Chain C, Recombination activating gene 1 - MBP chimera
Protein Classification
List of domain hits
| Name | Accession | Description | Interval | E-value | |||||||||
| RAG1 super family | cl20149 | Recombination-activation protein 1 (RAG1), recombinase; This family is one of the two ... |
528-1159 | 0e+00 | |||||||||
Recombination-activation protein 1 (RAG1), recombinase; This family is one of the two different components of the RAG1-RAG2 V(D)J recombinase complex. The RAG complex, consisting of two RAG1 and two RAG2 proteins is a multi-protein complex that mediates DNA cleavage during V(D)J (variable-diversity-joining) recombination. RAG1 mediates DNA-binding to the conserved recombination signal sequences (RSS). Many of the proteins in this family are fragments. Solution of the structure of the complex of RAG1 and RAG2 shows that each protein dimerizes with itself and each pair then complexes together to from the RAG1-RAG2 V(D)J recombinase enzyme. The different structural elements in RAG1 for UniProtKB:P15919 are: an N-terminal nonamer-binding domain from residues 391-459; a dimerization and DNA-binding domain from 459-515; an extended pre-RNase H domain from 515-588; the catalytic RNase H domain from 588-719; a ZnC2 domain from 719-791; and ZnH2 domain from 791-962; and a three-helix C-terminal domain from 962-1008. The actual alignment was detected with superfamily member pfam12940: Pssm-ID: 315595 Cd Length: 653 Bit Score: 1274.21 E-value: 0e+00
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| malE | PRK09474 | maltose/maltodextrin ABC transporter substrate-binding protein MalE; |
13-378 | 0e+00 | |||||||||
maltose/maltodextrin ABC transporter substrate-binding protein MalE; : Pssm-ID: 236533 [Multi-domain] Cd Length: 396 Bit Score: 835.43 E-value: 0e+00
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| RING-HC_RAG1 | cd16530 | RING finger, HC subclass, found in recombination activating gene-1 (RAG-1) and similar ... |
420-465 | 2.20e-25 | |||||||||
RING finger, HC subclass, found in recombination activating gene-1 (RAG-1) and similar proteins; RAG-1, also known as V(D)J recombination-activating protein 1, RING finger protein 74 (RNF74), or endonuclease RAG1, is the catalytic component of the RAG complex, a multiprotein complex that mediates the DNA cleavage phase during V(D)J recombination. RAG1 is a lymphoid-specific factor that mediates DNA-binding to conserved recombination signal sequences (RSS) and catalyzes DNA cleavage activities by introducing a double-strand break between the RSS and the adjacent coding segment. It also functions as an E3 ubiquitin-protein ligase that mediates monoubiquitination of histone H3, which is required for the joining step of V(D)J recombination. RAG-1 contains an N-terminal C3HC4-type RING-HC finger that mediates monoubiquitylation of histone H3, an adjacent C2H2-type zinc finger, and a nonamer binding (NBD) DNA-binding domain. : Pssm-ID: 319444 [Multi-domain] Cd Length: 46 Bit Score: 99.44 E-value: 2.20e-25
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| RAG1_imp_bd super family | cl13935 | RAG1 importin binding; This region of RAG1 is responsible for binding to importin alpha. |
398-421 | 1.78e-03 | |||||||||
RAG1 importin binding; This region of RAG1 is responsible for binding to importin alpha. The actual alignment was detected with superfamily member pfam12560: Pssm-ID: 463629 Cd Length: 287 Bit Score: 41.64 E-value: 1.78e-03
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| Name | Accession | Description | Interval | E-value | |||||||||
| RAG1 | pfam12940 | Recombination-activation protein 1 (RAG1), recombinase; This family is one of the two ... |
528-1159 | 0e+00 | |||||||||
Recombination-activation protein 1 (RAG1), recombinase; This family is one of the two different components of the RAG1-RAG2 V(D)J recombinase complex. The RAG complex, consisting of two RAG1 and two RAG2 proteins is a multi-protein complex that mediates DNA cleavage during V(D)J (variable-diversity-joining) recombination. RAG1 mediates DNA-binding to the conserved recombination signal sequences (RSS). Many of the proteins in this family are fragments. Solution of the structure of the complex of RAG1 and RAG2 shows that each protein dimerizes with itself and each pair then complexes together to from the RAG1-RAG2 V(D)J recombinase enzyme. The different structural elements in RAG1 for UniProtKB:P15919 are: an N-terminal nonamer-binding domain from residues 391-459; a dimerization and DNA-binding domain from 459-515; an extended pre-RNase H domain from 515-588; the catalytic RNase H domain from 588-719; a ZnC2 domain from 719-791; and ZnH2 domain from 791-962; and a three-helix C-terminal domain from 962-1008. Pssm-ID: 315595 Cd Length: 653 Bit Score: 1274.21 E-value: 0e+00
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| malE | PRK09474 | maltose/maltodextrin ABC transporter substrate-binding protein MalE; |
13-378 | 0e+00 | |||||||||
maltose/maltodextrin ABC transporter substrate-binding protein MalE; Pssm-ID: 236533 [Multi-domain] Cd Length: 396 Bit Score: 835.43 E-value: 0e+00
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| PBP2_MBP | cd13656 | The periplasmic binding component of ABC tansport system specific for maltose; possess the ... |
17-378 | 0e+00 | |||||||||
The periplasmic binding component of ABC tansport system specific for maltose; possess the type 2 periplasmic binidng fold; This group includes the periplasmic maltose-binding protein of an ATP-binding cassette transporter. Maltose is a disaccharide formed from two units of glucose. Members of this group belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Pssm-ID: 270374 [Multi-domain] Cd Length: 364 Bit Score: 739.79 E-value: 0e+00
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| MalE | COG2182 | Maltose-binding periplasmic protein MalE [Carbohydrate transport and metabolism]; |
2-378 | 2.54e-152 | |||||||||
Maltose-binding periplasmic protein MalE [Carbohydrate transport and metabolism]; Pssm-ID: 441785 [Multi-domain] Cd Length: 410 Bit Score: 461.34 E-value: 2.54e-152
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| SBP_bac_1 | pfam01547 | Bacterial extracellular solute-binding protein; This family also includes the bacterial ... |
29-301 | 6.57e-42 | |||||||||
Bacterial extracellular solute-binding protein; This family also includes the bacterial extracellular solute-binding protein family POTD/POTF. Pssm-ID: 460248 [Multi-domain] Cd Length: 294 Bit Score: 155.65 E-value: 6.57e-42
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| RING-HC_RAG1 | cd16530 | RING finger, HC subclass, found in recombination activating gene-1 (RAG-1) and similar ... |
420-465 | 2.20e-25 | |||||||||
RING finger, HC subclass, found in recombination activating gene-1 (RAG-1) and similar proteins; RAG-1, also known as V(D)J recombination-activating protein 1, RING finger protein 74 (RNF74), or endonuclease RAG1, is the catalytic component of the RAG complex, a multiprotein complex that mediates the DNA cleavage phase during V(D)J recombination. RAG1 is a lymphoid-specific factor that mediates DNA-binding to conserved recombination signal sequences (RSS) and catalyzes DNA cleavage activities by introducing a double-strand break between the RSS and the adjacent coding segment. It also functions as an E3 ubiquitin-protein ligase that mediates monoubiquitination of histone H3, which is required for the joining step of V(D)J recombination. RAG-1 contains an N-terminal C3HC4-type RING-HC finger that mediates monoubiquitylation of histone H3, an adjacent C2H2-type zinc finger, and a nonamer binding (NBD) DNA-binding domain. Pssm-ID: 319444 [Multi-domain] Cd Length: 46 Bit Score: 99.44 E-value: 2.20e-25
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| RING | smart00184 | Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and ... |
424-462 | 4.79e-10 | |||||||||
Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s) Pssm-ID: 214546 [Multi-domain] Cd Length: 40 Bit Score: 55.59 E-value: 4.79e-10
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| zf-C3HC4 | pfam00097 | Zinc finger, C3HC4 type (RING finger); The C3HC4 type zinc-finger (RING finger) is a ... |
424-462 | 2.18e-08 | |||||||||
Zinc finger, C3HC4 type (RING finger); The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid. Many proteins containing a RING finger play a key role in the ubiquitination pathway. Pssm-ID: 395049 [Multi-domain] Cd Length: 40 Bit Score: 51.20 E-value: 2.18e-08
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| rad18 | TIGR00599 | DNA repair protein rad18; All proteins in this family for which functions are known are ... |
403-462 | 3.08e-07 | |||||||||
DNA repair protein rad18; All proteins in this family for which functions are known are involved in nucleotide excision repair.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] Pssm-ID: 273165 [Multi-domain] Cd Length: 397 Bit Score: 54.24 E-value: 3.08e-07
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| RAD18 | COG5432 | RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]; |
412-462 | 1.91e-06 | |||||||||
RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]; Pssm-ID: 227719 [Multi-domain] Cd Length: 391 Bit Score: 51.63 E-value: 1.91e-06
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| RAG1_imp_bd | pfam12560 | RAG1 importin binding; This region of RAG1 is responsible for binding to importin alpha. |
398-421 | 1.78e-03 | |||||||||
RAG1 importin binding; This region of RAG1 is responsible for binding to importin alpha. Pssm-ID: 463629 Cd Length: 287 Bit Score: 41.64 E-value: 1.78e-03
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| PLN03208 | PLN03208 | E3 ubiquitin-protein ligase RMA2; Provisional |
424-472 | 2.25e-03 | |||||||||
E3 ubiquitin-protein ligase RMA2; Provisional Pssm-ID: 178747 [Multi-domain] Cd Length: 193 Bit Score: 40.45 E-value: 2.25e-03
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| Name | Accession | Description | Interval | E-value | |||||||||
| RAG1 | pfam12940 | Recombination-activation protein 1 (RAG1), recombinase; This family is one of the two ... |
528-1159 | 0e+00 | |||||||||
Recombination-activation protein 1 (RAG1), recombinase; This family is one of the two different components of the RAG1-RAG2 V(D)J recombinase complex. The RAG complex, consisting of two RAG1 and two RAG2 proteins is a multi-protein complex that mediates DNA cleavage during V(D)J (variable-diversity-joining) recombination. RAG1 mediates DNA-binding to the conserved recombination signal sequences (RSS). Many of the proteins in this family are fragments. Solution of the structure of the complex of RAG1 and RAG2 shows that each protein dimerizes with itself and each pair then complexes together to from the RAG1-RAG2 V(D)J recombinase enzyme. The different structural elements in RAG1 for UniProtKB:P15919 are: an N-terminal nonamer-binding domain from residues 391-459; a dimerization and DNA-binding domain from 459-515; an extended pre-RNase H domain from 515-588; the catalytic RNase H domain from 588-719; a ZnC2 domain from 719-791; and ZnH2 domain from 791-962; and a three-helix C-terminal domain from 962-1008. Pssm-ID: 315595 Cd Length: 653 Bit Score: 1274.21 E-value: 0e+00
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| malE | PRK09474 | maltose/maltodextrin ABC transporter substrate-binding protein MalE; |
13-378 | 0e+00 | |||||||||
maltose/maltodextrin ABC transporter substrate-binding protein MalE; Pssm-ID: 236533 [Multi-domain] Cd Length: 396 Bit Score: 835.43 E-value: 0e+00
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| PBP2_MBP | cd13656 | The periplasmic binding component of ABC tansport system specific for maltose; possess the ... |
17-378 | 0e+00 | |||||||||
The periplasmic binding component of ABC tansport system specific for maltose; possess the type 2 periplasmic binidng fold; This group includes the periplasmic maltose-binding protein of an ATP-binding cassette transporter. Maltose is a disaccharide formed from two units of glucose. Members of this group belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Pssm-ID: 270374 [Multi-domain] Cd Length: 364 Bit Score: 739.79 E-value: 0e+00
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| MalE | COG2182 | Maltose-binding periplasmic protein MalE [Carbohydrate transport and metabolism]; |
2-378 | 2.54e-152 | |||||||||
Maltose-binding periplasmic protein MalE [Carbohydrate transport and metabolism]; Pssm-ID: 441785 [Multi-domain] Cd Length: 410 Bit Score: 461.34 E-value: 2.54e-152
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| PBP2_ABC_oligosaccharides | cd13522 | The periplasmic-binding component of ABC transport systems specific for maltose and related ... |
18-378 | 8.12e-149 | |||||||||
The periplasmic-binding component of ABC transport systems specific for maltose and related oligosaccharides; possess type 2 periplasmic binding fold; This family represents the periplasmic binding component of ABC transport systems involved in uptake of oligosaccharides including maltose, trehalose, maltodextrin, and cyclodextrin. Members of this family belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Pssm-ID: 270240 [Multi-domain] Cd Length: 368 Bit Score: 450.71 E-value: 8.12e-149
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| PBP2_Maltose_binding_like | cd13586 | The periplasmic-binding component of ABC transport systems specific for maltose and related ... |
18-378 | 5.92e-140 | |||||||||
The periplasmic-binding component of ABC transport systems specific for maltose and related polysaccharides; possess type 2 periplasmic binding fold; This subfamily represents the periplasmic binding component of ABC transport systems involved in uptake of polysaccharides including maltose, maltodextrin, and cyclodextrin. Members of this family belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Pssm-ID: 270304 [Multi-domain] Cd Length: 367 Bit Score: 427.48 E-value: 5.92e-140
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| PBP2_CMBP | cd13658 | The periplasmic binding component of ABC transport systems specific for cyclo/maltodextrin; ... |
18-376 | 1.07e-89 | |||||||||
The periplasmic binding component of ABC transport systems specific for cyclo/maltodextrin; possess the type 2 periplasmic binding fold; This group includes the periplasmic cyclo/maltodextrin-binding protein of Thermoactinomyces vulgaris ATP-binding cassette transporter and related proteins. Cyclodextrins are a family of compounds composed of glucose units connected by 1, 4 glycosidic linkages to form a series of oligosaccharide rings, and their cavity is hydrophibic which allows cyclodextrins to accomodate hydrophobic molecules/moieties in the cavity. Members of this group belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Pssm-ID: 270376 [Multi-domain] Cd Length: 372 Bit Score: 293.62 E-value: 1.07e-89
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| PBP2_Maltodextrin | cd13657 | The periplasmic binding component of ABC transport system specific for maltodextrin; This ... |
18-377 | 5.84e-75 | |||||||||
The periplasmic binding component of ABC transport system specific for maltodextrin; This group includes the periplasmic maltodextrin-binding protein of a binding protein-dependent ATP-binding cassette transporter. Maltodextrin is a polysaccharide that is used as a food addtive and can be enzymatically produced from any starch . Members of this group belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Pssm-ID: 270375 [Multi-domain] Cd Length: 368 Bit Score: 252.68 E-value: 5.84e-75
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| PBP2_TMBP_like | cd13585 | The periplasmic-binding component of ABC transport systems specific for trehalose/maltose and ... |
18-377 | 5.58e-64 | |||||||||
The periplasmic-binding component of ABC transport systems specific for trehalose/maltose and similar oligosaccharides; possess type 2 periplasmic binding fold; This family includes the periplasmic trehalose/maltose-binding component of an ABC transport system and related proteins from archaea and bacteria. Members of this group belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Pssm-ID: 270303 [Multi-domain] Cd Length: 383 Bit Score: 222.28 E-value: 5.58e-64
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| PBP2_UgpB | cd14748 | The periplasmic-binding component of ABC transport system specific for sn-glycerol-3-phosphate; ... |
18-378 | 7.69e-60 | |||||||||
The periplasmic-binding component of ABC transport system specific for sn-glycerol-3-phosphate; possesses type 2 periplasmic binding fold; This group includes the periplasmic component of an ABC transport system specific for sn-glycerol-3-phosphate (G3P) and closely related proteins from archaea and bacteria. Under phophate starvation conditions, Escherichia coli can utilize G3P as phosphate source when exclusively imported by an ATP-binding cassette (ABC) transporter composed of the periplasmic binding protein, UgpB, the transmembrane subunits, UgpA and UgpE, and a homodimer of the nucleotide binding subunit, UgpC. Members of this group belong to the type 2 periplasmic-binding fold superfamily. PBP2 proteins are comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Pssm-ID: 270451 [Multi-domain] Cd Length: 385 Bit Score: 210.61 E-value: 7.69e-60
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| UgpB | COG1653 | ABC-type glycerol-3-phosphate transport system, periplasmic component [Carbohydrate transport ... |
2-325 | 1.21e-59 | |||||||||
ABC-type glycerol-3-phosphate transport system, periplasmic component [Carbohydrate transport and metabolism]; Pssm-ID: 441259 [Multi-domain] Cd Length: 363 Bit Score: 209.13 E-value: 1.21e-59
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| PBP2_XBP1_like | cd14749 | The periplasmic-binding component of ABC transport systems specific for xylo-oligosaccharides; ... |
18-378 | 4.24e-44 | |||||||||
The periplasmic-binding component of ABC transport systems specific for xylo-oligosaccharides; possesses type 2 periplasmic binding fold; This group represents the periplasmic component of an ABC transport system XBP1 that shows preference for xylo-oligosaccharides in the order of xylotriose > xylobiose > xylotetraose. Members of this group belong to the type 2 periplasmic-binding fold superfamily. PBP2 proteins are comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Pssm-ID: 270452 [Multi-domain] Cd Length: 388 Bit Score: 164.86 E-value: 4.24e-44
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| PBP2_MalE | cd14747 | Maltose-binding protein MalE; possesses type 2 periplasmic binding fold; This group includes ... |
18-378 | 1.67e-42 | |||||||||
Maltose-binding protein MalE; possesses type 2 periplasmic binding fold; This group includes the periplasmic maltose-binding component of an ABC transport system from the phytopathogen Xanthomonas citri and its related bacterial proteins. Members of this group belong to the type 2 periplasmic-binding fold superfamily. PBP2 proteins are comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Pssm-ID: 270450 [Multi-domain] Cd Length: 386 Bit Score: 160.17 E-value: 1.67e-42
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| SBP_bac_1 | pfam01547 | Bacterial extracellular solute-binding protein; This family also includes the bacterial ... |
29-301 | 6.57e-42 | |||||||||
Bacterial extracellular solute-binding protein; This family also includes the bacterial extracellular solute-binding protein family POTD/POTF. Pssm-ID: 460248 [Multi-domain] Cd Length: 294 Bit Score: 155.65 E-value: 6.57e-42
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| PBP2_TMBP | cd14750 | The periplasmic-binding component of ABC transport systems specific for trehalose/maltose; ... |
27-377 | 1.46e-41 | |||||||||
The periplasmic-binding component of ABC transport systems specific for trehalose/maltose; possesses type 2 periplasmic binding fold; This group represents the periplasmic trehalose/maltose-binding component of an ABC transport system and related proteins from archaea and bacteria. Members of this group belong to the type 2 periplasmic-binding fold superfamily. PBP2 proteins are comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Pssm-ID: 270453 [Multi-domain] Cd Length: 385 Bit Score: 157.46 E-value: 1.46e-41
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| SBP_bac_8 | pfam13416 | Bacterial extracellular solute-binding protein; This family includes bacterial extracellular ... |
34-327 | 8.69e-40 | |||||||||
Bacterial extracellular solute-binding protein; This family includes bacterial extracellular solute-binding proteins. Pssm-ID: 433189 [Multi-domain] Cd Length: 281 Bit Score: 149.09 E-value: 8.69e-40
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| PBP2_GacH | cd14751 | The periplasmic-binding component of the putative oligosacchride ABC transporter GacHFG; ... |
39-378 | 1.37e-33 | |||||||||
The periplasmic-binding component of the putative oligosacchride ABC transporter GacHFG; possesses type 2 periplasmic binding fold; This group represents the periplasmic component GacH of an ABC import system. GacH is identified as a maltose/maltodextrin-binding protein with a low affinity for acarbose. Members of this group belong to the type 2 periplasmic-binding fold superfamily. PBP2 proteins are comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Pssm-ID: 270454 [Multi-domain] Cd Length: 376 Bit Score: 134.04 E-value: 1.37e-33
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| PBP2_oligosaccharide_1 | cd13655 | The periplasmic binding component of ABC tansport system specific for an unknown ... |
18-352 | 1.29e-28 | |||||||||
The periplasmic binding component of ABC tansport system specific for an unknown oligosaccharide; possess the type 2 periplasmic binidng fold; This group represents an uncharacterized periplasmic-binding protein of an ATP-binding cassette transporter predicted to be involved in uptake of an unknown oligosaccharide molecule. Members of this group belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Pssm-ID: 270373 [Multi-domain] Cd Length: 363 Bit Score: 118.99 E-value: 1.29e-28
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| RING-HC_RAG1 | cd16530 | RING finger, HC subclass, found in recombination activating gene-1 (RAG-1) and similar ... |
420-465 | 2.20e-25 | |||||||||
RING finger, HC subclass, found in recombination activating gene-1 (RAG-1) and similar proteins; RAG-1, also known as V(D)J recombination-activating protein 1, RING finger protein 74 (RNF74), or endonuclease RAG1, is the catalytic component of the RAG complex, a multiprotein complex that mediates the DNA cleavage phase during V(D)J recombination. RAG1 is a lymphoid-specific factor that mediates DNA-binding to conserved recombination signal sequences (RSS) and catalyzes DNA cleavage activities by introducing a double-strand break between the RSS and the adjacent coding segment. It also functions as an E3 ubiquitin-protein ligase that mediates monoubiquitination of histone H3, which is required for the joining step of V(D)J recombination. RAG-1 contains an N-terminal C3HC4-type RING-HC finger that mediates monoubiquitylation of histone H3, an adjacent C2H2-type zinc finger, and a nonamer binding (NBD) DNA-binding domain. Pssm-ID: 319444 [Multi-domain] Cd Length: 46 Bit Score: 99.44 E-value: 2.20e-25
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| PotD | COG0687 | Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; |
15-356 | 1.95e-20 | |||||||||
Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Pssm-ID: 440451 [Multi-domain] Cd Length: 348 Bit Score: 94.21 E-value: 1.95e-20
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| AfuA | COG1840 | ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; ... |
37-301 | 8.09e-16 | |||||||||
ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Pssm-ID: 441445 [Multi-domain] Cd Length: 286 Bit Score: 79.21 E-value: 8.09e-16
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| PBP2_AlgQ_like_1 | cd13580 | Periplasmic-binding component of alginate-specific ABC uptake system-like; contains the type 2 ... |
37-309 | 1.92e-14 | |||||||||
Periplasmic-binding component of alginate-specific ABC uptake system-like; contains the type 2 periplasmic binding fold; This subgroup includes uncharacterized periplasmic-binding proteins that are closely related to high molecular weight (HMW) alginate bining proteins (AlgQ1 and AlgQ2) found in gram-negative soil bacteria. The HMW alginate uptake system is composed of a novel pit formed on the cell surface and a pit-dependent ATP-binding cassette (ABC) transporter in the inner membrane. The transportation of HMW alginate from the pit to the ABC transporter is mediated by periplasmic HMW alginate-binding proteins (AlgQ1 and AlgQ2). Alginate is an anionic polysaccharide that is made up of alpha-L-mannuronate and its 5'-epimer, alpha-L-guluronate. Alginate is present in the cell walls of brown seaweeds, where it forms a viscous gum by binding water. Alginate is also produced by two bacteria genera Pseudomonas and Azotobacter. AlgQ1 and AlgQ2 belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. However, unlike other bacterial periplasmic-binding proteins that deliver small solutes to ABC transporters, AlgQ1/2 can bind a macromolecule and may have specificity for either sugar or a certain type of polysaccharide. Pssm-ID: 270298 [Multi-domain] Cd Length: 471 Bit Score: 77.37 E-value: 1.92e-14
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| PBP2_PotD_PotF_like | cd13590 | The periplasmic-binding component of ABC transporters involved in uptake of polyamines; ... |
34-297 | 4.97e-13 | |||||||||
The periplasmic-binding component of ABC transporters involved in uptake of polyamines; possess the type 2 periplasmic binding fold; This family represents the periplasmic substrate-binding domain that functions as the primary high-affinity receptors of ABC-type polyamine transport systems. Polyamine transport plays an essential role in the regulation of intracellular polyamine levels which are known to be elevated in rapidly proliferating cells and tumors. Natural polyamines are putrescine, spermindine, and spermine. They are polycations that play multiple roles in cell growth, survival and proliferation, and plant stress and disease resistance. They can interact with negatively charged molecules, such as nucleic acids, to modulate their functions. Members of this family belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. Pssm-ID: 270308 [Multi-domain] Cd Length: 315 Bit Score: 71.50 E-value: 4.97e-13
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| PBP2_polyamine_RpCGA009 | cd13589 | The periplasmic-binding component of an uncharacterized ABC transport system from ... |
33-312 | 2.06e-12 | |||||||||
The periplasmic-binding component of an uncharacterized ABC transport system from Rhodopseudomonas palustris CGA009 and related proteins; contains the type 2 periplasmic-binding fold; This group represents the periplasmic binding domain that serves as the primary high-affinity receptor of an uncharacterized ABC-type polyamine transporter from Rhodopseudomonas palustris Cga009 and related proteins from other bacteria. Polyamine transport plays an essential role in the regulation of intracellular polyamine levels which are known to be elevated in rapidly proliferating cells and tumors. Natural polyamines are putrescine, spermindine, and spermine. They are polycations that play multiple roles in cell growth, survival and proliferation, and plant stress and disease resistance. They can interact with negatively charged molecules, such as nucleic acids, to modulate their functions. Members of this family belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. Pssm-ID: 270307 [Multi-domain] Cd Length: 268 Bit Score: 68.79 E-value: 2.06e-12
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| RING-HC_RAD16-like | cd16567 | RING finger, HC subclass, found in Saccharomyces cerevisiae DNA repair protein RAD16, ... |
424-466 | 5.56e-11 | |||||||||
RING finger, HC subclass, found in Saccharomyces cerevisiae DNA repair protein RAD16, Schizosaccharomyces pombe rhp16, and similar proteins; Budding yeast RAD16, also known as ATP-dependent helicase RAD16, is encoded by a yeast excision repair gene homologous to the recombinational repair gene RAD54 and to the SNF2 gene involved in transcriptional activation. It is a component of the global genome repair (GGR) complex that promotes global genome nucleotide excision repair (GG-NER) by removing DNA damage from non-transcribing DNA. RAD16 is involved in differential repair of DNA after UV damage, and repairs preferentially the MAT-alpha locus compared with the HML-alpha locus. Fission yeast rhp16, also known as ATP-dependent helicase rhp16, is a RAD16 homolog. It is involved in GGR via nucleotide excision repair (NER), in conjunction with rhp7, after UV irradiation. Both RAD16 and rhp16 contain a C3HC4-type RING-HC finger, as well as a DEAD-like helicase domain and a helicase superfamily C-terminal domain. Pssm-ID: 438229 [Multi-domain] Cd Length: 48 Bit Score: 58.51 E-value: 5.56e-11
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| PBP2_Fe3_thiamine_like | cd13518 | Substrate binding domain of iron and thiamine transporters-like, a member of the type 2 ... |
18-306 | 1.77e-10 | |||||||||
Substrate binding domain of iron and thiamine transporters-like, a member of the type 2 periplasmic binding fold superfamily; The periplasmic iron binding protein plays an essential role in the iron uptake pathway of Gram-negative pathogenic bacteria from the Pasteurellaceae and Neisseriaceae families and is critical for survival of these pathogens within the host. On the other hand, thiamin is an essential cofactor in all living systems. Thiamin diphosphate (ThDP)-dependent enzymes play an important role in carbohydrate and branched-chain amino acid metabolism. Most prokaryotes, plants, and fungi can synthesize thiamin, but it is not synthesized in vertebrates. These periplasmic domains have high affinities for their respective substrates and serve as the primary receptor for transport. After binding iron and thiamine with high affinity, they interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The iron- and thiamine-binding proteins belong to the PBPI2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. Pssm-ID: 270236 [Multi-domain] Cd Length: 260 Bit Score: 62.70 E-value: 1.77e-10
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| RING-HC | cd16449 | HC subclass of RING (RING-HC) finger and its variants; The RING finger is a specialized type ... |
423-462 | 2.34e-10 | |||||||||
HC subclass of RING (RING-HC) finger and its variants; The RING finger is a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc. It is defined by the "cross-brace" motif that chelates zinc atoms by eight amino acid residues, typically Cys or His, arranged in a characteristic spacing. Canonical RING motifs have been categorized into two major subclasses, RING-HC (C3HC4-type) and RING-H2 (C3H2C3-type), according to their Cys/His content. There are also many variants of RING fingers. Some have a different Cys/His pattern. Some lack a single Cys or His residue at typical Zn ligand positions, especially, the fourth or eighth zinc ligand is prevalently exchanged for an Asp, which can chelate Zn in a RING finger as well. This family corresponds to the HC subclass of RING (RING-HC) fingers that are characterized by containing C3HC4-type canonical RING-HC fingers or noncanonical RING-HC finger variants, including C4C4-, C3HC3D-, C2H2C4-, and C3HC5-type modified RING-HC fingers. The canonical RING-HC finger has been defined as C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C. It binds two Zn ions in a unique "cross-brace" arrangement, which distinguishes it from tandem zinc fingers and other similar motifs. RING-HC fingers can be found in a group of diverse proteins with a variety of cellular functions, including oncogenesis, development, viral replication, signal transduction, the cell cycle, and apoptosis. Many of them are ubiquitin-protein ligases (E3s) that serve as scaffolds for binding to ubiquitin-conjugating enzymes (E2s, also referred to as ubiquitin carrier proteins or UBCs) in close proximity to substrate proteins, which enables efficient transfer of ubiquitin from E2 to the substrates. Pssm-ID: 438113 [Multi-domain] Cd Length: 41 Bit Score: 56.73 E-value: 2.34e-10
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| RING | smart00184 | Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and ... |
424-462 | 4.79e-10 | |||||||||
Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s) Pssm-ID: 214546 [Multi-domain] Cd Length: 40 Bit Score: 55.59 E-value: 4.79e-10
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| PBP2_AlgQ_like | cd13521 | Periplasmic-binding component of alginate-specific ABC uptake system-like; contains the type 2 ... |
35-301 | 1.51e-09 | |||||||||
Periplasmic-binding component of alginate-specific ABC uptake system-like; contains the type 2 periplasmic binding fold; This family represents the periplasmic-binding component of high molecular weight (HMW) alginate uptake system found in gram-negative soil bacteria and related proteins. The HMW alginate uptake system is composed of a novel pit formed on the cell surface and a pit-dependent ATP-binding cassette (ABC) transporter in the inner membrane. In Sphingomonas sp. A1, the transportation of HMW alginate from the pit to the ABC transporter is mediated by periplasmic HMW alginate-binding proteins AlgQ1 and AlgQ2. Alginate is an anionic polysaccharide that is made up of alpha-L-mannuronate and its 5'-epimer, alpha-L-guluronate. Alginate is present in the cell walls of brown seaweeds, where it forms a viscous gum by binding water. Alginate is also produced by two bacteria genera Pseudomonas and Azotobacter. AlgQ1 and AlgQ2 belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. However, unlike other bacterial periplasmic-binding proteins that deliver small solutes to ABC transporters, AlgQ1/2 can bind a macromolecule and may have specificity for either sugar or a certain type of polysaccharide. Pssm-ID: 270239 [Multi-domain] Cd Length: 483 Bit Score: 61.70 E-value: 1.51e-09
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| RING-HC_TRIM77_C-IV | cd16543 | RING finger, HC subclass, found in tripartite motif-containing protein 77 (TRIM77) and similar ... |
422-468 | 3.41e-09 | |||||||||
RING finger, HC subclass, found in tripartite motif-containing protein 77 (TRIM77) and similar proteins; TRIM77 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including two consecutive zinc-binding domains, a C3HC4-type RING-HC finger and Bbox2, as well as a SPRY/B30.2 domain positioned C-terminal to the RBCC domain. Pssm-ID: 438205 [Multi-domain] Cd Length: 54 Bit Score: 53.55 E-value: 3.41e-09
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| RING-HC_RNF138 | cd16544 | RING finger, HC subclass, found in RING finger protein 138 (RNF138) and similar proteins; ... |
423-464 | 2.14e-08 | |||||||||
RING finger, HC subclass, found in RING finger protein 138 (RNF138) and similar proteins; RNF138, also known as Nemo-like kinase-associated RING finger protein (NARF) or NLK-associated RING finger protein, is an E3 ubiquitin-protein ligase that plays an important role in glioma cell proliferation, apoptosis, and cell cycle. It specifically cooperates with the E2 conjugating enzyme E2-25K (Hip-2/UbcH1), regulates the ubiquitylation and degradation of T cell factor/lymphoid enhancer factor (TCF/LEF), and further suppresses Wnt-beta-catenin signaling. RNF138, together with three closely related proteins: RNF114, RNF125 and RNF166, forms a novel family of ubiquitin ligases with a C3HC4-type RING-HC finger, a C2HC-, and two C2H2-type zinc fingers, as well as a ubiquitin interacting motif (UIM). Pssm-ID: 438206 [Multi-domain] Cd Length: 53 Bit Score: 51.25 E-value: 2.14e-08
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| zf-C3HC4 | pfam00097 | Zinc finger, C3HC4 type (RING finger); The C3HC4 type zinc-finger (RING finger) is a ... |
424-462 | 2.18e-08 | |||||||||
Zinc finger, C3HC4 type (RING finger); The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid. Many proteins containing a RING finger play a key role in the ubiquitination pathway. Pssm-ID: 395049 [Multi-domain] Cd Length: 40 Bit Score: 51.20 E-value: 2.18e-08
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| PBP2_polyamine_2 | cd13587 | The periplasmic-binding component of an uncharacterized ABC transporter involved in uptake of ... |
33-137 | 2.51e-08 | |||||||||
The periplasmic-binding component of an uncharacterized ABC transporter involved in uptake of polyamines; contains the type 2 periplasmic binding fold; This family represents the periplasmic binding domain that functions as the primary polyamine receptor of an uncharacterized ABC-type transport system. Polyamine transport plays an essential role in the regulation of intracellular polyamine levels which are known to be elevated in rapidly proliferating cells and tumors. Natural polyamines are putrescine, spermindine, and spermine. They are polycations that play multiple roles in cell growth, survival and proliferation, and plant stress and disease resistance. They can interact with negatively charged molecules, such as nucleic acids, to modulate their functions. Members of this family belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. Pssm-ID: 270305 [Multi-domain] Cd Length: 292 Bit Score: 56.67 E-value: 2.51e-08
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| mRING-HC-C3HC3D_TRAF6 | cd16643 | Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) ... |
424-471 | 4.08e-08 | |||||||||
Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) receptor-associated factor 6 (TRAF6) and similar proteins; TRAF6, also known as interleukin-1 signal transducer or RING finger protein 85 (RNF85), is a cytoplasmic adapter protein that mediates signals induced by the tumor necrosis factor receptor (TNFR) superfamily and Toll-like receptor (TLR)/interleukin-1 receptor (IL-1R) family. It functions as a mediator involved in the activation of mitogen-activated protein kinase (MAPK), phosphoinositide 3-kinase (PI3K), and interferon regulatory factor pathways, as well as in IL-1R-mediated activation of NF-kappaB. TRAF6 is also an oncogene that plays a vital role in K-RAS-mediated oncogenesis. TRAF6 contains an N-terminal domain with a modified C3HC3D-type RING-HC finger and several zinc fingers, and a C-terminal TRAF domain that comprises a coiled coil domain and a conserved TRAF-C domain. Pssm-ID: 438305 [Multi-domain] Cd Length: 58 Bit Score: 50.84 E-value: 4.08e-08
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| PBP2_polyamine_1 | cd13588 | The periplasmic-binding component of an uncharacterized ABC transporter involved in uptake of ... |
27-154 | 4.33e-08 | |||||||||
The periplasmic-binding component of an uncharacterized ABC transporter involved in uptake of polyamines; contains the type 2 periplasmic binding fold; This group represents the periplasmic binding domain that functions as the primary high-affinity receptor of an uncharactertized ABC-type polyamine transport system. Polyamine transport plays an essential role in the regulation of intracellular polyamine levels which are known to be elevated in rapidly proliferating cells and tumors. Natural polyamines are putrescine, spermindine, and spermine. They are polycations that play multiple roles in cell growth, survival and proliferation, and plant stress and disease resistance. They can interact with negatively charged molecules, such as nucleic acids, to modulate their functions. Members of this family belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. Pssm-ID: 270306 [Multi-domain] Cd Length: 279 Bit Score: 55.77 E-value: 4.33e-08
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| RING-HC_TRIM39_C-IV | cd16601 | RING finger, HC subclass, found in tripartite motif-containing protein 39 (TRIM39) and similar ... |
424-462 | 8.25e-08 | |||||||||
RING finger, HC subclass, found in tripartite motif-containing protein 39 (TRIM39) and similar proteins; TRIM39, also known as RING finger protein 23 (RNF23) or testis-abundant finger protein, is an E3 ubiquitin-protein ligase that plays a role in controlling DNA damage-induced apoptosis through inhibition of the anaphase promoting complex (APC/C), a multiprotein ubiquitin ligase that controls multiple cell cycle regulators, including cyclins, geminin, and others. TRIM39 also functions as a regulator of several key processes in the proliferative cycle. It directly regulates p53 stability. It modulates cell cycle progression and DNA damage responses via stabilizing p21. Moreover, TRIM39 negatively regulates the nuclear factor kappaB (NFkappaB)-mediated signaling pathway through stabilization of Cactin, an inhibitor of NFkappaB- and Toll-like receptor (TLR)-mediated transcription, which is induced by inflammatory stimulants such as tumor necrosis factor alpha. Furthermore, TRIM39 is a MOAP-1-binding protein that can promote apoptosis signaling through stabilization of MOAP-1 via the inhibition of its poly-ubiquitination process. TRIM39 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. Pssm-ID: 438263 [Multi-domain] Cd Length: 44 Bit Score: 49.41 E-value: 8.25e-08
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| RING-HC_LONFs_rpt2 | cd16514 | second RING finger, HC subclass, found in the LON peptidase N-terminal domain and RING finger ... |
424-466 | 9.08e-08 | |||||||||
second RING finger, HC subclass, found in the LON peptidase N-terminal domain and RING finger protein family; The LON peptidase N-terminal domain and RING finger protein family includes LONRF1 (also known as RING finger protein 191 or RNF191), LONRF2 (also known as RING finger protein 192, RNF192, or neuroblastoma apoptosis-related protease), LONRF3 (also known as RING finger protein 127 or RNF127), which are characterized by containing two C3HC4-type RING-HC fingers, four tetratricopeptide (TPR) repeats, and an ATP-dependent protease La (LON) substrate-binding domain at the C-terminus. Their biological functions remain unclear. This model corresponds to the second RING-HC finger. Pssm-ID: 438177 [Multi-domain] Cd Length: 45 Bit Score: 49.57 E-value: 9.08e-08
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| RING-HC_TRIM8_C-V | cd16580 | RING finger, HC subclass, found in tripartite motif-containing protein 8 (TRIM8) and similar ... |
424-464 | 1.85e-07 | |||||||||
RING finger, HC subclass, found in tripartite motif-containing protein 8 (TRIM8) and similar proteins; TRIM8, also known as glioblastoma-expressed RING finger protein (GERP) or RING finger protein 27 (RNF27), is a probable E3 ubiquitin-protein ligase that may promote proteasomal degradation of suppressor of cytokine signaling 1 (SOCS1) and further regulate interferon-gamma signaling. It functions as a new p53 modulator that stabilizes p53 impairing its association with MDM2 and inducing the reduction of cell proliferation. TRIM8 deficit dramatically impairs p53 stabilization and activation in response to chemotherapeutic drugs. TRIM8 also modulates tumor necrosis factor-alpha (TNFalpha) and interleukin-1beta (IL-1beta)-triggered nuclear factor-kappaB (NF- kappa B) activation by targeting transforming growth factor beta (TGFbeta) activated kinase 1 (TAK1) for K63-linked polyubiquitination. Moreover, TRIM8 modulates translocation of phosphorylated STAT3 into the nucleus through interaction with Hsp90beta and consequently regulates transcription of Nanog in embryonic stem cells. It also interacts with protein inhibitor of activated STAT3 (PIAS3), which inhibits IL-6-dependent activation of STAT3. TRIM8 belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil domain, as well as an uncharacterized region positioned C-terminal to the RBCC domain. The coiled coil domain is required for homodimerization and the region immediately C-terminal to the RING motif is sufficient to mediate the interaction with SOCS1. Pssm-ID: 438242 [Multi-domain] Cd Length: 67 Bit Score: 49.12 E-value: 1.85e-07
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| rad18 | TIGR00599 | DNA repair protein rad18; All proteins in this family for which functions are known are ... |
403-462 | 3.08e-07 | |||||||||
DNA repair protein rad18; All proteins in this family for which functions are known are involved in nucleotide excision repair.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] Pssm-ID: 273165 [Multi-domain] Cd Length: 397 Bit Score: 54.24 E-value: 3.08e-07
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| zf-C3HC4_2 | pfam13923 | Zinc finger, C3HC4 type (RING finger); |
424-462 | 3.70e-07 | |||||||||
Zinc finger, C3HC4 type (RING finger); Pssm-ID: 404756 [Multi-domain] Cd Length: 40 Bit Score: 47.43 E-value: 3.70e-07
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| RING-HC_AtRMA-like | cd16745 | RING finger, HC subclass, found in Arabidopsis thaliana RING membrane-anchor proteins (AtRMAs) ... |
424-462 | 8.63e-07 | |||||||||
RING finger, HC subclass, found in Arabidopsis thaliana RING membrane-anchor proteins (AtRMAs) and similar proteins; AtRMAs, including AtRma1, AtRma2, and AtRma3, are endoplasmic reticulum (ER)-localized Arabidopsis homologs of human outer membrane of the ER-anchor E3 ubiquitin-protein ligase, RING finger protein 5 (RNF5). AtRMAs possess E3 ubiquitin ligase activity, and may play a role in the growth and development of Arabidopsis. The AtRMA1 and AtRMA3 genes are predominantly expressed in major tissues, such as cotyledons, leaves, shoot-root junction, roots, and anthers, while AtRMA2 expression is restricted to the root tips and leaf hydathodes. AtRma1 probably functions with the Ubc4/5 subfamily of E2. AtRma2 is likely involved in the cellular regulation of ABP1 expression levels through interacting with auxin binding protein 1 (ABP1). AtRMA proteins contain an N-terminal C3HC4-type RING-HC finger and a trans-membrane-anchoring domain in their extreme C-terminal region. Pssm-ID: 438403 [Multi-domain] Cd Length: 45 Bit Score: 46.71 E-value: 8.63e-07
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| RING-HC_ScRAD18-like | cd23148 | RING finger, HC subclass, found in Saccharomyces cerevisiae radiation sensitivity protein 18 ... |
421-462 | 1.28e-06 | |||||||||
RING finger, HC subclass, found in Saccharomyces cerevisiae radiation sensitivity protein 18 (RAD18) and similar proteins; RAD18, also called RING-type E3 ubiquitin transferase RAD18, acts as a postreplication repair E3 ubiquitin-protein ligase that associates with the E2 ubiquitin conjugating enzyme UBC2/RAD6 to form the UBC2-RAD18 ubiquitin ligase complex involved in postreplicative repair (PRR) of damaged DNA. The UBC2-RAD18 complex cooperates with RAD5 and the UBC13-MMS2 dimer to attach mono-ubiquitin chains on 'Lys-164' of POL30, which is necessary for PRR. The UBC2-RAD18 complex is also involved in prevention of spontaneous mutations caused by 7,8-dihydro-8-oxoguanine. RAD18 is an E3 RING-finger protein belonging to the UBC2/RAD6 epistasis group. It contains a typical C3HC4-type RING-HC finger. Pssm-ID: 438510 [Multi-domain] Cd Length: 52 Bit Score: 46.37 E-value: 1.28e-06
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| RING-HC_HLTF | cd16509 | RING finger, HC subclass, found in helicase-like transcription factor (HLTF) and similar ... |
424-471 | 1.29e-06 | |||||||||
RING finger, HC subclass, found in helicase-like transcription factor (HLTF) and similar proteins; HLTF, also known as DNA-binding protein/plasminogen activator inhibitor 1 regulator, HIP116, RING finger protein 80, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 3, or sucrose nonfermenting protein 2-like 3, is a yeast RAD5 homolog found in mammals. It has both E3 ubiquitin ligase and DNA helicase activities, and plays a pivotal role in the template-switching pathway of DNA damage tolerance. It is involved in Lys-63-linked poly-ubiquitination of proliferating cell nuclear antigen (PCNA) at Lys-164 and in the regulation of DNA damage tolerance. It shows double-stranded DNA translocase activity with 3'-5' polarity, thereby facilitating regression of the replication fork. HLTF contains an N-terminal HIRAN (HIP116 and RAD5 N-terminal) domain, a SWI/SNF helicase domain that is divided into N- and C-terminal parts by an insertion of a C3HC4-type RING-HC finger involved in the poly-ubiquitination of PCNA. Pssm-ID: 438172 [Multi-domain] Cd Length: 53 Bit Score: 46.53 E-value: 1.29e-06
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| RING-HC_TRIM25_C-IV | cd16597 | RING finger, HC subclass, found in tripartite motif-containing protein TRIM25 and similar ... |
417-462 | 1.59e-06 | |||||||||
RING finger, HC subclass, found in tripartite motif-containing protein TRIM25 and similar proteins; TRIM25, also known as estrogen-responsive finger protein (EFP), RING finger protein 147 (RNF147), or RING-type E3 ubiquitin transferase, is an E3 ubiquitin/ISG15 ligase that is induced by estrogen and is therefore particularly abundant in placenta and uterus. TRIM25 regulates various cellular processes through E3 ubiquitin ligase activity, transferring ubiquitin and ISG15 to target proteins. It mediates K63-linked polyubiquitination of retinoic acid inducible gene I (RIG-I) that is crucial for downstream antiviral interferon signaling. It is also required for melanoma differentiation-associated gene 5 (MDA5) and mitochondrial antiviral signaling (MAVS, also known as IPS-1, VISA, Cardiff) mediated activation of nuclear factor-kappaB (NF-kappaB) and interferon production. Upon UV irradiation, TRIM25 interacts with mono-ubiquitinated PCNA and promotes its ISG15 modification (ISGylation), suggesting a crucial role in termination of error-prone translesion DNA synthesis. TRIM25 also functions as a novel regulator of p53 and Mdm2. It enhances p53 and Mdm2 abundance by inhibiting their ubiquitination and degradation in 26S proteasomes. Meanwhile, it inhibits p53's transcriptional activity and dampens the response to DNA damage, and is essential for medaka development and this dependence is rescued by silencing of p53. Moreover, TRIM25 is involved in the host cellular innate immune response against retroviral infection. It interferes with the late stage of feline leukemia virus (FeLV) replication. Furthermore, TRIM25 acts as an oncogene in gastric cancer. Its blockade by RNA interference inhibits migration and invasion of gastric cancer cells through transforming growth factor-beta (TGF-beta) signaling, suggesting it presents a novel target for the detection and treatment of gastric cancer. In addition, TRIM25 acts as an RNA-specific activator for Lin28a/TuT4-mediated uridylation. TRIM25 belongs to the C-IV subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. Pssm-ID: 438259 [Multi-domain] Cd Length: 71 Bit Score: 46.53 E-value: 1.59e-06
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| RAD18 | COG5432 | RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]; |
412-462 | 1.91e-06 | |||||||||
RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]; Pssm-ID: 227719 [Multi-domain] Cd Length: 391 Bit Score: 51.63 E-value: 1.91e-06
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| RING-HC_RNF39 | cd16592 | RING finger, HC subclass, found in RING finger protein 39 (RNF39) and similar proteins; RNF39, ... |
418-462 | 2.31e-06 | |||||||||
RING finger, HC subclass, found in RING finger protein 39 (RNF39) and similar proteins; RNF39, also called protein HZFw, may play a role in prolonged long term-potentiation (LTP) maintenance. It is involved in the etiology of Behcet's disease (BD). It may also be involved in HIV-1 replication. RNF39 acts as an E3 ubiquitin ligase that inhibits retinoic acid-inducible gene-I (RIG-I)-like receptor (RLR) pathways by mediating K48-linked ubiquitination and proteasomal degradation of DDX3X (DEAD-box RNA helicase 3, X-linked). RNF39 contains a typical C3HC4-type RING-HC finger. Pssm-ID: 438254 [Multi-domain] Cd Length: 58 Bit Score: 45.90 E-value: 2.31e-06
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| RING-HC_TRIM38_C-IV | cd16600 | RING finger, HC subclass, found in tripartite motif-containing protein 38 (TRIM38) and similar ... |
422-462 | 2.63e-06 | |||||||||
RING finger, HC subclass, found in tripartite motif-containing protein 38 (TRIM38) and similar proteins; TRIM38, also known as RING finger protein 15 (RNF15) or zinc finger protein RoRet, is an E3 ubiquitin-protein ligase that promotes K63- and K48-linked ubiquitination of cellular proteins and also catalyzes self-ubiquitination. It negatively regulates Tumor necrosis factor alpha (TNF-alpha)- and interleukin-1beta-triggered Nuclear factor-kappaB (NF-kappaB) activation by mediating lysosomal-dependent degradation of transforming growth factor beta (TGFbeta)-activated kinase 1 (TAK1)-binding protein (TAB)2/3, two critical components of the TAK1 kinase complex. It also inhibits TLR3/4-mediated activation of NF-kappaB and interferon regulatory factor 3 (IRF3) by mediating ubiquitin-proteasomal degradation of TNF receptor-associated factor 6 (Traf6) and NAK-associated protein 1 (Nap1), respectively. Moreover, TRIM38 negatively regulates TLR3-mediated interferon beta (IFN-beta) signaling by targeting ubiquitin-proteasomal degradation of TIR domain-containing adaptor inducing IFN-beta (TRIF). It functions as a valid target for autoantibodies in primary Sjogren's Syndrome. TRIM38 belongs the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, a B-box, and two coiled coil domains, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. Pssm-ID: 438262 [Multi-domain] Cd Length: 58 Bit Score: 45.53 E-value: 2.63e-06
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| RING-HC_TRIM13_like_C-V | cd16581 | RING finger, HC subclass, found in tripartite motif-containing proteins TRIM13, TRIM59 and ... |
422-463 | 3.36e-06 | |||||||||
RING finger, HC subclass, found in tripartite motif-containing proteins TRIM13, TRIM59 and similar proteins; TRIM13 and TRIM59, two closely related tripartite motif-containing proteins, belong to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domain, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, followed by a C-terminal transmembrane domain. TRIM13, also known as B-cell chronic lymphocytic leukemia tumor suppressor Leu5, leukemia-associated protein 5, putative tumor suppressor RFP2, RING finger protein 77 (RNF77), or Ret finger protein 2, is an endoplasmic reticulum (ER) membrane anchored E3 ubiquitin-protein ligase that interacts with proteins localized to the ER, including valosin-containing protein (VCP), a protein indispensable for ER-associated degradation (ERAD). TRIM59, also known as RING finger protein 104 (RNF104) or tumor suppressor TSBF-1, is a putative E3 ubiquitin-protein ligase that functions as a novel multiple cancer biomarker for immunohistochemical detection of early tumorigenesis. Pssm-ID: 438243 [Multi-domain] Cd Length: 50 Bit Score: 45.19 E-value: 3.36e-06
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| PBP2_TbpA | cd13545 | Substrate binding domain of thiamin transporter, a member of the type 2 periplasmic binding ... |
34-305 | 3.40e-06 | |||||||||
Substrate binding domain of thiamin transporter, a member of the type 2 periplasmic binding fold superfamily; Thiamin-binding protein TbpA is the periplasmic component of ABC-type transporter in E. coli, while the transmembrane permease and ATPase are ThiP and ThiQ, respectively. Thiamin (vitamin B1) is an essential confactor in all living systems that most prokaryotes, plants, and fungi can synthesized thiamin. However, in vertebrates, thiamine cannot be synthesized and must therefore be obtained through dietary absorption. In addition to thiamin biosynthesis, most organisms can import thiamin using specific transporters. After binding thiamine with high affinity, TbpA interacts with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The thiamine-binding proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. Pssm-ID: 270263 [Multi-domain] Cd Length: 269 Bit Score: 49.99 E-value: 3.40e-06
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| RING-HC_BRCA1 | cd16498 | RING finger, HC subclass, found in breast cancer type 1 susceptibility protein (BRCA1) and ... |
424-477 | 3.43e-06 | |||||||||
RING finger, HC subclass, found in breast cancer type 1 susceptibility protein (BRCA1) and similar proteins; BRCA1, also known as RING finger protein 53 (RNF53), is a RING finger protein encoded by the tumor suppressor gene BRCA1 that regulates all DNA double-strand break (DSB) repair pathways. BRCA1 is frequently mutated in patients with hereditary breast and ovarian cancer (HBOC). Its mutation is also associated with an increased risk of pancreatic, stomach, laryngeal, fallopian tube, and prostate cancer. It plays an important role in the DNA damage response signaling and has been implicated in various cellular processes such as cell cycle regulation, transcriptional regulation, chromatin remodeling, DNA DSBs, and apoptosis. BRCA1 contains an N-terminal C3HC4-type RING-HC finger, and two BRCT (BRCA1 C-terminus domain) repeats at the C-terminus. Pssm-ID: 438161 [Multi-domain] Cd Length: 94 Bit Score: 46.52 E-value: 3.43e-06
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| PBP2_AlgQ_like_4 | cd13583 | Periplasmic-binding component of alginate-specific ABC uptake system-like; contains the type 2 ... |
37-303 | 3.97e-06 | |||||||||
Periplasmic-binding component of alginate-specific ABC uptake system-like; contains the type 2 periplasmic binding fold; This subgroup includes uncharacterized periplasmic-binding proteins that are closely related to high molecular weight (HMW) alginate bining proteins (AlgQ1 and AlgQ2) found in gram-negative soil bacteria. The HMW alginate uptake system is composed of a novel pit formed on the cell surface and a pit-dependent ATP-binding cassette (ABC) transporter in the inner membrane. The transportation of HMW alginate from the pit to the ABC transporter is mediated by periplasmic HMW alginate-binding proteins (AlgQ1 and AlgQ2). Alginate is an anionic polysaccharide that is made up of alpha-L-mannuronate and its 5'-epimer, alpha-L-guluronate. Alginate is present in the cell walls of brown seaweeds, where it forms a viscous gum by binding water. Alginate is also produced by two bacteria genera Pseudomonas and Azotobacter. AlgQ1 and AlgQ2 belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. However, unlike other bacterial periplasmic-binding proteins that deliver small solutes to ABC transporters, AlgQ1/2 can bind a macromolecule and may have specificity for either sugar or a certain type of polysaccharide. Pssm-ID: 270301 [Multi-domain] Cd Length: 478 Bit Score: 50.82 E-value: 3.97e-06
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| RING-HC_TRIM21_C-IV | cd16596 | RING finger, HC subclass, found in tripartite motif-containing protein TRIM21 and similar ... |
422-471 | 4.36e-06 | |||||||||
RING finger, HC subclass, found in tripartite motif-containing protein TRIM21 and similar proteins; TRIM21, also known as 52 kDa Ro protein, 52 kDa ribonucleoprotein autoantigen Ro/SS-A, Ro(SS-A), RING finger protein 81 (RNF81), or Sjoegren syndrome type A antigen (SS-A), is a ubiquitously expressed E3 ubiquitin-protein ligase and a high affinity antibody receptor uniquely expressed in the cytosol of mammalian cells. As a cytosolic Fc receptor, TRIM21 binds the Fc of virus-associated antibodies and targets the complex in the cytosol for proteasomal degradation in a process known as antibody-dependent intracellular neutralization (ADIN), and provides an intracellular immune response to protect host defense against pathogen infection. It shows remarkably broad isotype specificity as it does not only bind IgG, but also IgM and IgA. Moreover, TRIM21 promotes the cytosolic DNA sensor cGAS and the cytosolic RNA sensor RIG-I sensing of viral genomes during infection by antibody-opsonized virus. It stimulates inflammatory signaling and activates innate transcription factors, such as nuclear factor-kappaB (NF-kappaB). TRIM21 also plays an essential role in p62-regulated redox homeostasis, suggesting it may be a viable target for treating pathological conditions resulting from oxidative damage. Furthermore, TRIM21 may have implications for various autoimmune diseases associated with uncontrolled antiviral signaling through the regulation of Nmi-IFI35 complex-mediated inhibition of innate antiviral response. TRIM21 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. Pssm-ID: 438258 [Multi-domain] Cd Length: 77 Bit Score: 45.66 E-value: 4.36e-06
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| RING-HC_CHR27-like | cd23142 | RING finger, HC subclass, found in Arabidopsis thaliana protein CHROMATIN REMODELING 27 (CHR27) ... |
424-466 | 4.67e-06 | |||||||||
RING finger, HC subclass, found in Arabidopsis thaliana protein CHROMATIN REMODELING 27 (CHR27) and similar proteins; CHR27, also called protein SNF2-RING-HELICASE-LIKE 1, is a probable helicase-like transcription factor involved in transcriptional gene silencing. It associates with SUVR2 and contributes to transcriptional gene silencing at RNA-directed DNA methylation (RdDM) target loci but also at RdDM-independent target loci. It may be involved in nucleosome positioning to form ordered nucleosome arrays on chromatin. It associates with SUVR2 and functions redundantly with FRG2. It is required for the efficient methylation of a broad range of RdDM target loci. CHR27 contains a typical C3HC4-type RING-HC finger. Pssm-ID: 438504 [Multi-domain] Cd Length: 55 Bit Score: 44.87 E-value: 4.67e-06
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| RING-HC_PEX10 | cd16527 | RING finger, HC subclass, found in peroxin-10 (PEX10) and similar proteins; PEX10, also known ... |
424-472 | 5.08e-06 | |||||||||
RING finger, HC subclass, found in peroxin-10 (PEX10) and similar proteins; PEX10, also known as peroxisome biogenesis factor 10, peroxisomal biogenesis factor 10, peroxisome assembly protein 10, or RING finger protein 69 (RNF69), is an integral peroxisomal membrane protein with two transmembrane regions and a C3HC4-type RING-HC finger within its cytoplasmically exposed C-terminus. It plays an essential role in peroxisome assembly, import of target substrates, and recycling or degradation of protein complexes and amino acids. It is an essential component of the spinal locomotor circuit, and thus its mutations may be involved in peroxisomal biogenesis disorders (PBD). Mutations in human PEX10 also result in autosomal recessive ataxia. Moreover, PEX10 functions as an E3-ubiquitin ligase with an E2, UBCH5C. It mono- or poly-ubiquitinates PEX5, a key player in peroxisomal matrix protein import, in a UBC4-dependent manner, to control PEX5 receptor recycling or degradation. It also links the E2 ubiquitin conjugating enzyme PEX4 to the protein import machinery of the peroxisome. Pssm-ID: 438190 [Multi-domain] Cd Length: 52 Bit Score: 44.53 E-value: 5.08e-06
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| RING-HC_RNF125 | cd16542 | RING finger, HC subclass, found in RING finger protein 125 (RNF125); RNF125, also known as ... |
424-467 | 5.11e-06 | |||||||||
RING finger, HC subclass, found in RING finger protein 125 (RNF125); RNF125, also known as T-cell RING activation protein 1 (TRAC-1), is an E3 ubiquitin-protein ligase that is predominantly expressed in lymphoid cells, and functions as a positive regulator of T cell activation. It also down-modulates HIV replication and inhibits pathogen-induced cytokine production. It negatively regulates type I interferon signaling, which conjugates Lys(48)-linked ubiquitination to retinoic acid-inducible gene-I (RIG-I) and subsequently leads to the proteasome-dependent degradation of RIG-I. Further, RNF125 conjugates ubiquitin to melanoma differentiation-associated gene 5 (MDA5), a family protein of RIG-I. It thus acts as a negative regulator of RIG-I signaling, and is a direct target of miR-15b in the context of Japanese encephalitis virus (JEV) infection. Moreover, RNF125 binds to and ubiquitinates JAK1, prompting its degradation and inhibition of receptor tyrosine kinase (RTK) expression. It also negatively regulates p53 function through physical interaction and ubiquitin-mediated proteasome degradation. Mutations in RNF125 may lead to overgrowth syndromes (OGS). RNF125, together with three closely related proteins: RNF114, RNF138 and RNF166, forms a novel family of ubiquitin ligases with a C3HC4-type RING-HC finger, a C2HC-, and two C2H2-type zinc fingers, as well as a ubiquitin interacting motif (UIM). The UIM of RNF125 binds K48-linked poly-ubiquitin chains and is, together with the RING domain, required for auto-ubiquitination. Pssm-ID: 438204 [Multi-domain] Cd Length: 50 Bit Score: 44.48 E-value: 5.11e-06
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| SBP_bac_6 | pfam13343 | Bacterial extracellular solute-binding protein; This family includes bacterial extracellular ... |
69-307 | 5.36e-06 | |||||||||
Bacterial extracellular solute-binding protein; This family includes bacterial extracellular solute-binding proteins. Pssm-ID: 463852 [Multi-domain] Cd Length: 247 Bit Score: 49.28 E-value: 5.36e-06
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| RING-HC_RNF170 | cd16553 | RING finger, HC subclass, found in RING finger protein 170 (RNF170) and similar proteins; ... |
423-467 | 5.81e-06 | |||||||||
RING finger, HC subclass, found in RING finger protein 170 (RNF170) and similar proteins; RNF170, also known as putative LAG1-interacting protein, is an endoplasmic reticulum (ER) membrane-bound E3 ubiquitin-protein ligase that mediates ubiquitination-dependent degradation of type-I inositol 1,4,5-trisphosphate (IP3) receptors (ITPR1) via the endoplasmic-reticulum-associated protein degradation (ERAD) pathway. A point mutation (arginine to cysteine at position 199) in the RNF170 gene is linked with autosomal-dominant sensory ataxia (ADSA), a disease characterized by neurodegeneration in the posterior columns of the spinal cord. RNF170 contains a C3HC4-type RING-HC finger. Pssm-ID: 438215 [Multi-domain] Cd Length: 57 Bit Score: 44.59 E-value: 5.81e-06
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| RING-HC_RNF146 | cd16546 | RING finger, HC subclass, found in RING finger protein 146 (RNF146) and similar proteins; ... |
424-472 | 5.87e-06 | |||||||||
RING finger, HC subclass, found in RING finger protein 146 (RNF146) and similar proteins; RNF146, also known as dactylidin, or iduna, is a cytoplasmic E3 ubiquitin-protein ligase that is responsible for PARylation-dependent ubiquitination (PARdU). It displays neuroprotective property due to its inhibition of Parthanatos, a PAR dependent cell death, via binding with Poly(ADP-ribose) (PAR). It also modulates PAR polymerase-1 (PARP-1)-mediated oxidative cell injury in cardiac myocytes. Moreover, RNF146 mediates tankyrase-dependent degradation of axin, thereby positively regulating Wnt signaling. It also facilitates DNA repair and protects against cell death induced by DNA damaging agents or gamma-irradiation by translocating to the nucleus after cellular injury and promoting the ubiquitination and degradation of various nuclear proteins involved in DNA damage repair. Furthermore, RNF146 is implicated in neurodegenerative disease and cancer development. It regulates the development and progression of non-small cell lung cancer (NSCLC) by enhancing cell growth, invasion, and survival. RNF146 contains an N-terminal C3HC4-type RING-HC finger followed by a WWE domain with a poly(ADP-ribose) (PAR) binding motif at the tail. Pssm-ID: 438208 [Multi-domain] Cd Length: 50 Bit Score: 44.30 E-value: 5.87e-06
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| RING-HC_TRIM7-like_C-IV | cd16594 | RING finger, HC subclass, found in tripartite motif-containing proteins, TRIM7, TRIM11 and ... |
422-464 | 6.26e-06 | |||||||||
RING finger, HC subclass, found in tripartite motif-containing proteins, TRIM7, TRIM11 and TRIM27, and similar proteins; TRIM7, TRIM11 and TRIM27, closely related tripartite motif-containing proteins, belong to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox2, and a coiled coil region, as well as a SPRY/B30.2 domain positioned C-terminal to the RBCC domain. TRIM7, also known as glycogenin-interacting protein (GNIP) or RING finger protein 90 (RNF90), is an E3 ubiquitin-protein ligase that mediates c-Jun/AP-1 activation by Ras signalling. Its phosphorylation and activation by MSK1 in response to direct activation by the Ras-Raf-MEK-ERK pathway can stimulate TRIM7 E3 ubiquitin ligase activity in mediating Lys63-linked ubiquitination of the AP-1 coactivator RACO-1, leading to RACO-1 protein stabilization. Moreover, TRIM7 binds and activates glycogenin, the self-glucosylating initiator of glycogen biosynthesis. TRIM11, also known as protein BIA1, or RING finger protein 92 (RNF92), is an E3 ubiquitin-protein ligase involved in the development of the central nervous system. It is overexpressed in high-grade gliomas and promotes proliferation, invasion, migration and glial tumor growth. TRIM11 acts as a potential therapeutic target for congenital central hypoventilation syndrome (CCHS) by mediating the degradation of CCHS-associated polyalanine-expanded Phox2b. TRIM11 modulates the function of neurogenic transcription factor Pax6 through the ubiquitin-proteosome system, and thus plays an essential role for Pax6-dependent neurogenesis. It also binds to and destabilizes a key component of the activator-mediated cofactor complex (ARC105), humanin, a neuroprotective peptide against Alzheimer's disease-relevant insults, and further regulates ARC105 function in transforming growth factor beta (TGFbeta) signaling. Moreover, TRIM11 negatively regulates retinoic acid-inducible gene-I (RIG-I)-mediated interferon-beta (IFNbeta) production and antiviral activity by targeting TANK-binding kinase-1 (TBK1). It may contribute to the endogenous restriction of retroviruses in cells. It enhances N-tropic murine leukemia virus (N-MLV) entry by interfering with Ref1 restriction. It also suppresses the early steps of human immunodeficiency virus HIV-1 transduction, resulting in decreased reverse transcripts. TRIM27, also known as RING finger protein 76 (RNF76), RET finger protein (RFP), or zinc finger protein RFP, is a nuclear E3 ubiquitin-protein ligase that is highly expressed in testis and in various tumor cell lines. Expression of TRIM27 is associated with prognosis of colon and endometrial cancers. TRIM27 was first identified as a fusion partner of the RET receptor tyrosine kinase. It functions as a transcriptional repressor and associates with several proteins involved in transcriptional activity, such as enhancer of polycomb 1 (Epc1), a member of the Polycomb group proteins, and Mi-2beta, a main component of the nucleosome remodeling and deacetylase (NuRD) complex, and the cell cycle regulator retinoblastoma protein (RB1). It also interacts with HDAC1, leading to downregulation of thioredoxin binding protein 2 (TBP-2), which inhibits the function of thioredoxin. Moreover, TRIM27 mediates Pax7-induced ubiquitination of MyoD in skeletal muscle atrophy. In addition, it inhibits muscle differentiation by modulating serum response factor (SRF) and Epc1. TRIM27 promotes a non-canonical polyubiquitination of PTEN, a lipid phosphatase that catalyzes PtdIns(3,4,5)P3 (PIP3) to PtdIns(4,5)P2 (PIP2). It is an IKKepsilon-interacting protein that regulates IkappaB kinase (IKK) function and negatively regulates signaling involved in the antiviral response and inflammation. TRIM27 also forms a protein complex with MBD4 or MBD2 or MBD3, and thus plays an important role in the enhancement of transcriptional repression through MBD proteins in tumorigenesis, spermatogenesis, and embryogenesis. It is a component of an estrogen receptor 1 (ESR1) regulatory complex that is involved in estrogen receptor-mediated transcription in MCF-7 cells. Pssm-ID: 438256 [Multi-domain] Cd Length: 61 Bit Score: 44.60 E-value: 6.26e-06
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| RING-HC_TRIM10_C-IV | cd16593 | RING finger, HC subclass, found in tripartite motif-containing protein 10 (TRIM10) and similar ... |
417-468 | 6.63e-06 | |||||||||
RING finger, HC subclass, found in tripartite motif-containing protein 10 (TRIM10) and similar proteins; TRIM10, also known as B30-RING finger protein (RFB30), RING finger protein 9 (RNF9), or hematopoietic RING finger 1 (HERF1), is a novel hematopoiesis-specific RING finger protein required for terminal differentiation of erythroid cells. TRIM10 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. Pssm-ID: 438255 [Multi-domain] Cd Length: 61 Bit Score: 44.51 E-value: 6.63e-06
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| vRING-HC-C4C4_RBBP6 | cd16620 | Variant RING finger, HC subclass (C4C4-type), found in retinoblastoma-binding protein 6 (RBBP6) ... |
415-464 | 8.48e-06 | |||||||||
Variant RING finger, HC subclass (C4C4-type), found in retinoblastoma-binding protein 6 (RBBP6) and similar proteins; RBBP6, also known as proliferation potential-related protein, protein P2P-R, retinoblastoma-binding Q protein 1 (RBQ-1), or p53-associated cellular protein of testis (PACT), is a nuclear E3 ubiquitin-protein ligase involved in multiple processes, such as the control of gene expression, mitosis, cell differentiation, and cell apoptosis. It plays a role in both promoting and inhibiting apoptosis in many human cancers, including esophageal, lung, hepatocellular, and colon cancers, familial myeloproliferative neoplasms, as well as in human immunodeficiency virus-associated nephropathy (HIVAN). It functions as an Rb- and p53-binding protein that plays an important role in chaperone-mediated ubiquitination and possibly in protein quality control. It acts as a scaffold protein to promote the assembly of the p53/TP53-MDM2 complex, resulting in an increase of MDM2-mediated ubiquitination and degradation of p53/TP53, and leading to both apoptosis and cell growth. It is also a double-stranded RNA-binding protein that plays a role in mRNA processing by regulating the human polyadenylation machinery and modulating expression of mRNAs with AU-rich 3' untranslated regions (UTRs). Moreover, RBBP6 ubiquitinates and destabilizes the transcriptional repressor ZBTB38 that negatively regulates transcription and levels of the MCM10 replication factor on chromatin. Furthermore, RBBP6 is involved in tunicamycin-induced apoptosis by mediating protein kinase (PKR) activation. RBBP6 contains an N-terminal ubiquitin-like domain and a C4C4-type RING finger, whose overall folding is similar to that of the typical C3HC4-type RING-HC finger. RBBP6 interacts with chaperones Hsp70 and Hsp40 through its N-terminal ubiquitin-like domain. It promotes the ubiquitination of p53 by Hdm2 in an E4-like manner through its RING finger. It also interacts directly with the pro-proliferative transcription factor Y-box-binding protein-1 (YB-1) via its RING finger. Pssm-ID: 438282 [Multi-domain] Cd Length: 55 Bit Score: 44.32 E-value: 8.48e-06
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| RING-HC_TRIM40-C-V | cd16583 | RING finger, HC subclass, found in tripartite motif-containing protein 40 (TRIM40) and similar ... |
424-462 | 8.71e-06 | |||||||||
RING finger, HC subclass, found in tripartite motif-containing protein 40 (TRIM40) and similar proteins; TRIM40, also known as probable E3 NEDD8-protein ligase or RING finger protein 35 (RNF35), is highly expressed in the gastrointestinal tract including the stomach, small intestine, and large intestine. It enhances neddylation of inhibitor of nuclear factor kappaB kinase subunit gamma (IKKgamma), inhibits the activity of nuclear factor-kappaB (NF-kappaB)-mediated transcription, and thus prevents inflammation-associated carcinogenesis in the gastrointestinal tract. TRIM40 belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domain, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as an uncharacterized region positioned C-terminal to the RBCC domain. Pssm-ID: 438245 [Multi-domain] Cd Length: 63 Bit Score: 44.44 E-value: 8.71e-06
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| RING-HC_TRIM5-like_C-IV | cd16591 | RING finger, HC subclass, found in tripartite motif-containing proteins TRIM5, TRIM6, TRIM22, ... |
422-471 | 8.94e-06 | |||||||||
RING finger, HC subclass, found in tripartite motif-containing proteins TRIM5, TRIM6, TRIM22, TRIM34 and similar proteins; TRIM5, TRIM6, TRIM22, and TRIM34, four closely related tripartite motif-containing proteins, belong to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. TRIM5, also known as RING finger protein 88 (RNF88), is a capsid-specific restriction factor that prevents infection from non-host-adapted retroviruses in a species-specific manner by binding to and destabilizing the retroviral capsid lattice before reverse transcription is completed. Its retroviral restriction activity correlates with the ability to activate TAK1-dependent innate immune signaling. TRIM5 also acts as a pattern recognition receptor that activates innate immune signaling in response to the retroviral capsid lattice. Moreover, TRIM5 plays a role in regulating autophagy through activation of autophagy regulator BECN1 by causing its dissociation from its inhibitors BCL2 and TAB2. It also plays a role in autophagy by acting as a selective autophagy receptor which recognizes and targets HIV-1 capsid protein p24 for autophagic destruction. TRIM6, also known as RING finger protein 89 (RNF89), is an E3-ubiquitin ligase that cooperates with the E2-ubiquitin conjugase UbE2K to catalyze the synthesis of unanchored K48-linked polyubiquitin chains, and further stimulates the interferon-I kappa B kinase epsilon (IKKepsilon) kinase-mediated antiviral response. It also regulates the transcriptional activity of Myc during the maintenance of embryonic stem (ES) cell pluripotency, and may act as a novel regulator for Myc-mediated transcription in ES cells. TRIM22, also known as 50 kDa-stimulated trans-acting factor (Staf-50) or RING finger protein 94 (RNF94), is an E3 ubiquitin-protein ligase that plays an integral role in the host innate immune response to viruses. It has been shown to inhibit the replication of a number of viruses, including HIV-1, hepatitis B, and influenza A. TRIM22 acts as a suppressor of basal HIV-1 long terminal repeat (LTR)-driven transcription by preventing the transcription factor specificity protein 1 (Sp1) binding to the HIV-1 promoter. It also controls FoxO4 activity and cell survival by directing Toll-like receptor 3 (TLR3)-stimulated cells toward type I interferon (IFN) type I gene induction or apoptosis. Moreover, TRIM22 can activate the noncanonical nuclear factor-kappaB (NF-kappaB) pathway by activating I kappa B kinase alpha (IKKalpha). It also regulates nucleotide binding oligomerization domain containing 2 (NOD2)-dependent activation of interferon-beta signaling and nuclear factor-kappaB. TRIM34, also known as interferon-responsive finger protein 1 or RING finger protein 21 (RNF21), may function as antiviral protein that contribute to the defense against retroviral infections. Pssm-ID: 438253 [Multi-domain] Cd Length: 72 Bit Score: 44.74 E-value: 8.94e-06
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| RING-HC_RNF5-like | cd16534 | RING finger, HC subclass, found in RING finger protein RNF5, RNF185 and similar proteins; RNF5 ... |
424-463 | 1.02e-05 | |||||||||
RING finger, HC subclass, found in RING finger protein RNF5, RNF185 and similar proteins; RNF5 and RNF185 are E3 ubiquitin-protein ligases that are anchored to the outer membrane of the endoplasmic reticulum (ER). RNF5 acts at early stages of cystic fibrosis (CF) transmembrane conductance regulator (CFTR) biosynthesis, and functions as a target for therapeutic modalities to antagonize mutant CFTR proteins in CF patients carrying the F508del allele. RNF185 controls the degradation of CFTR and CFTR F508del allele in a RING- and proteasome-dependent manner, but does not control that of other classical endoplasmic reticulum-associated degradation (ERAD) model substrates. Moreover, both RNF5 and RNF185 play important roles in cell adhesion and migration through the modulation of cell migration by ubiquitinating paxillin. Arabidopsis thaliana RING membrane-anchor proteins (AtRMAs) are also included in this family. They possess E3 ubiquitin-protein ligase activity and may play a role in the growth and development of Arabidopsis. All members of this family contain a C3HC4-type RING-HC finger. Pssm-ID: 438196 [Multi-domain] Cd Length: 44 Bit Score: 43.44 E-value: 1.02e-05
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| RING-HC_RNF151 | cd16547 | RING finger, HC subclass, found in RING finger protein 151 (RNF151) and similar proteins; ... |
424-468 | 1.11e-05 | |||||||||
RING finger, HC subclass, found in RING finger protein 151 (RNF151) and similar proteins; RNF151 is a testis-specific RING finger protein that interacts with dysbindin, a synaptic and microtubular protein that binds brain snapin, a SNARE-binding protein that mediates intracellular membrane fusion in both neuronal and non-neuronal cells. Thus, it may be involved in acrosome formation of spermatids by interacting with multiple proteins participating in membrane biogenesis and microtubule organization. RNF151 contains a C3HC4-type RING finger domain, a putative nuclear localization signal (NLS), and a TNF receptor associated factor (TRAF)-type zinc finger domain. Pssm-ID: 438209 [Multi-domain] Cd Length: 49 Bit Score: 43.60 E-value: 1.11e-05
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| RING-HC_COP1 | cd16504 | RING finger, HC subclass, found in constitutive photomorphogenesis protein 1 (COP1) and ... |
422-466 | 1.20e-05 | |||||||||
RING finger, HC subclass, found in constitutive photomorphogenesis protein 1 (COP1) and similar proteins; COP1, also known as RING finger and WD repeat domain protein 2 (RFWD2) or RING finger protein 200 (RNF200), is a central regulator of photomorphogenic development in plants, which targets key transcription factors for proteasome-dependent degradation. It is localized predominantly in the nucleus, but may also be present in the cytosol. Mammalian COP1 functions as an E3 ubiquitin-protein ligase that interacts with Jun transcription factors and modulates their transcriptional activity. It also interacts with and negatively regulates the tumor-suppressor protein p53. Moreover, COP1 associates with COP9 signalosome subunit 6 (CSN6), and is involved in 14-3-3sigma ubiquitin-mediated degradation. The CSN6-COP1 link enhances ubiquitin-mediated degradation of p27(Kip1), a critical CDK inhibitor involved in cell cycle regulation, to promote cancer cell growth. Furthermore, COP1 functions as the negative regulator of ETV1 and influences prognosis in triple-negative breast cancer. COP1 contains an N-terminal extension, a C3HC4-type RING-HC finger, a coiled coil domain, and seven WD40 repeats. In human COP1, a classic leucine-rich NES, and a novel bipartite NLS is bridged by the RING-HC finger. Pssm-ID: 438167 [Multi-domain] Cd Length: 47 Bit Score: 43.38 E-value: 1.20e-05
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| RING-HC_RING1-like | cd16531 | RING finger, HC subclass, found in really interesting new gene proteins RING1, RING2 and ... |
422-485 | 1.38e-05 | |||||||||
RING finger, HC subclass, found in really interesting new gene proteins RING1, RING2 and similar proteins; RING1, also known as polycomb complex protein RING1, RING finger protein 1 (RNF1), or RING finger protein 1A (RING1A), is a transcriptional repressor that is associated with the Polycomb group (PcG) protein complex involved in stable repression of gene activity. RING2, also known as huntingtin-interacting protein 2-interacting protein 3, HIP2-interacting protein 3, protein DinG, RING finger protein 1B (RING1B), RING finger protein 2 (RNF2), or RING finger protein BAP-1, is an E3 ubiquitin-protein ligase that interacts with both nucleosomal DNA and an acidic patch on histone H4 to achieve the specific monoubiquitination of K119 on histone H2A (H2AK119ub), thereby playing a central role in histone code and gene regulation. Both RING1 and RING2 are core components of polycomb repressive complex 1 (PRC1) that functions as an E3-ubuiquitin ligase transferring the mono-ubuiquitin mark to the C-terminal tail of Histone H2A at K118/K119. PRC1 is also capable of chromatin compaction, a function not requiring histone tails, and this activity appears important in gene silencing. RING2 acts as the main E3 ubiquitin ligase on histone H2A of the PRC1 complex, while RING1 may rather act as a modulator of RNF2/RING2 activity. Members of this family contain a C3HC4-type RING-HC finger. Pssm-ID: 438193 [Multi-domain] Cd Length: 66 Bit Score: 43.80 E-value: 1.38e-05
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| RING-HC_TRIM62_C-IV | cd16608 | RING finger, HC subclass, found in tripartite motif-containing protein 62 (TRIM62) and similar ... |
422-464 | 1.64e-05 | |||||||||
RING finger, HC subclass, found in tripartite motif-containing protein 62 (TRIM62) and similar proteins; TRIM62, also known as Ductal Epithelium Associated Ring Chromosome 1 (DEAR1), is a cytoplasmic E3 ubiquitin-protein ligase that was identified as a dominant regulator of acinar morphogenesis in the mammary gland. It is implicated in the inflammatory response of immune cells by regulating the Toll-like receptor 4 (TLR4) signaling pathway, leading to increased activity of the activator protein 1 (AP-1) transcription factor in primary macrophages. It is also involved in muscular protein homeostasis, especially during inflammation-induced atrophy, and may play a role in the pathogenesis of ICU-acquired weakness (ICUAW) by activating and maintaining inflammation in myocytes. Moreover, TRIM62 facilitates K27-linked poly-ubiquitination of CARD9 and also regulates CARD9-mediated anti-fungal immunity and intestinal inflammation. It also functions as a chromosome 1p35 tumor suppressor and negatively regulates transforming growth factor beta (TGFbeta)-driven epithelial-mesenchymal transition (EMT) by binding to and promoting the ubiquitination of SMAD3, a major effector of TGFbeta-mediated EMT. TRIM62 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. Pssm-ID: 438270 [Multi-domain] Cd Length: 52 Bit Score: 43.26 E-value: 1.64e-05
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| PBP2_AEPn_like | cd13548 | Substrate binding domain of a putative 2-amnioethylphosphonate-bindinig transporter, a member ... |
39-300 | 1.66e-05 | |||||||||
Substrate binding domain of a putative 2-amnioethylphosphonate-bindinig transporter, a member of the type 2 periplasmic binding fold superfamily; The substrate domain of this group shows a high homology to the periplasmic component of ferric iron transporter (Fbp), but its biochemical characterization has not been performed. The periplasmic iron binding protein plays an essential role in the iron uptake pathway of Gram-negative pathogenic bacteria from the Pasteurellaceae and Neisseriaceae families and is critical for survival of these pathogens within the host. After binding iron with high affinity, Fbp interacts with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The ferric iron-binding proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. Pssm-ID: 270266 [Multi-domain] Cd Length: 310 Bit Score: 48.33 E-value: 1.66e-05
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| RING-HC_TRIM47-like_C-IV | cd16604 | RING finger, HC subclass, found in tripartite motif-containing protein 47 (TRIM47) and similar ... |
424-464 | 1.81e-05 | |||||||||
RING finger, HC subclass, found in tripartite motif-containing protein 47 (TRIM47) and similar proteins; TRIM47, also known as gene overexpressed in astrocytoma protein (GOA) or RING finger protein 100 (RNF100), belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, a B-box, and two coiled coil domains, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. It plays an important role in the process of dedifferentiation that is associated with astrocytoma tumorigenesis. This subfamily also includes RING finger protein 135 (RNF135). RNF135, also known as RIG-I E3 ubiquitin ligase (REUL) or Riplet, is a widely expressed E3 ubiquitin-protein ligase that consists of an N-terminal C3HC4-type RING-HC finger and C-terminal B30.2/SPRY and PRY motifs, but lacks the B-box and coiled-coil domains that are also typically present in TRIM proteins. RNF135 serves as a specific retinoic acid-inducible gene-I (RIG-I)-interacting protein that ubiquitinates RIG-I and specifically stimulates RIG-I-mediated innate antiviral activity to produce antiviral type-I interferon (IFN) during the early phase of viral infection. It also has been identified as a bio-marker and therapy target of glioblastoma. It associates with the ERK signal transduction pathway and plays a role in glioblastoma cell proliferation, migration and cell cycle. Pssm-ID: 438266 [Multi-domain] Cd Length: 49 Bit Score: 43.18 E-value: 1.81e-05
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| RING-HC_PCGF | cd16525 | RING finger, HC subclass, found in Polycomb Group RING finger homologs (PCGF1, 2, 3, 4, 5 and ... |
423-463 | 1.87e-05 | |||||||||
RING finger, HC subclass, found in Polycomb Group RING finger homologs (PCGF1, 2, 3, 4, 5 and 6), and similar proteins; This subfamily includes six Polycomb Group (PcG) RING finger homologs (PCGF1/NSPc1, PCGF2/Mel-18, PCGF3, PCGF4/BMI1, PCGF5, and PCGF6/MBLR) that use epigenetic mechanisms to maintain or repress expression of their target genes. They were first discovered in fruit flies and are well known for silencing Hox genes through modulation of chromatin structure during embryonic development. PCGF homologs play important roles in cell proliferation, differentiation, and tumorigenesis. They all have been found to associate with ring finger protein 2 (RNF2). The RNF2-PCGF heterodimer is catalytically competent as an E3 ubiquitin transferase and is the scaffold for the assembly of additional components. Moreover, PCGF homologs are critical components in the assembly of distinct Polycomb Repression Complex 1 (PRC1) related complexes which is involved in the maintenance of gene repression and which target different genes through distinct mechanisms. The Drosophila PRC1 core complex is formed by the Polycomb (Pc), Polyhomeotic (Ph), Posterior sex combs (Psc), and Sex combs extra (Sce, also known as Ring) subunits. In mammals, the composition of PRC1 is much more diverse and varies depending on the cellular context. All PRC1 complexes contain homologs of the Drosophila Ring protein. Ring1A/RNF1 and Ring1B/RNF2 are E3 ubiquitin ligases that mark lysine 119 of histone H2A with a single ubiquitin group (H2AK119ub). Mammalian homologs of the Drosophila Psc protein, such as PCGF2/Mel-18 or PCGF4/BMI1, regulate PRC1 enzymatic activity. PRC1 complexes can be divided into at least two classes according to the presence or absence of CBX proteins, which are homologs of Drosophila Pc. Canonical PRC1 complexes contain CBX proteins that recognize and bind H3K27me3, the mark deposited by PRC2. Therefore, canonical PRC1 complexes and PRC2 can act together to repress gene transcription and maintain this repression through cell division. Non-canonical PRC1 complexes, containing RYBP (together with additional proteins, such as L3mbtl2 or Kdm2b) rather than the CBX proteins have recently been described in mammals. PCGF homologs contain a C3HC4-type RING-HC finger. Pssm-ID: 438188 [Multi-domain] Cd Length: 42 Bit Score: 42.60 E-value: 1.87e-05
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| RING-HC_RNF10 | cd16536 | RING finger, HC subclass, found in RING finger protein 10 (RNF10) and similar proteins; RNF10 ... |
422-471 | 1.90e-05 | |||||||||
RING finger, HC subclass, found in RING finger protein 10 (RNF10) and similar proteins; RNF10 is an E3 ubiquitin-protein ligase that interacts with mesenchyme Homeobox 2 (MEOX2) transcription factor, a regulator of the proliferation, differentiation and migration of vascular smooth muscle cells and cardiomyocytes; it enhances Meox2 activation of the p21 promoter. It also regulates the expression of myelin-associated glycoprotein (MAG) genes and is required for myelin production in Schwann cells of the peripheral nervous system. Moreover, RNF10 regulates retinoic acid-induced neuronal differentiation and the cell cycle exit of P19 embryonic carcinoma cells. RNF10 contains a C3HC4-type RING-HC finger and three putative nuclear localization signals. Pssm-ID: 438198 [Multi-domain] Cd Length: 54 Bit Score: 43.00 E-value: 1.90e-05
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| RING-HC_RNF113A_B | cd16539 | RING finger, HC subclass, found in RING finger proteins RNF113A, RNF113B, and similar proteins; ... |
423-464 | 2.21e-05 | |||||||||
RING finger, HC subclass, found in RING finger proteins RNF113A, RNF113B, and similar proteins; RNF113A, also known as zinc finger protein 183 (ZNF183), is an E3 ubiquitin-protein ligase that physically interacts with the E2 protein, UBE2U. A nonsense mutation in RNF113A is associated with an X-linked trichothiodystrophy (TTD). Its yeast ortholog Cwc24p is predicted to have a spliceosome function and acts in a complex with Cef1p to participate in pre-U3 snoRNA splicing, indirectly affecting pre-rRNA processing. It is also important for the U2 snRNP binding to primary transcripts and co-migrates with spliceosomes. Moreover, the ortholog of RNF113A in fruit flies may also act as a spliceosome and is hypothesized to be involved in splicing, namely within the central nervous system. The ortholog in Caenorhabditis elegans is involved in DNA repair of inter-strand crosslinks. RNF113B, also known as zinc finger protein 183-like 1, shows high sequence similarity with RNF113A. Both RNF113A and RNF113B contain a CCCH-type zinc finger, which is commonly found in RNA-binding proteins involved in splicing, and a C3HC4-type RING-HC finger, which is frequently found in E3 ubiquitin ligases. Pssm-ID: 438201 [Multi-domain] Cd Length: 54 Bit Score: 42.96 E-value: 2.21e-05
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| RING-HC_TRIM65_C-IV | cd16609 | RING finger, HC subclass, found in tripartite motif-containing protein TRIM65 and similar ... |
423-464 | 2.29e-05 | |||||||||
RING finger, HC subclass, found in tripartite motif-containing protein TRIM65 and similar proteins; TRIM65 is an E3 ubiquitin-protein ligase that interacts with the innate immune receptor MDA5, enhancing its ability to stimulate interferon-beta signaling. It functions as a potential oncogenic protein that negatively regulates p53 through ubiquitination, providing insight into the development of novel approaches targeting TRIM65 for non-small cell lung carcinoma (NSCLC) treatment, and also overcoming chemotherapy resistance. Moreover, TRIM65 negatively regulates microRNA-driven suppression of mRNA translation by targeting TNRC6 proteins for ubiquitination and degradation. TRIM65 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. Pssm-ID: 438271 [Multi-domain] Cd Length: 58 Bit Score: 43.13 E-value: 2.29e-05
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| RING-HC_TRIM26_C-IV | cd16598 | RING finger, HC subclass, found in tripartite motif-containing protein 26 (TRIM26) and similar ... |
422-462 | 2.50e-05 | |||||||||
RING finger, HC subclass, found in tripartite motif-containing protein 26 (TRIM26) and similar proteins; TRIM26, also known as acid finger protein (AFP), RING finger protein 95 (RNF95), or zinc finger protein 173 (ZNF173), is an E3 ubiquitin-protein ligase that negatively regulates interferon-beta production and antiviral response through polyubiquitination and degradation of nuclear transcription factor IRF3. It functions as an important regulator for RNA virus-triggered innate immune response by bridging TBK1 to NEMO (NF-kappaB essential modulator, also known as IKKgamma) and mediating TBK1 activation. It also acts as a novel tumor suppressor of hepatocellular carcinoma by regulating cancer cell proliferation, colony forming ability, migration, and invasion. TRIM26 belongs the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, a B-box, and two coiled coil domains, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. Pssm-ID: 438260 [Multi-domain] Cd Length: 64 Bit Score: 43.23 E-value: 2.50e-05
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| zf-RING_UBOX | pfam13445 | RING-type zinc-finger; This zinc-finger is a typical RING-type of plant ubiquitin ligases. |
424-460 | 2.91e-05 | |||||||||
RING-type zinc-finger; This zinc-finger is a typical RING-type of plant ubiquitin ligases. Pssm-ID: 463881 [Multi-domain] Cd Length: 38 Bit Score: 42.00 E-value: 2.91e-05
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| PBP2_polyamines | cd13523 | The periplasmic-binding component of ABC transporters involved in uptake of polyamines; ... |
38-297 | 2.94e-05 | |||||||||
The periplasmic-binding component of ABC transporters involved in uptake of polyamines; possess the type 2 periplasmic binding fold; This family represents the periplasmic substrate-binding proteins that function as the primary high-affinity receptors of ABC-type polyamine transport systems. Polyamine transport plays an essential role in the regulation of intracellular polyamine levels which are known to be elevated in rapidly proliferating cells and tumors. Natural polyamines are putrescine, spermindine, and spermine. They are polycations that play multiple roles in cell growth, survival and proliferation, as well as plant stress and disease resistance. They can interact with negatively charged molecules, such as nucleic acids, to modulate their functions. Members of this family belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. Pssm-ID: 270241 [Multi-domain] Cd Length: 268 Bit Score: 47.05 E-value: 2.94e-05
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| RING-HC_TRAF3 | cd16640 | RING finger, HC subclass, found in tumor necrosis factor (TNF) receptor-associated factor 3 ... |
424-463 | 2.97e-05 | |||||||||
RING finger, HC subclass, found in tumor necrosis factor (TNF) receptor-associated factor 3 (TRAF3) and similar proteins; TRAF3, also known as CAP-1, CD40 receptor-associated factor 1 (CRAF1), CD40-binding protein (CD40BP), or LMP1-associated protein 1 (LAP1), is a member of the TRAF protein family, which mainly functions in the immune system, where it mediates signaling through tumor necrosis factor receptors (TNFRs) and interleukin-1/Toll-like receptors (IL-1/TLRs). It also plays a unique cell type-specific and critical role in the restraint of B-cell homeostatic survival, a role with important implications for both B-cell differentiation and the pathogenesis of B-cell malignancies. TRAF3 differentially regulates differentiation of specific T cell subsets. It is required for iNKT cell development, restrains Treg cell development in the thymus, and plays an essential role in the homeostasis of central memory CD8+ T cells. TRAF3 contains an N-terminal domain with a typical C3HC4-type RING-HC finger and several zinc fingers, and a C-terminal TRAF domain that comprises a coiled coil domain, and a conserved TRAF-C domain. Pssm-ID: 438302 [Multi-domain] Cd Length: 42 Bit Score: 42.19 E-value: 2.97e-05
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| PBP2_PotD_PotF_like_3 | cd13664 | TThe periplasmic substrate-binding component of an uncharacterized active transport system ... |
34-94 | 4.10e-05 | |||||||||
TThe periplasmic substrate-binding component of an uncharacterized active transport system closely related to spermidine and putrescine transporters; contains the type 2 periplasmic binding fold; This family represents the periplasmic substrate-binding domain that functions as the primary high-affinity receptors of ABC-type polyamine transport systems. Polyamine transport plays an essential role in the regulation of intracellular polyamine levels which are known to be elevated in rapidly proliferating cells and tumors. Natural polyamines are putrescine, spermindine, and spermine. They are polycations that play multiple roles in cell growth, survival and proliferation, and plant stress and disease resistance. They can interact with negatively charged molecules, such as nucleic acids, to modulate their functions. Members of this family belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. Pssm-ID: 270382 [Multi-domain] Cd Length: 315 Bit Score: 46.97 E-value: 4.10e-05
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| RING-HC_LONFs_rpt1 | cd16513 | first RING finger, HC subclass, found in the LON peptidase N-terminal domain and RING finger ... |
422-469 | 5.45e-05 | |||||||||
first RING finger, HC subclass, found in the LON peptidase N-terminal domain and RING finger protein family; The LON peptidase N-terminal domain and RING finger protein family includes LONRF1 (also known as RING finger protein 191 or RNF191), LONRF2 (also known as RING finger protein 192, RNF192, or neuroblastoma apoptosis-related protease), LONRF3 (also known as RING finger protein 127 or RNF127), which are characterized by containing two C3HC4-type RING-HC fingers, four tetratricopeptide (TPR) repeats, and an ATP-dependent protease La (LON) substrate-binding domain at the C-terminus. Their biological functions remain unclear. This model corresponds to the first RING-HC finger. Pssm-ID: 438176 [Multi-domain] Cd Length: 47 Bit Score: 41.52 E-value: 5.45e-05
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| RING-HC_TRIM59_C-V | cd16763 | RING finger, HC subclass, found in tripartite motif-containing protein 59 (TRIM59) and similar ... |
422-462 | 5.46e-05 | |||||||||
RING finger, HC subclass, found in tripartite motif-containing protein 59 (TRIM59) and similar proteins; TRIM59, also known as RING finger protein 104 (RNF104) or tumor suppressor TSBF-1, is a putative E3 ubiquitin-protein ligase that functions as a novel multiple cancer biomarker for immunohistochemical detection of early tumorigenesis. It is upregulated in gastric cancer and promotes gastric carcinogenesis by interacting with and targeting the P53 tumor suppressor for its ubiquitination and degradation. It also acts as a novel accessory molecule involved in cytotoxicity of BCG-activated macrophages (BAM). Moreover, TRIM59 may serve as a multifunctional regulator for innate immune signaling pathways. It interacts with ECSIT and negatively regulates nuclear factor-kappaB (NF- kappa B) and interferon regulatory factor (IRF)-3/7-mediated signal pathways. TRIM59 belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domain, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region. In addition, TRIM59 contains a C-terminal transmembrane domain. Pssm-ID: 438419 [Multi-domain] Cd Length: 56 Bit Score: 41.82 E-value: 5.46e-05
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| RING-HC_AtBARD1-like | cd23146 | RING finger, HC subclass, found in Arabidopsis thaliana BRCA1-associated RING domain protein 1 ... |
423-464 | 7.94e-05 | |||||||||
RING finger, HC subclass, found in Arabidopsis thaliana BRCA1-associated RING domain protein 1 (AtBARD1) and similar proteins; AtBARD1, also called protein REPRESSOR OF WUSCHEL 1, binds specifically to H3K4me3 regions of target gene (e.g. WUS and WOX5) promoters to repress their transcription via chromatin remodeling. It is required for the shoot apical meristem (SAM) organization and maintenance, by confining WUS expression to the organizing center, and for the quiescent center (QC) development in the root apical meristem (RAM), by repressing WOX5 expression in the root proximal meristem. AtBARD1 plays a role in DNA repair and in cell-cycle control. It is required for the repair of DNA double-strand breaks (DSBs), both natural and induced by genotoxic stress, by homologous recombination (HR). AtBARD1 contains a typical C3HC4-type RING-HC finger. Pssm-ID: 438508 [Multi-domain] Cd Length: 54 Bit Score: 41.30 E-value: 7.94e-05
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| RING-HC_MSL2 | cd16522 | RING finger found in Drosophila melanogaster male-specific lethal-2 (MSL2) and similar ... |
418-462 | 9.38e-05 | |||||||||
RING finger found in Drosophila melanogaster male-specific lethal-2 (MSL2) and similar proteins; MSL2, also known as RING finger protein 184 (RNF184), is a putative DNA-binding protein required for X chromosome dosage compensation in Drosophila males. Its expression is sex specifically regulated by Sex-lethal. Drosophila dosage compensation proteins MOF, MSL1, MSL2, and MSL3 are essential for elevating transcription of the single X chromosome in the male (X chromosome dosage compensation). MSL2 plays a critical role in translation and/or stability of MSL1 in males. In complex with MSL1, it acts as an E3 ubiquitin ligase that promotes ubiquitination of histone H2B. MSL2 contains a C3HC4-type RING-HC finger and a metallothionein-like domain with eight conserved and two non-conserved cysteines, as well as a positively and a negatively charged amino acid residue cluster and a coiled coil domain that may be involved in protein-protein interactions. This subfamily also includes many male-specific lethal-2 homologs from bilaterians. Pssm-ID: 438185 Cd Length: 60 Bit Score: 41.27 E-value: 9.38e-05
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| RING-HC_CHFR | cd16503 | RING finger, HC subclass, found in checkpoint with forkhead and RING finger domains protein ... |
423-466 | 9.76e-05 | |||||||||
RING finger, HC subclass, found in checkpoint with forkhead and RING finger domains protein (CHFR); CHFR, also known as RING finger protein 196 (RNF196), is a checkpoint protein that delays entry into mitosis in response to stress. It functions as an E3 ubiquitin ligase that ubiquitinates and degrades its target proteins, such as Aurora-A, Plk1, Kif22, and PARP-1, which are critical for proper mitotic transitions. It also plays an important role in cell cycle progression and tumor suppression, and is negatively regulated by SUMOylation-mediated proteasomal ubiquitylation. Moreover, CHFR is involved in the early stage of the DNA damage response, which mediates the crosstalk between ubiquitination and poly-ADP-ribosylation. CHFR contains a fork head associated (FHA) domain and a C3HC4-type RING-HC finger. Pssm-ID: 438166 [Multi-domain] Cd Length: 55 Bit Score: 41.20 E-value: 9.76e-05
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| RING-HC_UHRF | cd16613 | RING finger, HC subclass, found in ubiquitin-like PHD and RING finger domain-containing ... |
423-466 | 9.97e-05 | |||||||||
RING finger, HC subclass, found in ubiquitin-like PHD and RING finger domain-containing proteins, UHRF1 and UHRF2, and similar proteins; UHRF1 is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumor suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of transcription factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF2 was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation, but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) by interacting with the HBV core protein and promoting its degradation. Both UHRF1 and UHRF2 contain an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET- and RING-associated (SRA) domain, and a C-terminal C3HC4-type RING-HC finger. Pssm-ID: 438275 [Multi-domain] Cd Length: 46 Bit Score: 40.80 E-value: 9.97e-05
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| RING-HC_LNX3 | cd16718 | RING finger, HC subclass, found in ligand of numb protein X 3 (LNX3); LNX3, also known as PDZ ... |
424-460 | 1.00e-04 | |||||||||
RING finger, HC subclass, found in ligand of numb protein X 3 (LNX3); LNX3, also known as PDZ domain-containing RING finger protein 3 (PDZRN3), or Semaphorin cytoplasmic domain-associated protein 3 (SEMACAP3), is an E3 ubiquitin-protein ligase that was first identified as a Semaphorin-binding partner. It is also responsible for the ubiquitination and degradation of Numb, a component of the Notch signaling pathway that functions in the specification of cell fates during development and is known to control cell numbers during neurogenesis in vertebrates. LNX3 acts as a negative regulator of osteoblast differentiation by inhibiting Wnt-beta-catenin signaling. LNX3 also plays an important role in neuromuscular junction formation. It interacts with and ubiquitinates the muscle specific tyrosine kinase (MuSK), thus promoting its endocytosis and negatively regulating the cell surface expression of this key regulator of postsynaptic assembly. LNX3 contains an N-terminal C3HC4-type RING-HC finger, two PDZ domains, and a C-terminal LNX3 homology (LNX3H) domain. Pssm-ID: 438378 [Multi-domain] Cd Length: 47 Bit Score: 40.74 E-value: 1.00e-04
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| RING-HC_EHV1-like | cd23130 | RING finger, HC subclass, found in Equid alphaherpesvirus 1 (Equine herpesvirus 1/EHV-1) ... |
424-464 | 1.13e-04 | |||||||||
RING finger, HC subclass, found in Equid alphaherpesvirus 1 (Equine herpesvirus 1/EHV-1) regulatory protein and similar proteins; EHV-1 regulatory protein belongs to the Vmw110 (IPC0) protein family. It contains a typical C3HC4-type RING-HC finger and binds zinc stably. Pssm-ID: 438492 [Multi-domain] Cd Length: 51 Bit Score: 40.80 E-value: 1.13e-04
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| mRING-HC-C3HC3D_TRAF7 | cd16644 | Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) ... |
420-466 | 1.21e-04 | |||||||||
Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) receptor-associated factor 7 (TRAF7) and similar proteins; TRAF7, also known as RING finger and WD repeat-containing protein 1 or RING finger protein 119 (RNF119), is an E3 ubiquitin-protein ligase involved in signal transduction pathways that lead either to activation or repression of NF-kappaB transcription factor by promoting K29-linked ubiquitination of several cellular targets, including the NF-kappaB essential modulator (NEMO) and the p65 subunit of NF-kappaB transcription factor. It is also involved in K29-linked polyubiquitination that has been implicated in lysosomal degradation of proteins. Moreover, TRAF7 is required for K48-linked ubiquitination of p53, a key tumor suppressor and a master regulator of various signaling pathways, such as those related to apoptosis, cell cycle and DNA repair. It is also required for tumor necrosis factor alpha (TNFalpha)-induced Jun N-terminal kinase activation and promotes cell death by regulating polyubiquitination and lysosomal degradation of c-FLIP protein. Furthermore, TRAF7 functions as small ubiquitin-like modifier (SUMO) E3 ligase involved in other post-translational modification, such as sumoylation. It binds to and stimulates sumoylation of the proto-oncogene product c-Myb, a transcription factor regulating proliferation and differentiation of hematopoietic cells. It potentiates MEKK3-induced AP1 and CHOP activation and induces apoptosis. Meanwhile, TRAF7 mediates MyoD1 regulation of the pathway and cell-cycle progression in myoblasts. It also plays a role in Toll-like receptors (TLR) signaling. TRAF7 contains an N-terminal domain with a modified C3HC3D-type RING-HC finger and an adjacent zinc finger, and a unique C-terminal domain that comprises a coiled coil domain and seven WD40 repeats. Pssm-ID: 438306 [Multi-domain] Cd Length: 47 Bit Score: 40.80 E-value: 1.21e-04
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| mRING-HC-C4C4_TRIM37_C-VIII | cd16619 | Modified RING finger, HC subclass (C4C4-type), found in tripartite motif-containing protein 37 ... |
422-462 | 1.29e-04 | |||||||||
Modified RING finger, HC subclass (C4C4-type), found in tripartite motif-containing protein 37 (TRIM37) and similar proteins; TRIM37, also known as mulibrey nanism protein, or MUL, is a peroxisomal E3 ubiquitin-protein ligase that is involved in the tumorigenesis of several cancer types, including pancreatic ductal adenocarcinoma (PDAC), hepatocellular carcinoma (HCC), breast cancer, and sporadic fibrothecoma. It mono-ubiquitinates histone H2A, a chromatin modification associated with transcriptional repression. Moreover, TRIM37 possesses anti-HIV-1 activity, and interferes with viral DNA synthesis. Mutations in the human TRIM37 gene (also known as MUL) cause Mulibrey (muscle-liver-brain-eye) nanism, a rare growth disorder of prenatal onset characterized by dysmorphic features, pericardial constriction, and hepatomegaly. TRIM37 belongs to the C-VIII subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C4C4-type RING finger, whose overall folding is similar to that of the typical C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a MATH (meprin and TRAF-C homology) domain positioned C-terminal to the RBCC domain. Its MATH domain has been shown to interact with the TRAF (TNF-Receptor-Associated Factor) domain of six known TRAFs in vitro. Pssm-ID: 438281 [Multi-domain] Cd Length: 43 Bit Score: 40.42 E-value: 1.29e-04
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| RING-HC_BARD1 | cd16496 | RING finger, HC subclass, found in BRCA1-associated RING domain protein 1 (BARD-1) and similar ... |
418-489 | 1.31e-04 | |||||||||
RING finger, HC subclass, found in BRCA1-associated RING domain protein 1 (BARD-1) and similar proteins; BARD-1 is a critical factor in BRCA1-mediated tumor suppression and may also serve as a target for tumorigenic lesions in some human cancers. It associates with BRCA1 (breast cancer-1) to form a heterodimeric BRCA1/BARD1 complex that is responsible for maintaining genomic stability through nuclear functions involving DNA damage signaling and repair, transcriptional regulation, and cell cycle control. The BRCA1/BARD1 complex catalyzes autoubiquitination of BRCA1 and trans ubiquitination of other protein substrates. Its E3 ligase activity is dramatically reduced in the presence of UBX domain protein 1 (UBXN1). BARD-1 contains an C3HC4-type RING-HC finger that binds BRCA1 at its N-terminus and three tandem ankyrin repeats and tandem BRCT repeat domains at its C-terminus. The BRCT repeats bind CstF-50 (cleavage stimulation factor) to modulate mRNA processing and RNAP II stability in response to DNA damage. Pssm-ID: 438159 [Multi-domain] Cd Length: 86 Bit Score: 41.94 E-value: 1.31e-04
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| RING-HC_PCGF5 | cd16737 | RING finger found in polycomb group RING finger protein 5 (PCGF5) and similar proteins; PCGF5, ... |
417-473 | 1.53e-04 | |||||||||
RING finger found in polycomb group RING finger protein 5 (PCGF5) and similar proteins; PCGF5, also known as RING finger protein 159 (RNF159), is one of six PcG RING finger (PCGF) homologs (PCGF1/NSPc1, PCGF2/Mel-18, PCGF3, PCGF4/BMI1, PCGF5, and PCGF6/MBLR) and serves as the core component of a Polycomb repressive complex 1 (PRC1). Like other PCGF homologs, PCGF5 associates with ring finger protein 2 (RNF2) to form a RNF2-PCGF heterodimer, which is catalytically competent as an E3 ubiquitin transferase and is the scaffold for the assembly of additional components. PCGF5 contains a C3HC4-type RING-HC finger. Pssm-ID: 438395 [Multi-domain] Cd Length: 95 Bit Score: 41.67 E-value: 1.53e-04
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| RING-HC_RNF114 | cd16540 | RING finger, HC subclass, found in RING finger protein 114 (RNF114) and similar proteins; ... |
423-466 | 1.66e-04 | |||||||||
RING finger, HC subclass, found in RING finger protein 114 (RNF114) and similar proteins; RNF114, also known as zinc finger protein 228 (ZNF228) or zinc finger protein 313 (ZNF313), is a p21(WAF1)-targeting ubiquitin E3 ligase that interacts with X-linked inhibitor of apoptosis (XIAP)-associated factor 1 (XAF1) and may play a role in p53-mediated cell-fate decisions. It is involved in the immune response to double-stranded RNA in disease pathogenesis. Moreover, RNF114 interacts with A20 and modulates its ubiquitylation. It negatively regulates nuclear factor-kappaB (NF-kappaB)-dependent transcription and positively regulates T-cell activation. RNF114 may play a putative role in the regulation of immune responses, since it corresponds to a novel psoriasis susceptibility gene, ZNF313. RNF114, together with three closely related proteins: RNF125, RNF138 and RNF166, forms a novel family of ubiquitin ligases with a C3HC4-type RING-HC finger, a C2HC-, and two C2H2-type zinc fingers, as well as a ubiquitin interacting motif (UIM). Pssm-ID: 438202 [Multi-domain] Cd Length: 46 Bit Score: 40.13 E-value: 1.66e-04
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| RING-HC_BAR | cd16497 | RING finger, HC subclass, found in bifunctional apoptosis regulator (BAR); BAR, also known as ... |
424-467 | 1.68e-04 | |||||||||
RING finger, HC subclass, found in bifunctional apoptosis regulator (BAR); BAR, also known as RING finger protein 47, was originally identified as an inhibitor of Bax-induced apoptosis. It participates in the block of apoptosis induced by TNF-family death receptors (extrinsic pathway) and mitochondria-dependent apoptosis (intrinsic pathway). BAR is predominantly expressed by neurons in the central nervous system and is involved in the regulation of neuronal survival. It is an endoplasmic reticulum (ER)-associated RING-type E3 ubiquitin ligase that interacts with BI-1 protein and post-translationally regulates its stability, as well as functioning in ER stress. BAR contains an N-terminal C3HC4-type RING-HC finger, a SAM domain, a coiled-coil domain, and a C-terminal transmembrane (TM) domain. This model corresponds to the RING-HC finger responsible for the binding of ubiquitin conjugating enzymes (E2s). Pssm-ID: 438160 [Multi-domain] Cd Length: 52 Bit Score: 40.57 E-value: 1.68e-04
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| RING-HC_TRIM72_C-IV | cd16612 | RING finger, HC subclass, found in tripartite motif-containing protein 72 (TRIM72) and similar ... |
423-462 | 1.72e-04 | |||||||||
RING finger, HC subclass, found in tripartite motif-containing protein 72 (TRIM72) and similar proteins; TRIM72, also known as Mitsugumin-53 (MG53), is a muscle-specific protein that plays a central role in cell membrane repair by nucleating the assembly of the repair machinery at muscle injury sites. It is required in repair of alveolar epithelial cells under plasma membrane stress failure. It interacts with dysferlin to regulate sarcolemmal repair. Upregulation of TRIM72 develops obesity, systemic insulin resistance, dyslipidemia, and hyperglycemia, as well as induces diabetic cardiomyopathy through transcriptional activation of the peroxisome proliferation-activated receptor alpha (PPAR-alpha) signaling pathway. Compensation for the absence of AKT signaling by ERK signaling during TRIM72 overexpression leads to pathological hypertrophy. Moreover, TRIM72 functions as a novel negative feedback regulator of myogenesis by targeting insulin receptor substrate-1 (IRS-1). It is transcriptionally activated by the synergism of myogenin (MyoD) and myocyte enhancer factor 2 (MEF2). TRIM72 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. Pssm-ID: 438274 [Multi-domain] Cd Length: 60 Bit Score: 40.49 E-value: 1.72e-04
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| PBP2_TpPotD_like | cd13662 | The periplasmic substrate-binding component of an ABC-type polyamine transport system from ... |
37-165 | 1.76e-04 | |||||||||
The periplasmic substrate-binding component of an ABC-type polyamine transport system from Treponema pallidum and related proteins; contains the type 2 periplasmic binding fold; This group includes the polyamine-binding component of an ABC-type polyamine transport system from Treponema pallidum and closely related proteins, which is homologous to the spermidine-preferring periplasmic substrate-binding protein component (PotD)of ABC transport system. Polyamine transport plays an essential role in the regulation of intracellular polyamine levels which are known to be elevated in rapidly proliferating cells and tumors. Natural polyamines are putrescine, spermindine, and spermine. They are polycations that play multiple roles in cell growth, survival and proliferation, as well as plant stress and disease resistance. They can interact with negatively charged molecules, such as nucleic acids, to modulate their functions. Members of this family belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. Pssm-ID: 270380 Cd Length: 312 Bit Score: 45.20 E-value: 1.76e-04
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| RING-HC_TRIM2_like_C-VII | cd16586 | RING finger, HC subclass, found in tripartite motif-containing protein TRIM2, TRIM3, and ... |
422-462 | 1.79e-04 | |||||||||
RING finger, HC subclass, found in tripartite motif-containing protein TRIM2, TRIM3, and similar proteins; TRIM2, also known as RING finger protein 86 (RNF86), is an E3 ubiquitin-protein ligase that ubiquitinates the neurofilament light chain, a component of the intermediate filament in axons. Loss of function of TRIM2 results in early-onset axonal neuropathy. TRIM3, also known as brain-expressed RING finger protein (BERP), RING finger protein 97 (RNF97), or RING finger protein 22 (RNF22), is an E3 ubiquitin-protein ligase involved in the pathogenesis of various cancers. It also plays an important role in the central nervous system (CNS). In addition, TRIM3 may be involved in vesicular trafficking via its association with the cytoskeleton-associated-recycling or transport (CART) complex that is necessary for efficient transferrin receptor recycling, but not for epidermal growth factor receptor (EGFR) degradation. Both TRIM2 and TRIM3 belong to the C-VII subclass of the TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain. Pssm-ID: 438248 [Multi-domain] Cd Length: 45 Bit Score: 40.13 E-value: 1.79e-04
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| PRK15046 | PRK15046 | 2-aminoethylphosphonate ABC transporter substrate-binding protein; Provisional |
37-308 | 1.87e-04 | |||||||||
2-aminoethylphosphonate ABC transporter substrate-binding protein; Provisional Pssm-ID: 237887 [Multi-domain] Cd Length: 349 Bit Score: 45.06 E-value: 1.87e-04
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| zf-C3HC4_3 | pfam13920 | Zinc finger, C3HC4 type (RING finger); |
423-465 | 1.93e-04 | |||||||||
Zinc finger, C3HC4 type (RING finger); Pssm-ID: 464042 [Multi-domain] Cd Length: 50 Bit Score: 40.05 E-value: 1.93e-04
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| RING-HC_ORTHRUS_rpt1 | cd23138 | first RING finger, HC subclass, found in Arabidopsis thaliana ORTHRUS and similar proteins; ... |
424-462 | 2.18e-04 | |||||||||
first RING finger, HC subclass, found in Arabidopsis thaliana ORTHRUS and similar proteins; This subfamily includes Arabidopsis thaliana ORTHRUS 1-5. They are E3 ubiquitin-protein ligases that may participate in CpG methylation-dependent transcriptional regulation and/or epigenetic transcriptional silencing. ORTHRUS 1 mediates ubiquitination with the E2 ubiquitin-conjugating enzymes UBC11, UBC8 and UBC8 homologs (e.g. UBC10, UBC11, UBC28 and UBC29) but not with UBC27, UBC30, UBC32, UBC34 and UBC36. ORTHRUS 2 and 5 mediate ubiquitination with the E2 ubiquitin-conjugating enzyme UBC11. ORTHRUS 1 and 2 promote methylation-mediated gene silencing leading, for example, to early flowering. They can bind to CpG, CpNpG, and CpNpN DNA motifs, with a strong preference for methylated forms, and with highest affinity for CpG substrates. Members of this subfamily contain two typical C3HC4-type RING-HC fingers. This model corresponds to the first one. Pssm-ID: 438500 [Multi-domain] Cd Length: 48 Bit Score: 40.12 E-value: 2.18e-04
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| RING-HC_TRIM41-like_C-IV | cd16602 | RING finger, HC subclass, found in tripartite motif-containing proteins TRIM41, TRIM52 and ... |
424-464 | 2.34e-04 | |||||||||
RING finger, HC subclass, found in tripartite motif-containing proteins TRIM41, TRIM52 and similar proteins; TRIM41 and TRIM52, two closely related tripartite motif-containing proteins, have dramatically expanded RING domains compared with the rest of the TRIM family proteins. TRIM41 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. In contrast, TRIM52 lacks the putative viral recognition SPRY/B30.2 domain, and thus has been classified to the C-V subclass of the TRIM family that contains only RBCC domains. TRIM41, also known as RING finger-interacting protein with C kinase (RINCK), is an E3 ubiquitin-protein ligase that promotes the ubiquitination of protein kinase C (PKC) isozymes in cells. It specifically recognizes the C1 domain of PKC isozymes. It controls the amplitude of PKC signaling by controlling the amount of PKC in the cell. TRIM52, also known as RING finger protein 102 (RNF102), is encoded by a novel, noncanonical antiviral TRIM52 gene in primate genomes with unique specificity determined by the rapidly evolving RING domain. Pssm-ID: 438264 [Multi-domain] Cd Length: 53 Bit Score: 39.91 E-value: 2.34e-04
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| RING-HC_TRIM4_C-IV | cd16590 | RING finger, HC subclass, found in tripartite motif-containing protein TRIM4 and similar ... |
417-471 | 2.52e-04 | |||||||||
RING finger, HC subclass, found in tripartite motif-containing protein TRIM4 and similar proteins; TRIM4 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox2, and a coiled coil region, as well as a SPRY/B30.2 domain positioned C-terminal to the RBCC domain. TRIM4, also known as RING finger protein 87 (RNF87), is a cytoplasmic E3 ubiquitin-protein ligase that has recently evolved and is present only in higher mammals. It transiently interacts with mitochondria, induces mitochondrial aggregation and sensitizes the cells to hydrogen peroxide (H2O2) induced death. Its interaction with peroxiredoxin 1 (PRX1) is critical for the regulation of H2O2 induced cell death. Moreover, TRIM4 functions as a positive regulator of RIG-I-mediated type I interferon induction. It regulates the K63-linked ubiquitination of RIG-1 and assembly of antiviral signaling complex at the mitochondria. Pssm-ID: 438252 [Multi-domain] Cd Length: 61 Bit Score: 40.40 E-value: 2.52e-04
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| PEX10 | COG5574 | RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, ... |
403-472 | 2.63e-04 | |||||||||
RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]; Pssm-ID: 227861 [Multi-domain] Cd Length: 271 Bit Score: 44.11 E-value: 2.63e-04
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| RING-HC_TRIM69_C-IV | cd16611 | RING finger, HC subclass, found in tripartite motif-containing protein 69 (TRIM69) and similar ... |
424-464 | 2.73e-04 | |||||||||
RING finger, HC subclass, found in tripartite motif-containing protein 69 (TRIM69) and similar proteins; TRIM69, also known as RFP-like domain-containing protein trimless or RING finger protein 36 (RNF36), is a testis E3 ubiquitin-protein ligase that plays a specific role in apoptosis and may also play an important role in germ cell homeostasis during spermatogenesis. TRIM69 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. Pssm-ID: 438273 [Multi-domain] Cd Length: 59 Bit Score: 40.13 E-value: 2.73e-04
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| PBP2_Fbp_like_5 | cd13551 | Substrate binding domain of an uncharacterized ferric iron transporter, a member of the type 2 ... |
83-293 | 3.19e-04 | |||||||||
Substrate binding domain of an uncharacterized ferric iron transporter, a member of the type 2 periplasmic binding fold superfamily; The periplasmic iron binding protein plays an essential role in the iron uptake pathway of Gram-negative pathogenic bacteria from the Pasteurellaceae and Neisseriaceae families and is critical for survival of these pathogens within the host. This periplasmic domain (Fbp) has high affinity for ferric iron and serves as the primary receptor for transport. After binding iron with high affinity, Fbp interacts with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The ferric iron-binding proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. Pssm-ID: 270269 [Multi-domain] Cd Length: 267 Bit Score: 43.93 E-value: 3.19e-04
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| RING-HC_TRIM35_C-IV | cd16599 | RING finger, HC subclass, found in tripartite motif-containing protein 35 (TRIM35) and similar ... |
422-471 | 3.76e-04 | |||||||||
RING finger, HC subclass, found in tripartite motif-containing protein 35 (TRIM35) and similar proteins; TRIM35, also known as hemopoietic lineage switch protein 5 (HLS5), is a putative hepatocellular carcinoma (HCC) suppressor that inhibits phosphorylation of pyruvate kinase isoform M2 (PKM2), which is involved in aerobic glycolysis of cancer cells and further suppresses the Warburg effect and tumorigenicity in HCC. It also negatively regulates Toll-like receptor 7 (TLR7)- and TLR9-mediated type I interferon production by suppressing the stability of interferon regulatory factor 7 (IRF7). Moreover, TRIM35 regulates erythroid differentiation by modulating globin transcription factor 1 (GATA-1) activity. TRIM35 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. Pssm-ID: 438261 [Multi-domain] Cd Length: 66 Bit Score: 39.75 E-value: 3.76e-04
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| RING-HC_RNF168 | cd16550 | RING finger, HC subclass, found in RING finger protein 168 (RNF168) and similar proteins; ... |
422-462 | 4.13e-04 | |||||||||
RING finger, HC subclass, found in RING finger protein 168 (RNF168) and similar proteins; RNF168 is an E3 ubiquitin-protein ligase that promotes noncanonical K27 ubiquitination to signal DNA damage. It, together with RNF8, functions as a DNA damage response (DDR) factor that promotes a series of ubiquitylation events on substrates, such as H2A and H2AX with H2AK13/15 ubiquitylation, facilitates recruitment of repair factors p53-binding protein 1 (53BP1) or the RAP80-BRCA1 complex to sites of double-strand breaks (DSBs), and inhibits homologous recombination (HR) in cells deficient in the tumor suppressor BRCA1. RNF168 also promotes H2A neddylation, which antagonizes ubiquitylation of H2A and regulates DNA damage repair. Moreover, RNF168 forms a functional complex with RAD6A or RAD6B during the DNA damage response. RNF168 contains an N-terminal C3HC4-type RING-HC finger that catalyzes H2A-K15ub and interacts with H2A, and two MIU (motif interacting with ubiquitin) domains responsible for the interaction with K63 linked poly-ubiquitin. Pssm-ID: 438212 [Multi-domain] Cd Length: 48 Bit Score: 39.28 E-value: 4.13e-04
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| zf-RING_2 | pfam13639 | Ring finger domain; |
423-463 | 4.46e-04 | |||||||||
Ring finger domain; Pssm-ID: 433370 [Multi-domain] Cd Length: 44 Bit Score: 38.93 E-value: 4.46e-04
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| RING-HC_AtBRCA1-like | cd23147 | RING finger, HC subclass, found in Arabidopsis thaliana protein BREAST CANCER SUSCEPTIBILITY 1 ... |
420-465 | 4.54e-04 | |||||||||
RING finger, HC subclass, found in Arabidopsis thaliana protein BREAST CANCER SUSCEPTIBILITY 1 homolog (AtBRCA1) and similar proteins; AtBRCA1 plays a role in DNA repair and in cell-cycle control. It is required for the repair of DNA double-strand breaks (DSBs), both natural and induced by genotoxic stress, by homologous recombination (HR). AtBRCA1 contains a typical C3HC4-type RING-HC finger. Pssm-ID: 438509 [Multi-domain] Cd Length: 54 Bit Score: 39.37 E-value: 4.54e-04
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| RING-HC_PCGF3 | cd16735 | RING finger found in polycomb group RING finger protein 3 (PCGF3) and similar proteins; PCGF3, ... |
422-470 | 4.93e-04 | |||||||||
RING finger found in polycomb group RING finger protein 3 (PCGF3) and similar proteins; PCGF3, also known as RING finger protein 3A (RNF3A), is one of six PcG RING finger (PCGF) homologs (PCGF1, PCGF2/Mel-18, PCGF3, PCGF4/BMI1, PCGF5, and PCGF6) and serves as the core component of a Polycomb repressive complex 1 (PRC1). Like other PCGF homologs, PCGF3 associates with ring finger protein 2 (RNF2) to form a RNF2-PCGF heterodimer, which is catalytically competent as an E3 ubiquitin transferase and is the scaffold for the assembly of additional components. PCGF3 contains a C3HC4-type RING-HC finger. Pssm-ID: 438393 [Multi-domain] Cd Length: 66 Bit Score: 39.36 E-value: 4.93e-04
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| mRING-HC-C3HC3D_LNX1-like | cd16637 | Modified RING finger, HC subclass (C3HC3D-type), found in ligand of Numb protein LNX1, LNX2, ... |
423-451 | 5.01e-04 | |||||||||
Modified RING finger, HC subclass (C3HC3D-type), found in ligand of Numb protein LNX1, LNX2, and similar proteins; The ligand of Numb protein X (LNX) family, also known as PDZ and RING (PDZRN) family, includes LNX1-5, which can interact with Numb, a key regulator of neurogenesis and neuronal differentiation. LNX5 (also known as PDZK4 or PDZRN4L) shows high sequence homology to LNX3 and LNX4, but it lacks the RING domain. LNX1-4 proteins function as E3 ubiquitin ligases and have a unique domain architecture consisting of an N-terminal RING-HC finger for E3 ubiquitin ligase activity and either two or four PDZ domains necessary for substrate-binding. LNX1/LNX2-like proteins contain a modified C3HC3D-type RING-HC finger and four PDZ domains. This model corresponds to the RING finger. Pssm-ID: 438299 [Multi-domain] Cd Length: 42 Bit Score: 38.92 E-value: 5.01e-04
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| RING-HC_SPL2-like | cd23145 | RING finger, HC subclass, found in Arabidopsis thaliana SP1-like protein 2 (SPL2) and similar ... |
423-464 | 6.10e-04 | |||||||||
RING finger, HC subclass, found in Arabidopsis thaliana SP1-like protein 2 (SPL2) and similar proteins; SPL2, also known as RING-type E3 ubiquitin transferase SPL2, acts as an E3 ubiquitin-protein ligase that mediates E2-dependent protein ubiquitination. SPL2 contains a typical C3HC4-type RING-HC finger. Pssm-ID: 438507 [Multi-domain] Cd Length: 47 Bit Score: 38.72 E-value: 6.10e-04
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| RING-HC_TRIM2 | cd16767 | RING finger, HC subclass, found in tripartite motif-containing protein 2 (TRIM2); TRIM2, also ... |
422-464 | 6.18e-04 | |||||||||
RING finger, HC subclass, found in tripartite motif-containing protein 2 (TRIM2); TRIM2, also known as RING finger protein 86 (RNF86), is an E3 ubiquitin-protein ligase that ubiquitinates the neurofilament light chain, a component of the intermediate filament in axons. Loss of function of TRIM2 results in early-onset axonal neuropathy. TRIM2 also plays a role in mediating the p42/p44 MAPK-dependent ubiquitination of the cell death-promoting protein Bcl-2-interacting mediator of cell death (Bim) in rapid ischemic tolerance. TRIM2 belongs to the C-VII subclass of the TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain. Pssm-ID: 438423 [Multi-domain] Cd Length: 51 Bit Score: 38.84 E-value: 6.18e-04
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| PBP2_Fbp_like_1 | cd13544 | Substrate binding domain of a putative ferric iron transporter, a member of the type 2 ... |
38-347 | 6.24e-04 | |||||||||
Substrate binding domain of a putative ferric iron transporter, a member of the type 2 periplasmic binding fold superfamily; The substrate domain of this group shows a high homology to the periplasmic component of ferric iron transporter (Fbp), but its biochemical characterization has not been performed. The periplasmic iron binding protein plays an essential role in the iron uptake pathway of Gram-negative pathogenic bacteria from the Pasteurellaceae and Neisseriaceae families and is critical for survival of these pathogens within the host. After binding iron with high affinity, Fbp interacts with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The ferric iron-binding proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. Pssm-ID: 270262 [Multi-domain] Cd Length: 292 Bit Score: 42.97 E-value: 6.24e-04
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| RING-HC_ScPSH1-like | cd16568 | RING finger, HC subclass, found in Saccharomyces cerevisiae POB3/SPT16 histone-associated ... |
418-467 | 6.79e-04 | |||||||||
RING finger, HC subclass, found in Saccharomyces cerevisiae POB3/SPT16 histone-associated protein 1 (ScPSH1) and similar proteins; ScPSH1 is a Cse4-specific E3 ubiquitin ligase that interacts with the kinetochore protein Pat1 and targets the degradation of budding yeast centromeric histone H3 variant, CENP-ACse4, which is essential for faithful chromosome segregation. ScPSH1 contains a C3HC4-type RING-HC finger and a DNA directed RNA polymerase domain. Pssm-ID: 438230 [Multi-domain] Cd Length: 54 Bit Score: 38.89 E-value: 6.79e-04
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| RING_Ubox | cd00162 | RING finger (Really Interesting New Gene) domain and U-box domain superfamily; The RING finger ... |
424-462 | 7.33e-04 | |||||||||
RING finger (Really Interesting New Gene) domain and U-box domain superfamily; The RING finger is a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc. It is defined by the "cross-brace" motif that chelates zinc atoms by eight amino acid residues, typically Cys or His, arranged in a characteristic spacing. Canonical RING motifs have been categorized into two major subclasses, RING-HC (C3HC4-type) and RING-H2 (C3H2C3-type), according to their Cys/His content. There are also many variants of RING fingers: some have different Cys/His patterns while some lack a single Cys or His residue at typical Zn ligand positions (the fourth or eighth zinc ligand is prevalently exchanged for an Asp, which can indeed chelate Zn in a RING finger as well). C4C4-, C3HC3D-, C2H2C4-, and C3HC5-type RING fingers are closely related to RING-HC fingers. In contrast, C4HC3- (RING-CH alias RINGv), C3H3C2-, C3H2C2D-, C3DHC3-, and C4HC2H-type RING fingers are more closely related to RING-H2 fingers. However, not all RING finger-containing proteins display regular RING finger features, and the RING finger family has turned out to be multifarious. The degenerate RING fingers of the Siz/PIAS RING (SP-RING) family proteins and sporulation protein RMD5, are characterized by lacking the second, fifth, and sixth Zn2+ ion-coordinating residues. They bind only one Zn2+ ion. On the other hand, the RING fingers of the human APC11 and RBX1 proteins can bind a third Zn atom since they harbor four additional Zn ligands. U-box is a modified form of the RING finger domain that lacks metal chelating Cys and His residues. It resembles the cross-brace RING structure consisting of three beta-sheets and a single alpha-helix, which would be stabilized by salt bridges instead of chelated metal ions. U-box proteins are widely distributed among eukaryotic organisms and show a higher prevalence in plants than in other organisms. RING finger/U-box-containing proteins are a group of diverse proteins with a variety of cellular functions, including oncogenesis, development, viral replication, signal transduction, the cell cycle and apoptosis. Many of them are ubiquitin-protein ligases (E3s) that serve as scaffolds for binding to ubiquitin-conjugating enzymes (E2s, also referred to as ubiquitin carrier proteins or UBCs) in close proximity to substrate proteins, which enable efficient transfer of ubiquitin from E2 to the substrates. Pssm-ID: 438111 [Multi-domain] Cd Length: 42 Bit Score: 38.21 E-value: 7.33e-04
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| RING-HC_RNF169 | cd16551 | RING finger, HC subclass, found in RING finger protein 169 (RNF169) and similar proteins; ... |
423-462 | 8.05e-04 | |||||||||
RING finger, HC subclass, found in RING finger protein 169 (RNF169) and similar proteins; RNF169 is an uncharacterized E3 ubiquitin-protein ligase paralogous to RNF168. It functions as a negative regulator of the DNA damage signaling cascade. RNF169 recognizes polyubiquitin structures but does not itself contribute to double-strand break (DSB)-induced chromatin ubiquitylation. It contributes to regulation of the DSB repair pathway utilization via functionally competing with recruiting repair factors, 53BP1 and RAP80-BRCA1, for association with RNF168-modified chromatin independent of its catalytic activity, limiting the magnitude of the RNF8/RNF168-dependent signaling response to DSBs. RNF169 contains an N-terminal C3HC4-type RING-HC finger and a C-terminal MIU (motif interacting with ubiquitin) domain. Pssm-ID: 438213 [Multi-domain] Cd Length: 55 Bit Score: 38.68 E-value: 8.05e-04
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| RING-HC_ORTHRUS_rpt2 | cd23139 | second RING finger, HC subclass, found in Arabidopsis thaliana ORTHRUS and similar proteins; ... |
418-448 | 8.14e-04 | |||||||||
second RING finger, HC subclass, found in Arabidopsis thaliana ORTHRUS and similar proteins; This subfamily includes Arabidopsis thaliana ORTHRUS 1-5. They are E3 ubiquitin-protein ligases that may participate in CpG methylation-dependent transcriptional regulation and/or epigenetic transcriptional silencing. ORTHRUS 1 mediates ubiquitination with the E2 ubiquitin-conjugating enzymes UBC11, UBC8 and UBC8 homologs (e.g. UBC10, UBC11, UBC28 and UBC29) but not with UBC27, UBC30, UBC32, UBC34 and UBC36. ORTHRUS 2 and 5 mediate ubiquitination with the E2 ubiquitin-conjugating enzyme UBC11. ORTHRUS 1 and 2 promote methylation-mediated gene silencing leading, for example, to early flowering. They can bind to CpG, CpNpG, and CpNpN DNA motifs, with a strong preference for methylated forms, and with highest affinity for CpG substrates. Members of this subfamily contain two typical C3HC4-type RING-HC fingers. This model corresponds to the second one. Pssm-ID: 438501 [Multi-domain] Cd Length: 72 Bit Score: 38.98 E-value: 8.14e-04
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| RING-HC_RING2 | cd16740 | RING finger, HC subclass, found in really interesting new gene 2 protein (RING2) and similar ... |
415-485 | 8.31e-04 | |||||||||
RING finger, HC subclass, found in really interesting new gene 2 protein (RING2) and similar proteins; RING2, also known as huntingtin-interacting protein 2-interacting protein 3, HIP2-interacting protein 3, protein DinG, RING finger protein 1B (RING1B), RING finger protein 2 (RNF2), or RING finger protein BAP-1, is an E3 ubiquitin-protein ligase that interacts with both nucleosomal DNA and an acidic patch on histone H4 to achieve the specific monoubiquitination of K119 on histone H2A (H2AK119ub), thereby playing a central role in histone code and gene regulation. RING2 is a core component of polycomb repressive complex 1 (PRC1) that functions as an E3-ubuiquitin ligase transferring the mono-ubuiquitin mark to the C-terminal tail of Histone H2A at K118/K119. PRC1 is also capable of chromatin compaction, a function not requiring histone tails, and this activity appears important in gene silencing. The enzymatic activity of RING2 is enhanced by the interaction with BMI1/PCGF4, and it is dispensable for early embryonic development and much of the gene repression activity of PRC1. Moreover, RING2 plays a key role in terminating neural precursor cell (NPC)-mediated production of subcerebral projection neurons (SCPNs) during neocortical development. It also plays a critical role in nonhomologous end-joining (NHEJ)-mediated end-to-end chromosome fusions. Furthermore, RING2 is essential for expansion of hepatic stem/progenitor cells. It promotes hepatic stem/progenitor cell expansion through simultaneous suppression of cyclin-dependent kinase inhibitors (CDKIs) Cdkn1a and Cdkn2a, known negative regulators of cell proliferation. RING2 also negatively regulates p53 expression through directly binding with both p53 and MDM2 and promoting MDM2-mediated p53 ubiquitination in selective cancer cell types to stimulate tumor development. RING2 contains a C3HC4-type RING-HC finger. Pssm-ID: 438398 [Multi-domain] Cd Length: 77 Bit Score: 39.30 E-value: 8.31e-04
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| RING-HC_RAD18 | cd16529 | RING finger, HC subclass, found in postreplication repair protein RAD18 and similar proteins; ... |
417-471 | 8.84e-04 | |||||||||
RING finger, HC subclass, found in postreplication repair protein RAD18 and similar proteins; RAD18, also known as HR18 or RING finger protein 73 (RNF73), is an E3 ubiquitin-protein ligase involved in post replication repair of UV-damaged DNA via its recruitment to stalled replication forks. It associates to the E2 ubiquitin conjugating enzyme UBE2B to form the UBE2B-RAD18 ubiquitin ligase complex involved in mono-ubiquitination of DNA-associated PCNA on K164. It also interacts with another E2 ubiquitin conjugating enzyme RAD6 to form a complex that monoubiquitinates proliferating cell nuclear antigen at stalled replication forks in DNA translesion synthesis. Moreover, Rad18 is a key factor in double-strand break DNA damage response (DDR) pathways via its association with K63-linked polyubiquitylated chromatin proteins. It can function as a mediator for DNA damage response signals to activate the G2/M checkpoint in order to maintain genome integrity and cell survival after ionizing radiation (IR) exposure. RAD18 contains a C3HC4-type RING-HC finger, a ubiquitin-binding zinc finger domain (UBZ), a SAP (SAF-A/B, Acinus and PIAS) domain, and a RAD6-binding domain (R6BD). Pssm-ID: 438192 [Multi-domain] Cd Length: 54 Bit Score: 38.44 E-value: 8.84e-04
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| RING-HC_LNX3-like | cd16512 | RING finger, HC subclass, found in ligand of Numb protein LNX3, LNX4, and similar proteins; ... |
424-464 | 8.99e-04 | |||||||||
RING finger, HC subclass, found in ligand of Numb protein LNX3, LNX4, and similar proteins; The ligand of Numb protein X (LNX) family, also known as PDZ and RING (PDZRN) family, includes LNX1-5, which can interact with Numb, a key regulator of neurogenesis and neuronal differentiation. LNX5 (also known as PDZK4, or PDZRN4L) shows high sequence homology to LNX3 and LNX4, but it lacks the RING domain. LNX1-4 proteins function as E3 ubiquitin ligases and have a unique domain architecture consisting of an N-terminal RING-HC finger for E3 ubiquitin ligase activity and either two or four PDZ domains necessary for the substrate-binding. This family corresponds to LNX3/LNX4-like proteins, which contains a C3HC4-type RING-HC finger and two PDZ domains. Pssm-ID: 438175 [Multi-domain] Cd Length: 43 Bit Score: 38.16 E-value: 8.99e-04
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| RING-HC_RNF213 | cd16561 | RING finger, HC subclass, found in RING finger protein 213 (RNF213) and similar proteins; ... |
424-469 | 9.62e-04 | |||||||||
RING finger, HC subclass, found in RING finger protein 213 (RNF213) and similar proteins; RNF213, also known as ALK lymphoma oligomerization partner on chromosome 17 or Moyamoya steno-occlusive disease-associated AAA+ and RING finger protein (mysterin), is an intracellular soluble protein that functions as an E3 ubiquitin-protein ligase and AAA+ ATPase, which possibly contributes to vascular development through mechanical processes in the cell. It plays a unique role in endothelial cells for proper gene expression in response to inflammatory signals from the environment. Mutations in RNF213 may be associated with Moyamoya disease (MMD), an idiopathic cerebrovascular occlusive disorder prevalent in East Asia. It also acts as a nuclear marker for acanthomorph phylogeny. RNF213 contains two tandem enzymatically active AAA+ ATPase modules and a C3HC4-type RING-HC finger. It can form a huge ring-shaped oligomeric complex. Pssm-ID: 438223 [Multi-domain] Cd Length: 50 Bit Score: 38.03 E-value: 9.62e-04
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| RING-HC_MmTRIM43-like | cd23133 | RING finger, HC subclass, found in Mus musculus tripartite motif-containing protein 43 (TRIM43) ... |
422-467 | 9.71e-04 | |||||||||
RING finger, HC subclass, found in Mus musculus tripartite motif-containing protein 43 (TRIM43) and similar propteins; This subfamily includes TRIM43A, TRIM43B and TRIM43C, which are expressed specifically in mouse preimplantation embryos. They contain a typical C3HC4-type RING-HC finger. Pssm-ID: 438495 [Multi-domain] Cd Length: 57 Bit Score: 38.35 E-value: 9.71e-04
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| TbpA | COG4143 | ABC-type thiamine transport system, periplasmic component TbpA [Coenzyme transport and ... |
33-152 | 1.14e-03 | |||||||||
ABC-type thiamine transport system, periplasmic component TbpA [Coenzyme transport and metabolism]; Pssm-ID: 443315 [Multi-domain] Cd Length: 343 Bit Score: 42.53 E-value: 1.14e-03
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| RING-HC_RNF37 | cd16537 | RING finger, HC subclass, found in RING finger protein 37 (RNF37); RNF37, also known as ... |
424-464 | 1.17e-03 | |||||||||
RING finger, HC subclass, found in RING finger protein 37 (RNF37); RNF37, also known as KIAA0860, U-box domain-containing protein 5 (UBOX5), UbcM4-interacting protein 5 (UIP5), or ubiquitin-conjugating enzyme 7-interacting protein 5, is an E3 ubiquitin-protein ligase found exclusively in the nucleus as part of a nuclear dot-like structure. It interacts with the molecular chaperone VCP/p97 protein. RNF37 contains a U-box domain followed by a potential nuclear location signal (NLS) and a C-terminal C3HC4-type RING-HC finger. The U-box domain is a modified RING finger domain that lacks the hallmark metal-chelating cysteines and histidines of the latter, and is likely to adopt a RING finger-like conformation. The presence of the U-box, but not of the RING finger, is required for the E3 activity. The U-box domain can directly interact with several E2 enzymes, including UbcM2, UbcM3, UbcM4, UbcH5, and UbcH8, suggesting a similar function as the RING finger in the ubiquitination pathway. This model corresponds to the RING-HC finger. Pssm-ID: 438199 Cd Length: 52 Bit Score: 38.19 E-value: 1.17e-03
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| RING-HC_LNX4 | cd16719 | RING finger, HC subclass, found in ligand of numb protein X 4 (LNX4); LNX4, also known as PDZ ... |
421-471 | 1.39e-03 | |||||||||
RING finger, HC subclass, found in ligand of numb protein X 4 (LNX4); LNX4, also known as PDZ domain-containing RING finger protein 4 (PDZRN4), or SEMACAP3-like protein (SEMCAP3L), is an E3 ubiquitin-protein ligase responsible for the ubiquitination and degradation of Numb, a component of the Notch signaling pathway that functions in the specification of cell fates during development and is known to control cell numbers during neurogenesis in vertebrates. LNX4 contains an N-terminal C3HC4-type RING-HC finger, two PDZ domains, and a C-terminal LNX3 homology (LNX3H) domain. Pssm-ID: 438379 [Multi-domain] Cd Length: 53 Bit Score: 37.99 E-value: 1.39e-03
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| mRING-C3HGC3_RFWD3 | cd16450 | Modified RING finger, C3HGC3-type, found in RING finger and WD repeat domain-containing ... |
421-473 | 1.45e-03 | |||||||||
Modified RING finger, C3HGC3-type, found in RING finger and WD repeat domain-containing protein 3 (RFWD3) and similar proteins; RFWD3, also known as RING finger protein 201 (RNF201) or FLJ10520, is an E3 ubiquitin-protein ligase that forms a complex with Mdm2 and p53 to synergistically ubiquitinate p53 and acts as a positive regulator of p53 stability in response to DNA damage. It is phosphorylated by checkpoint kinase ATM/ATR and the phosphorylation mutant fails to stimulate p53 ubiquitination. RFWD3 also functions as a novel replication protein A (RPA)-associated protein involved in DNA replication checkpoint control. RFWD3 contains an N-terminal SQ-rich region followed by a RING finger domain that exhibits robust E3 ubiquitin ligase activity toward p53, a coiled-coil domain and three WD40 repeats in the C-terminus, the latter two of which may be responsible for protein-protein interaction. The RING finger in this family is a modified C3HGC3-type RING finger, but not a canonical C3H2C3-type RING-H2 finger or C3HC4-type RING-HC finger. Pssm-ID: 438114 [Multi-domain] Cd Length: 61 Bit Score: 37.98 E-value: 1.45e-03
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| mRING-HC-C3HC3D_Nrdp1 | cd16634 | Modified RING finger, HC subclass (C3HC3D-type), found in neuregulin receptor degradation ... |
422-460 | 1.68e-03 | |||||||||
Modified RING finger, HC subclass (C3HC3D-type), found in neuregulin receptor degradation protein-1 (Nrdp1) and similar proteins; Nrdp1 (referred to as FLRF in mice), also known as RING finger protein 41 (RNF41), is an E3 ubiquitin-protein ligase that plays a critical role in the regulation of cell growth and apoptosis, inflammation and production of reactive oxygen species (ROS), as well as in doxorubicin (DOX)-induced cardiac injury. It promotes the degradation of the epidermal growth factor receptor (EGFR/ErbB) family member, ErbB3, which is independent of growth factor stimulation. It also promotes M2 macrophage polarization by ubiquitinating and activating transcription factor CCAAT/enhancer-binding protein beta (C/EBPbeta) via Lys-63-linked ubiquitination. Moreover, Nrdp1 interacts with and modulates the activity of Parkin, a causative protein for early onset recessive juvenile parkinsonism (AR-JP). It also interacts with ubiquitin-specific protease 8 (USP8), which is involved in trafficking of various transmembrane proteins. Furthermore, Nrdp1 inhibits basal lysosomal degradation and enhances ectodomain shedding of JAK2-associated cytokine receptors. Its phosphorylation by the kinase Par-1b (also known as MARK2) is required for epithelial cell polarity. Nrdp1 contains an N-terminal modified C3HC3D-type RING-HC finger required for enhancing ErbB3 degradation, a B-box, a coiled-coil domain responsible for Nrdp1 oligomerization, and a C-terminal ErbB3-binding domain. Pssm-ID: 438296 [Multi-domain] Cd Length: 43 Bit Score: 37.40 E-value: 1.68e-03
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| RING-HC_RNF180 | cd16554 | RING finger, HC subclass, found in RING finger protein 180 (RNF180) and similar proteins; ... |
423-464 | 1.73e-03 | |||||||||
RING finger, HC subclass, found in RING finger protein 180 (RNF180) and similar proteins; RNF180, also known as Rines, is a membrane-bound E3 ubiquitin-protein ligase well conserved among vertebrates. It is a critical regulator of the monoaminergic system, as well as emotional and social behavior. It interacts with brain monoamine oxidase A (MAO-A) and targets it for ubiquitination and degradation. It also functions as a novel tumor suppressor in gastric carcinogenesis. The hypermethylated CpG site count of the RNF180 DNA promoter can be used to predict survival of gastric cancer. RNF180 contains a novel conserved dual specificity protein phosphatase Rines conserved (DSPRC) domain, a basic coiled-coil domain, a C3HC4-type RING-HC finger, and a C-terminal hydrophobic region that is predicted to be a transmembrane domain. Pssm-ID: 438216 [Multi-domain] Cd Length: 59 Bit Score: 37.68 E-value: 1.73e-03
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| RAG1_imp_bd | pfam12560 | RAG1 importin binding; This region of RAG1 is responsible for binding to importin alpha. |
398-421 | 1.78e-03 | |||||||||
RAG1 importin binding; This region of RAG1 is responsible for binding to importin alpha. Pssm-ID: 463629 Cd Length: 287 Bit Score: 41.64 E-value: 1.78e-03
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| RING-HC_PRT1-like | cd23132 | RING finger, HC subclass, found in Arabidopsis thaliana proteolysis 1 protein (PRT1) and ... |
423-462 | 1.97e-03 | |||||||||
RING finger, HC subclass, found in Arabidopsis thaliana proteolysis 1 protein (PRT1) and similar proteins; PRT1, also called RING-type E3 ubiquitin transferase PRT1, is an E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of target proteins. It functions in the N-end rule pathway of protein degradation, where it specifically recognizes and ubiquitinates proteins with an N-terminal bulky aromatic amino acid (Phe). It does not act on aliphatic hydrophobic and basic N-terminal residues (Arg or Leu) containing proteins. PRT1 contains a typical C3HC4-type RING-HC finger. Pssm-ID: 438494 [Multi-domain] Cd Length: 52 Bit Score: 37.40 E-value: 1.97e-03
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| RING-HC_TRIM13_C-V | cd16762 | RING finger, HC subclass, found in tripartite motif-containing protein 13 (TRIM13) and similar ... |
422-464 | 2.18e-03 | |||||||||
RING finger, HC subclass, found in tripartite motif-containing protein 13 (TRIM13) and similar proteins; TRIM13, also known as B-cell chronic lymphocytic leukemia tumor suppressor Leu5, leukemia-associated protein 5, putative tumor suppressor RFP2, RING finger protein 77 (RNF77), or Ret finger protein 2, is an endoplasmic reticulum (ER) membrane anchored E3 ubiquitin-protein ligase that interacts with proteins localized to the ER, including valosin-containing protein (VCP), a protein indispensable for ER-associated degradation (ERAD). It also targets the known ER proteolytic substrate CD3-delta, but not the N-end rule substrate Ub-R-YFP (yellow fluorescent protein) for degradation. Moreover, TRIM13 regulates ubiquitination and degradation of NEMO to suppress tumor necrosis factor (TNF) induced nuclear factor-kappaB (NF- kappa B) activation. It is also involved in NF-kappaB p65 activation and nuclear factor of activated T-cells (NFAT)-dependent activation of c-Rel upon T-cell receptor engagement. Furthermore, TRIM13 negatively regulates melanoma differentiation-associated gene 5 (MDA5)-mediated type I interferon production. It also regulates caspase-8 ubiquitination, translocation to autophagosomes, and activation during ER stress induced cell death. Meanwhile, TRIM13 enhances ionizing radiation-induced apoptosis by increasing p53 stability and decreasing AKT kinase activity through MDM2 and AKT degradation. TRIM13 belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domain, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region. In addition, TRIM13 contains a C-terminal transmembrane domain. Pssm-ID: 438418 [Multi-domain] Cd Length: 56 Bit Score: 37.59 E-value: 2.18e-03
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| RING-H2_RNF115 | cd16800 | RING finger, H2 subclass, found in RING finger protein 115 (RNF115) and similar proteins; ... |
424-467 | 2.21e-03 | |||||||||
RING finger, H2 subclass, found in RING finger protein 115 (RNF115) and similar proteins; RNF115, also known as Rab7-interacting ring finger protein (Rabring 7), or zinc finger protein 364 (ZNF364), or breast cancer-associated gene 2 (BCA2), is an E3 ubiquitin-protein ligase that is an endogenous inhibitor of adenosine monophosphate-activated protein kinase (AMPK) activation and its inhibition increases the efficacy of metformin in breast cancer cells. It also functions as a co-factor in the restriction imposed by tetherin on HIV-1, and targets HIV-1 Gag for lysosomal degradation, impairing virus assembly and release, in a tetherin-independent manner. Moreover, RNF115 is a Rab7-binding protein that stimulates c-Myc degradation through mono-ubiquitination of MM-1. It also plays crucial roles as a Rab7 target protein in vesicle traffic to late endosome/lysosome and lysosome biogenesis. Furthermore, RNF115 and the related protein, RNF126 associate with the epidermal growth factor receptor (EGFR) and promote ubiquitylation of EGFR, suggesting they play a role in the ubiquitin-dependent sorting and downregulation of membrane receptors. RNF115 contains an N-terminal BCA2 Zinc-finger domain (BZF), the AKT-phosphorylation sites, and the C-terminal C3H2C3-type RING-H2 finger. Pssm-ID: 438452 [Multi-domain] Cd Length: 50 Bit Score: 37.23 E-value: 2.21e-03
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| PLN03208 | PLN03208 | E3 ubiquitin-protein ligase RMA2; Provisional |
424-472 | 2.25e-03 | |||||||||
E3 ubiquitin-protein ligase RMA2; Provisional Pssm-ID: 178747 [Multi-domain] Cd Length: 193 Bit Score: 40.45 E-value: 2.25e-03
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| RING-HC_TRIM56_C-V | cd16584 | RING finger, HC subclass, found in tripartite motif-containing protein 56 (TRIM56) and similar ... |
422-466 | 2.68e-03 | |||||||||
RING finger, HC subclass, found in tripartite motif-containing protein 56 (TRIM56) and similar proteins; TRIM56, also known as RING finger protein 109 (RNF109), is a virus-inducible E3 ubiquitin ligase that restricts pestivirus infection. It positively regulates the Toll-like receptor 3 (TLR3) antiviral signaling pathway, and possesses antiviral activity against bovine viral diarrhea virus (BVDV), a ruminant pestivirus classified within the family Flaviviridae shared by tick-borne encephalitis virus (TBEV). It also possesses antiviral activity against two classical flaviviruses, yellow fever virus (YFV) and dengue virus (DENV), as well as a human coronavirus, HCoV-OC43, which is responsible for a significant share of common cold cases. It may not act on positive-strand RNA viruses indiscriminately. Moreover, TRIM56 is an interferon-inducible E3 ubiquitin ligase that modulates STING to confer double-stranded DNA-mediated innate immune responses. TRIM56 belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domain, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as an uncharacterized region positioned C-terminal to the RBCC domain. Pssm-ID: 438246 [Multi-domain] Cd Length: 56 Bit Score: 37.27 E-value: 2.68e-03
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| RING-HC_UHRF2 | cd16770 | RING finger, HC subclass, found in ubiquitin-like PHD and RING finger domain-containing ... |
424-483 | 3.06e-03 | |||||||||
RING finger, HC subclass, found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); UHRF2, also known as Np95/ICBP90-like RING finger protein (NIRF), Np95-like RING finger protein, nuclear protein 97, nuclear zinc finger protein Np97, RING finger protein 107, or E3 ubiquitin-protein ligase UHRF2, was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation, but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) through interacting with HBV core protein and promoting its degradation. UHRF2 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) domain, a SET- and RING-associated (SRA) domain, and a C-terminal C3HC4-type RING-HC finger. Pssm-ID: 438426 [Multi-domain] Cd Length: 65 Bit Score: 37.10 E-value: 3.06e-03
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| RING-HC_PCGF2 | cd16734 | RING finger found in polycomb group RING finger protein 2 (PCGF2) and similar proteins; PCGF2, ... |
404-474 | 3.30e-03 | |||||||||
RING finger found in polycomb group RING finger protein 2 (PCGF2) and similar proteins; PCGF2, also known as DNA-binding protein Mel-18, RING finger protein 110 (RNF110), or zinc finger protein 144 (ZNF144), is one of six PcG RING finger (PCGF) homologs (PCGF1/NSPc1, PCGF2/Mel-18, PCGF3, PCGF4/BMI1, PCGF5, and PCGF6/MBLR). It serves as the core component of a canonical Polycomb repressive complex 1 (PRC1), which is composed of a chromodomain-containing protein (CBX2, CBX4, CBX6, CBX7 or CBX8) and a Polyhomeotic protein (PHC1, PHC2, or PHC3). Like other PCGF homologs, PCGF2 associates with ring finger protein 2 (RNF2) to form a RNF2-PCGF heterodimer, which is catalytically competent as an E3 ubiquitin transferase and is the scaffold for the assembly of additional components. Moreover, PCGF2 uniquely regulates PRC1 to specify mesoderm cell fate in embryonic stem cells. It is required for PRC1 stability and maintenance of gene repression in embryonic stem cells (ESCs) and essential for ESC differentiation into early cardiac-mesoderm precursors. PCGF2 also plays a significant role in the angiogenic function of endothelial cells (ECs) by regulating endothelial gene expression. Furthermore, PCGF2 is a SUMO-dependent regulator of hormone receptors. It facilitates the deSUMOylation process by inhibiting PCGF4/BMI1-mediated ubiquitin-proteasomal degradation of SUMO1/sentrin-specific protease 1 (SENP1). It is also a novel negative regulator of breast cancer stem cells (CSCs) that inhibits the stem cell population and in vitro and in vivo self-renewal through the inactivation of Wnt-mediated Notch signaling. PCGF2 contains a C3HC4-type RING-HC finger. Pssm-ID: 438392 [Multi-domain] Cd Length: 80 Bit Score: 37.66 E-value: 3.30e-03
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| RING-HC_TRIM31_C-V | cd16582 | RING finger, HC subclass, found in tripartite motif-containing protein 31 (TRIM31) and similar ... |
422-462 | 3.36e-03 | |||||||||
RING finger, HC subclass, found in tripartite motif-containing protein 31 (TRIM31) and similar proteins; TRIM31 is an E3 ubiquitin-protein ligase that primarily localizes to the cytoplasm, but is also associated with the mitochondria. It can negatively regulate cell proliferation and may be a potential biomarker of gastric cancer as it is overexpressed from the early stage of gastric carcinogenesis. TRIM31 is downregulated in non-small cell lung cancer and serves as a potential tumor suppressor. It interacts with p52 (Shc) and inhibits Src-induced anchorage-independent growth. TRIM31 belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domain, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as an uncharacterized region positioned C-terminal to the RBCC domain. Pssm-ID: 438244 [Multi-domain] Cd Length: 44 Bit Score: 36.34 E-value: 3.36e-03
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| RING-HC_Cbl-c | cd16710 | RING finger, HC subclass, found in E3 ubiquitin-protein ligase Cbl-c and similar proteins; ... |
424-462 | 3.54e-03 | |||||||||
RING finger, HC subclass, found in E3 ubiquitin-protein ligase Cbl-c and similar proteins; Cbl-c, also known as RING finger protein 57 (RNF57), SH3-binding protein Cbl-3, SH3-binding protein Cbl-c, or signal transduction protein Cbl-c, is an E3 ubiquitin-protein ligase expressed exclusively in epithelial cells. It contains a tyrosine-kinase-binding domain (TKB, also known as the phosphotyrosine binding PTB domain, composed of a four helix-bundle, a Ca2+ binding EF-hand and a highly variant SH2 domain), a C3HC4-type RING-HC finger, and a short proline-rich region, but lacks the ubiquitin-associated (UBA) leucine zipper motif that are present in Cbl and Cbl-b. Cbl-c acts as a regulator of epidermal growth factor receptor (EGFR)-mediated signal transduction. It also suppresses v-Src-induced transformation through ubiquitin-dependent protein degradation. Moreover, Cbl-c ubiquitinates and downregulates RETMEN2A and implicates Enigma (PDLIM7) as a positive regulator of RETMEN2A by blocking Cbl-mediated ubiquitination and degradation. The ubiquitin ligase activity of Cbl-c is increased via the interaction of its RING-HC finger domain with a LIM domain of the paxillin homolog, hydrogen peroxide induced construct 5 (Hic-5). Pssm-ID: 438370 [Multi-domain] Cd Length: 65 Bit Score: 36.99 E-value: 3.54e-03
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| RING-HC_TRIM17_C-IV | cd16595 | RING finger, HC subclass, found in tripartite motif-containing protein TRIM17 and similar ... |
423-448 | 3.67e-03 | |||||||||
RING finger, HC subclass, found in tripartite motif-containing protein TRIM17 and similar proteins; TRIM17, also known as RING finger protein 16 (RNF16) or testis RING finger protein (Terf), is a crucial E3 ubiquitin ligase that is necessary and sufficient for neuronal apoptosis and contributes to Mcl-1 ubiquitination in cerebellar granule neurons (CGNs). It interacts in a SUMO-dependent manner with nuclear factor of activated T cell NFATc3 transcription factor, and thus inhibits the activity of NFATc3 by preventing its nuclear localization. In contrast, it binds to and inhibits NFATc4 transcription factor in a SUMO-independent manner. Moreover, TRIM17 stimulates degradation of kinetochore protein ZW10 interacting protein (ZWINT), a known component of the kinetochore complex required for the mitotic spindle checkpoint, and negatively regulates cell proliferation. TRIM17 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. Pssm-ID: 438257 [Multi-domain] Cd Length: 70 Bit Score: 37.28 E-value: 3.67e-03
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| RING-HC_TRIM43-like_C-IV | cd16603 | RING finger, HC subclass, found in tripartite motif-containing proteins TRIM43, TRIM48, TRIM49, ... |
420-462 | 4.54e-03 | |||||||||
RING finger, HC subclass, found in tripartite motif-containing proteins TRIM43, TRIM48, TRIM49, TRIM51, TRIM64 and similar proteins; The family includes a group of closely related uncharacterized tripartite motif-containing proteins, TRIM43, TRIM43B, TRIM48/RNF101, TRIM49/RNF18, TRIM49B, TRIM49C/TRIM49L2, TRIM49D/TRIM49L, TRIM51/SPRYD5, TRIM64, TRIM64B, and TRIM64C, whose biological function remain unclear. TRIM49, also known as testis-specific RING-finger protein, has moderate similarity with SS-A/Ro52 antigen, suggesting it may be one of the target proteins of autoantibodies in the sera of patients with these autoimmune disorders. All family members belong to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains as well as a SPRY/B30.2 domain positioned C-terminal to the RBCC domain. In RBCC region, they all have a C3HC4-type RING-HC finger. Pssm-ID: 438265 [Multi-domain] Cd Length: 59 Bit Score: 36.69 E-value: 4.54e-03
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| RING-HC_TRIM58_C-IV | cd16606 | RING finger, HC subclass, found in tripartite motif-containing protein TRIM58 and similar ... |
424-462 | 4.76e-03 | |||||||||
RING finger, HC subclass, found in tripartite motif-containing protein TRIM58 and similar proteins; TRIM58, also known as protein BIA2, is an erythroid E3 ubiquitin-protein ligase induced during late erythropoiesis. It binds and ubiquitinates the intermediate chain of the microtubule motor dynein (DYNC1LI1/DYNC1LI2), stimulating the degradation of the dynein holoprotein complex. It may participate in the erythroblast enucleation process through regulation of nuclear polarization. TRIM58 belongs to the C-IV subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. Pssm-ID: 438268 [Multi-domain] Cd Length: 53 Bit Score: 36.38 E-value: 4.76e-03
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| RING-HC_RNF4 | cd16533 | RING finger, HC subclass, found in RING finger protein 4 (RNF4) and similar proteins; RNF4, ... |
420-467 | 6.90e-03 | |||||||||
RING finger, HC subclass, found in RING finger protein 4 (RNF4) and similar proteins; RNF4, also known as small nuclear ring finger protein (SNURF), is a SUMO-targeted E3 ubiquitin-protein ligase with a pivotal function in the DNA damage response (DDR) by interacting with the deubiquitinating enzyme ubiquitin-specific protease 11 (USP11), a known DDR-component, and further facilitating DNA repair. It plays a novel role in preventing the loss of intact chromosomes and ensures the maintenance of chromosome integrity. Moreover, RNF4 is responsible for the UbcH5A-catalyzed formation of K48 chains that target SUMO-modified promyelocytic leukemia (PML) protein for proteasomal degradation in response to arsenic treatment. It also interacts with telomeric repeat binding factor 2 (TRF2) in a small ubiquitin-like modifier (SUMO)-dependent manner and preferentially targets SUMO-conjugated TRF2 for ubiquitination through SUMO-interacting motifs (SIMs). Furthermore, RNF4 can form a complex with a Ubc13-ubiquitin conjugate and Ube2V2. It catalyzes K63-linked polyubiquitination by the Ube2V2-Ubc13 (ubiquitin-loaded) complex. Meanwhile, RNF4 negatively regulates nuclear factor kappa B (NF-kappaB) signaling by down-regulating transforming growth factor beta (TGF-beta)-activated kinase 1 (TAK1)-TAK1-binding protein2 (TAB2). RNF4 contains four SIMs followed by a C3HC4-type RING-HC finger at the C-terminus. Pssm-ID: 438195 [Multi-domain] Cd Length: 57 Bit Score: 36.03 E-value: 6.90e-03
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| RING-HC_RNF220 | cd16563 | RING finger, HC subclass, found in RING finger protein 220 (RNF220) and similar proteins; ... |
424-473 | 7.01e-03 | |||||||||
RING finger, HC subclass, found in RING finger protein 220 (RNF220) and similar proteins; RNF220 is an E3 ubiquitin-protein ligase that promotes the ubiquitination and proteasomal degradation of Sin3B, a scaffold protein of the Sin3/HDAC (histone deacetylase) corepressor complex. It can also bind E2 and mediate auto-ubiquitination of itself. Moreover, RNF220 specifically interacts with beta-catenin, and enhances canonical Wnt signaling through ubiquitin-specific protease 7 (USP7)-mediated deubiquitination and stabilization of beta-catenin, which is independent of its E3 ligase activity. RNF220 contains a characteristic C3HC4-type RING-HC finger at its C-terminus. Pssm-ID: 438225 [Multi-domain] Cd Length: 52 Bit Score: 35.89 E-value: 7.01e-03
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| RING-HC_Bre1-like | cd16499 | RING finger, HC subclass, found in yeast Bre1 and its homologs from eukaryotes; Bre1 is an E3 ... |
422-464 | 8.88e-03 | |||||||||
RING finger, HC subclass, found in yeast Bre1 and its homologs from eukaryotes; Bre1 is an E3 ubiquitin-protein ligase that catalyzes monoubiquitination of histone H2B in concert with the E2 ubiquitin-conjugating enzyme, Rad6. The Rad6-Bre1-mediated histone H2B ubiquitylation modulates the formation of double-strand breaks (DSBs) during meiosis in yeast. it is also required, indirectly, for the methylation of histone 3 on lysine 4 (H3K4) and 79. RNF20, also known as BRE1A and RNF40, also known as BRE1B, are the mammalian homologs of Bre1. They work together to form a heterodimeric Bre1 complex that facilitate the K120 monoubiquitination of histone H2B (H2Bub1), a DNA damage-induced histone modification that is crucial for recruitment of the chromatin remodeler SNF2h to DNA double-strand break (DSB) damage sites. Moreover, the Bre1 complex acts as a tumor suppressor, augmenting expression of select tumor suppressor genes and suppressing select oncogenes. Deficiency in the mammalian histone H2B ubiquitin ligase Bre1 leads to replication stress and chromosomal instability. All subfamily members contain a C3HC4-type RING-HC finger at its C-terminus. Pssm-ID: 438162 [Multi-domain] Cd Length: 59 Bit Score: 35.61 E-value: 8.88e-03
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| RING-HC_DTX3L | cd16712 | RING finger, HC subclass, found in protein Deltex-3-like (DTX3L) and similar proteins; DTX3L, ... |
424-463 | 9.23e-03 | |||||||||
RING finger, HC subclass, found in protein Deltex-3-like (DTX3L) and similar proteins; DTX3L, also known as B-lymphoma- and BAL-associated protein (BBAP) or Rhysin-2 (Rhysin2), is a RING-domain E3 ubiquitin-protein ligase that regulates endosomal sorting of the G protein-coupled receptor CXCR4 from endosomes to lysosomes. It also regulates subcellular localization of its partner protein, B aggressive lymphoma (BAL), by a dynamic nucleocytoplasmic trafficking mechanism. DTX3L has a unique N-terminus, but lacks the highly basic N-terminal motif and the central proline-rich motif present in other Deltex (DTX) family members, such as DTX1, DTX2, and DTX4. Moreover, its C-terminal region is highly homologous to DTX3. It includes a C3HC4-type RING-HC finger, and a previously unidentified C-terminal domain. DTX3L can associate with DTX1 through its unique N-terminus and further enhance self-ubiquitination. Pssm-ID: 438372 [Multi-domain] Cd Length: 56 Bit Score: 35.48 E-value: 9.23e-03
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