SNF2 domain-containing protein / helicase domain-containing protein / zinc finger protein-like protein [Arabidopsis thaliana]
Protein Classification
DEAD/DEAH box helicase; DEXDc_SHPRH-like domain-containing protein( domain architecture ID 12784972)
DEAD/DEAH box containing ATP-dependent helicase catalyzes the unwinding of DNA or RNA; such as human DNA excision repair protein ERCC-6-like and DNA repair and recombination protein RAD54-like; DEXDc_SHPRH-like domain-containing protein
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||||||||
| HepA | COG0553 | Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ... |
547-1256 | 3.19e-113 | ||||||||||
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair]; : Pssm-ID: 440319 [Multi-domain] Cd Length: 682 Bit Score: 370.32 E-value: 3.19e-113
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| RING-HC_CHR27-like | cd23142 | RING finger, HC subclass, found in Arabidopsis thaliana protein CHROMATIN REMODELING 27 (CHR27) ... |
984-1035 | 6.05e-20 | ||||||||||
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: 84.55 E-value: 6.05e-20
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| Name | Accession | Description | Interval | E-value | ||||||||||
| HepA | COG0553 | Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ... |
547-1256 | 3.19e-113 | ||||||||||
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair]; Pssm-ID: 440319 [Multi-domain] Cd Length: 682 Bit Score: 370.32 E-value: 3.19e-113
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| DEXDc_SHPRH-like | cd18008 | DEXH-box helicase domain of SHPRH-like proteins; The SHPRH-like subgroup belongs to the ... |
556-880 | 1.65e-82 | ||||||||||
DEXH-box helicase domain of SHPRH-like proteins; The SHPRH-like subgroup belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350766 [Multi-domain] Cd Length: 241 Bit Score: 269.93 E-value: 1.65e-82
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| SNF2-rel_dom | pfam00176 | SNF2-related domain; This domain is found in proteins involved in a variety of processes ... |
559-958 | 8.91e-55 | ||||||||||
SNF2-related domain; This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1). SNF2 functions as the ATPase component of the SNF2/SWI multisubunit complex, which utilizes energy derived from ATP hydrolysis to disrupt histone-DNA interactions, resulting in the increased accessibility of DNA to transcription factors. Pssm-ID: 425504 [Multi-domain] Cd Length: 289 Bit Score: 192.90 E-value: 8.91e-55
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| PLN03142 | PLN03142 | Probable chromatin-remodeling complex ATPase chain; Provisional |
782-1247 | 3.77e-25 | ||||||||||
Probable chromatin-remodeling complex ATPase chain; Provisional Pssm-ID: 215601 [Multi-domain] Cd Length: 1033 Bit Score: 113.36 E-value: 3.77e-25
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| RING-HC_CHR27-like | cd23142 | RING finger, HC subclass, found in Arabidopsis thaliana protein CHROMATIN REMODELING 27 (CHR27) ... |
984-1035 | 6.05e-20 | ||||||||||
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: 84.55 E-value: 6.05e-20
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| HELICc | smart00490 | helicase superfamily c-terminal domain; |
1139-1220 | 3.33e-16 | ||||||||||
helicase superfamily c-terminal domain; Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 74.56 E-value: 3.33e-16
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| RING | smart00184 | Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and ... |
986-1023 | 1.69e-08 | ||||||||||
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: 51.36 E-value: 1.69e-08
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| zf-RING_UBOX | pfam13445 | RING-type zinc-finger; This zinc-finger is a typical RING-type of plant ubiquitin ligases. |
986-1022 | 6.06e-06 | ||||||||||
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: 44.31 E-value: 6.06e-06
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| PEX10 | COG5574 | RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, ... |
986-1022 | 5.44e-04 | ||||||||||
RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]; Pssm-ID: 227861 [Multi-domain] Cd Length: 271 Bit Score: 43.34 E-value: 5.44e-04
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| Name | Accession | Description | Interval | E-value | ||||||||||
| HepA | COG0553 | Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ... |
547-1256 | 3.19e-113 | ||||||||||
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair]; Pssm-ID: 440319 [Multi-domain] Cd Length: 682 Bit Score: 370.32 E-value: 3.19e-113
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| DEXDc_SHPRH-like | cd18008 | DEXH-box helicase domain of SHPRH-like proteins; The SHPRH-like subgroup belongs to the ... |
556-880 | 1.65e-82 | ||||||||||
DEXH-box helicase domain of SHPRH-like proteins; The SHPRH-like subgroup belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350766 [Multi-domain] Cd Length: 241 Bit Score: 269.93 E-value: 1.65e-82
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| DEXHc_TTF2 | cd18072 | DEAH-box helicase domain of TTF2; Transcription termination factor 2 (TTF2 also called ... |
556-880 | 2.24e-59 | ||||||||||
DEAH-box helicase domain of TTF2; Transcription termination factor 2 (TTF2 also called Forkhead-box E1/FOXE1 ) is a transcription termination factor that couples ATP hydrolysis with the removal of RNA polymerase II from the DNA template. Single nucleotide polymorphism (SNP) within the 5'-UTR of TTF2 is associated with thyroid cancer risk.TTF2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350830 [Multi-domain] Cd Length: 241 Bit Score: 204.25 E-value: 2.24e-59
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| SNF2-rel_dom | pfam00176 | SNF2-related domain; This domain is found in proteins involved in a variety of processes ... |
559-958 | 8.91e-55 | ||||||||||
SNF2-related domain; This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1). SNF2 functions as the ATPase component of the SNF2/SWI multisubunit complex, which utilizes energy derived from ATP hydrolysis to disrupt histone-DNA interactions, resulting in the increased accessibility of DNA to transcription factors. Pssm-ID: 425504 [Multi-domain] Cd Length: 289 Bit Score: 192.90 E-value: 8.91e-55
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| DEXHc_HLTF1_SMARC3 | cd18071 | DEXH-box helicase domain of HLTF1; Helicase like transcription factor (HLTF1, also known as ... |
556-880 | 3.17e-54 | ||||||||||
DEXH-box helicase domain of HLTF1; Helicase like transcription factor (HLTF1, also known as HIP116 or SMARCA3) has both helicase and E3 ubiquitin ligase activities and ATP-dependent nucleosome-remodeling activity. HLTF1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350829 [Multi-domain] Cd Length: 239 Bit Score: 189.22 E-value: 3.17e-54
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| SF2_C_SNF | cd18793 | C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ... |
1119-1230 | 6.57e-52 | ||||||||||
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) family includes chromatin-remodeling factors, such as CHD proteins and SMARCA proteins, recombination proteins Rad54, and many others. They are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. Pssm-ID: 350180 [Multi-domain] Cd Length: 135 Bit Score: 178.44 E-value: 6.57e-52
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| DEXQc_SHPRH | cd18070 | DEXQ-box helicase domain of SHPRH; E3 ubiquitin-protein ligase SHPRH is a ubiquitously ... |
556-879 | 1.68e-50 | ||||||||||
DEXQ-box helicase domain of SHPRH; E3 ubiquitin-protein ligase SHPRH is a ubiquitously expressed protein that contains motifs characteristic of several DNA repair proteins, transcription factors, and helicases. SHPRH is a functional homolog of S. cerevisiae RAD5 and is involved in DNA repair. SHPRH is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350828 [Multi-domain] Cd Length: 257 Bit Score: 179.46 E-value: 1.68e-50
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| DEXQc_arch_SWI2_SNF2 | cd18012 | DEAQ-box helicase domain of archaeal and bacterial SNF2-related proteins; Proteins belonging ... |
557-882 | 1.17e-42 | ||||||||||
DEAQ-box helicase domain of archaeal and bacterial SNF2-related proteins; Proteins belonging to SNF2 family of DNA dependent ATPases are important members of the chromatin remodeling complexes that are implicated in epigenetic control of gene expression. The Snf2 family comprises a large group of ATP-hydrolyzing proteins that are ubiquitous in eukaryotes, but also present in eubacteria and archaea. Archaeal SWI2 and SNF2 are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350770 [Multi-domain] Cd Length: 218 Bit Score: 155.42 E-value: 1.17e-42
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| DEXHc_Snf | cd17919 | DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting ... |
559-844 | 1.70e-36 | ||||||||||
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting (SNF) proteins DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350677 [Multi-domain] Cd Length: 182 Bit Score: 136.16 E-value: 1.70e-36
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| DEXHc_ERCC6L2 | cd18005 | DEXH-box helicase domain of ERCC6L2; ERCC excision repair 6 like 2 (ERCC6L2, also known as ... |
556-880 | 4.50e-26 | ||||||||||
DEXH-box helicase domain of ERCC6L2; ERCC excision repair 6 like 2 (ERCC6L2, also known as RAD26L) may play a role in DNA repair and mitochondrial function. In humans, mutations in the ERCC6L2 gene are associated with bone marrow failure syndrome 2. ERCC6L2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350763 [Multi-domain] Cd Length: 245 Bit Score: 108.62 E-value: 4.50e-26
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| DEXHc_Mot1 | cd17999 | DEXH-box helicase domain of Mot1; Modifier of transcription 1 (Mot1, also known as TAF172 in ... |
580-839 | 3.59e-25 | ||||||||||
DEXH-box helicase domain of Mot1; Modifier of transcription 1 (Mot1, also known as TAF172 in eukaryotes) regulates transcription in association with TATA binding protein (TBP). Mot1, Ino80C, and NC2 function coordinately to regulate pervasive transcription in yeast and mammals. Mot1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350757 [Multi-domain] Cd Length: 232 Bit Score: 105.51 E-value: 3.59e-25
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| PLN03142 | PLN03142 | Probable chromatin-remodeling complex ATPase chain; Provisional |
782-1247 | 3.77e-25 | ||||||||||
Probable chromatin-remodeling complex ATPase chain; Provisional Pssm-ID: 215601 [Multi-domain] Cd Length: 1033 Bit Score: 113.36 E-value: 3.77e-25
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| DEXHc_ERCC6 | cd18000 | DEXH-box helicase domain of ERCC6; ERCC excision repair 6, chromatin remodeling factor (ERCC6, ... |
556-844 | 1.37e-23 | ||||||||||
DEXH-box helicase domain of ERCC6; ERCC excision repair 6, chromatin remodeling factor (ERCC6, also known Cockayne syndrome group B (CSB), Rad26 in Saccharomyces cerevisiae, and Rhp26 in Schizosaccharomyces pombe) is a DNA-binding protein that is important in transcription-coupled excision repair. ERCC6 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350758 [Multi-domain] Cd Length: 193 Bit Score: 99.71 E-value: 1.37e-23
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| Helicase_C | pfam00271 | Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
1123-1220 | 7.51e-23 | ||||||||||
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase. Pssm-ID: 459740 [Multi-domain] Cd Length: 109 Bit Score: 94.58 E-value: 7.51e-23
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| DEXQc_SRCAP | cd18003 | DEXH/Q-box helicase domain of SRCAP; Snf2-related CBP activator (SRCAP, also known as SWR1 or ... |
557-880 | 2.63e-20 | ||||||||||
DEXH/Q-box helicase domain of SRCAP; Snf2-related CBP activator (SRCAP, also known as SWR1 or DOMO1) is the core catalytic component of the multiprotein chromatin-remodeling SRCAP complex, that is necessary for the incorporation of the histone variant H2A.Z into nucleosomes. SRCAP is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350761 [Multi-domain] Cd Length: 223 Bit Score: 90.87 E-value: 2.63e-20
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| RING-HC_CHR27-like | cd23142 | RING finger, HC subclass, found in Arabidopsis thaliana protein CHROMATIN REMODELING 27 (CHR27) ... |
984-1035 | 6.05e-20 | ||||||||||
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: 84.55 E-value: 6.05e-20
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| DEXHc_SMARCA1_SMARCA5 | cd17997 | DEAH-box helicase domain of SMARCA1 and SMARCA5; SWI/SNF related, matrix associated, actin ... |
564-882 | 1.54e-17 | ||||||||||
DEAH-box helicase domain of SMARCA1 and SMARCA5; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1 and 5 (SMARCA1 and SMARCA5) are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350755 [Multi-domain] Cd Length: 222 Bit Score: 83.14 E-value: 1.54e-17
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| DEXHc_ERCC6L | cd18001 | DEXH-box helicase domain of ERCC6L; ERCC excision repair 6 like, spindle assembly checkpoint ... |
556-839 | 4.65e-17 | ||||||||||
DEXH-box helicase domain of ERCC6L; ERCC excision repair 6 like, spindle assembly checkpoint helicase (ERCC6L, also known as RAD26L) is an essential component of the mitotic spindle assembly checkpoint, by acting as a tension sensor that associates with catenated DNA which is stretched under tension until it is resolved during anaphase. ERCC6L is proposed to stimulate cancer cell proliferation by promoting cell cycle through a way of RAB31-MAPK-CDK2. ERCC6L is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350759 [Multi-domain] Cd Length: 232 Bit Score: 82.03 E-value: 4.65e-17
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| HELICc | smart00490 | helicase superfamily c-terminal domain; |
1139-1220 | 3.33e-16 | ||||||||||
helicase superfamily c-terminal domain; Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 74.56 E-value: 3.33e-16
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| DEXHc_HELLS_SMARCA6 | cd18009 | DEXH-box helicase domain of HELLS; HELLS (helicase, lymphoid specific, also known as Lsh or ... |
556-882 | 1.09e-14 | ||||||||||
DEXH-box helicase domain of HELLS; HELLS (helicase, lymphoid specific, also known as Lsh or SMARCA6) is a major epigenetic regulator crucial for normal heterochromatin structure and function. HELLS is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350767 [Multi-domain] Cd Length: 236 Bit Score: 75.12 E-value: 1.09e-14
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| DEXHc_CHD6_7_8_9 | cd17995 | DEXH-box helicase domain of the chromodomain helicase DNA binding protein 6, 7, 8 and 9; ... |
557-880 | 1.96e-14 | ||||||||||
DEXH-box helicase domain of the chromodomain helicase DNA binding protein 6, 7, 8 and 9; Chromodomain-helicase-DNA-binding protein 6-9 (CHD6, CHD7, CHD8, and CHD9) are members of the DEAD-like helicases superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350753 [Multi-domain] Cd Length: 223 Bit Score: 73.82 E-value: 1.96e-14
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| DEXHc_RAD54 | cd18004 | DEXH-box helicase domain of RAD54; RAD54 proteins play a role in recombination. They are ... |
557-880 | 9.68e-14 | ||||||||||
DEXH-box helicase domain of RAD54; RAD54 proteins play a role in recombination. They are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350762 [Multi-domain] Cd Length: 240 Bit Score: 72.32 E-value: 9.68e-14
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| DEXHc_CHD8 | cd18060 | DEAH-box helicase domain of the chromodomain helicase DNA binding protein 8; ... |
668-880 | 1.51e-12 | ||||||||||
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 8; Chromodomain-helicase-DNA-binding protein 8 (CHD8) is a DNA helicase that acts as a chromatin remodeling factor and regulates transcription. It also acts as a transcription repressor by remodeling chromatin structure and recruiting histone H1 to target genes. It suppresses p53/TP53-mediated apoptosis by recruiting histone H1 and preventing p53/TP53 transactivation activity and of STAT3 activity by suppressing the LIF-induced STAT3 transcriptional activity. It also acts as a negative regulator of Wnt signaling pathway and CTNNB1-targeted gene expression. CHD8 is also involved in both enhancer blocking and epigenetic remodeling at chromatin boundary via its interaction with CTCF. It also acts as a transcription activator via its interaction with ZNF143 by participating in efficient U6 RNA polymerase III transcription. CHD8 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350818 [Multi-domain] Cd Length: 222 Bit Score: 68.54 E-value: 1.51e-12
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| DEXHc_CHD6 | cd18058 | DEAH-box helicase domain of the chromodomain helicase DNA binding protein 6; ... |
668-880 | 1.55e-12 | ||||||||||
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 6; Chromodomain-helicase-DNA-binding protein 6 (CHD6) is a DNA-dependent ATPase that plays a role in chromatin remodeling. It regulates transcription by disrupting nucleosomes in a largely non-sliding manner which strongly increases the accessibility of chromatin. It activates transcription of specific genes in response to oxidative stress through interaction with NFE2L2.2 and acts as a transcriptional repressor of different viruses including influenza virus or papillomavirus. During influenza virus infection, the viral polymerase complex localizes CHD6 to inactive chromatin where it gets degraded in a proteasome independent-manner. CHD6 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350816 [Multi-domain] Cd Length: 222 Bit Score: 68.53 E-value: 1.55e-12
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| DEXHc_CHD1L | cd18006 | DEAH/Q-box helicase domain of CHD1L; Chromodomain helicase DNA binding protein 1 like (CHD1L, ... |
559-880 | 2.33e-12 | ||||||||||
DEAH/Q-box helicase domain of CHD1L; Chromodomain helicase DNA binding protein 1 like (CHD1L, also known as ALC1) is involved in DNA repair by regulating chromatin relaxation following DNA damage. CHD1L is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350764 [Multi-domain] Cd Length: 216 Bit Score: 67.85 E-value: 2.33e-12
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| DEXHc_CHD7 | cd18059 | DEAH-box helicase domain of the chromodomain helicase DNA binding protein 7; ... |
668-880 | 9.63e-12 | ||||||||||
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 7; Chromodomain-helicase-DNA-binding protein 7 (CHD7) is a probable transcription regulator. It may be involved in the 45S precursor rRNA production. CHD7 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350817 [Multi-domain] Cd Length: 222 Bit Score: 66.21 E-value: 9.63e-12
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| DEXDc | smart00487 | DEAD-like helicases superfamily; |
555-837 | 9.71e-12 | ||||||||||
DEAD-like helicases superfamily; Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 65.59 E-value: 9.71e-12
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| DEXQc_INO80 | cd18002 | DEAQ-box helicase domain of INO80; INO80 is the catalytic ATPase subunit of the INO80 ... |
556-880 | 3.97e-11 | ||||||||||
DEAQ-box helicase domain of INO80; INO80 is the catalytic ATPase subunit of the INO80 chromatin remodeling complex. INO80 removes histone H3-containing nucleosomes from associated chromatin, promotes CENP-ACnp1 chromatin assembly at the centromere in a redundant manner with another chromatin-remodeling factor Chd1Hrp1. INO80 mutants have severe defects in oxygen consumption and promiscuous cell division that is no longer coupled with metabolic status. INO80 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350760 [Multi-domain] Cd Length: 229 Bit Score: 64.45 E-value: 3.97e-11
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| DEXHc_HARP_SMARCAL1 | cd18010 | DEXH-box helicase domain of SMARCAL1; SMARCAL1 (SWI/SNF related, matrix associated, actin ... |
668-880 | 7.02e-11 | ||||||||||
DEXH-box helicase domain of SMARCAL1; SMARCAL1 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a like 1, also known as HARP) is recruited to stalled replication forks to promote repair and helps restart replication. It plays a role in DNA repair, telomere maintenance and replication fork stability in response to DNA replication stress. Mutations cause Schimke Immunoosseous Dysplasia. SMARCAL1 is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350768 [Multi-domain] Cd Length: 213 Bit Score: 63.38 E-value: 7.02e-11
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| DEXHc_SMARCAD1 | cd17998 | DEXH-box helicase domain of SMARCAD1; SWI/SNF-related matrix-associated actin-dependent ... |
559-844 | 1.17e-10 | ||||||||||
DEXH-box helicase domain of SMARCAD1; SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 (SMARCAD1, also known as ATP-dependent helicase 1 or Hel1) possesses intrinsic ATP-dependent nucleosome-remodeling activity and is required for both DNA repair and heterochromatin organization. SMARCAD1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350756 [Multi-domain] Cd Length: 187 Bit Score: 62.02 E-value: 1.17e-10
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| RING-HC_RAD16-like | cd16567 | RING finger, HC subclass, found in Saccharomyces cerevisiae DNA repair protein RAD16, ... |
985-1030 | 4.43e-10 | ||||||||||
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: 56.20 E-value: 4.43e-10
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| DEXHc_ATRX-like | cd18007 | DEXH-box helicase domain of ATRX-like proteins; This family includes ATRX-like members such as ... |
662-880 | 5.33e-10 | ||||||||||
DEXH-box helicase domain of ATRX-like proteins; This family includes ATRX-like members such as transcriptional regulator ATRX (also called alpha thalassemia/mental retardation syndrome X-linked and X-linked nuclear protein or XNP) which is involved in transcriptional regulation and chromatin remodeling, and ARIP4 (also called androgen receptor-interacting protein 4, RAD54 like 2 or RAD54L2) which modulates androgen receptor (AR)-dependent transactivation in a promoter-dependent manner. They are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350765 [Multi-domain] Cd Length: 239 Bit Score: 61.15 E-value: 5.33e-10
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| DEXHc_SMARCA5 | cd18064 | DEAH-box helicase domain of SMARCA5; SWI/SNF related, matrix associated, actin dependent ... |
784-897 | 7.03e-10 | ||||||||||
DEAH-box helicase domain of SMARCA5; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5 (SMARCA5, also called SNF2H) is the catalytic subunit of the four known chromatin-remodeling complexes: CHRAC, RSF, ACF/WCRF, and WICH. SMARCA5 plays a major role organising arrays of nucleosomes adjacent to the binding sites for the architectural transcription factor CTCF sites and acts to promote CTCF binding SMARCA5 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350822 [Multi-domain] Cd Length: 244 Bit Score: 60.83 E-value: 7.03e-10
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| DEXHc_SMARCA2_SMARCA4 | cd17996 | DEXH-box helicase domain of SMARCA2 and SMARCA4; SWI/SNF related, matrix associated, actin ... |
580-882 | 7.60e-10 | ||||||||||
DEXH-box helicase domain of SMARCA2 and SMARCA4; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, members 2 and 4 (SMARCA2 and SMARCA4) are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350754 [Multi-domain] Cd Length: 233 Bit Score: 60.85 E-value: 7.60e-10
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| DEXHc_CHD9 | cd18061 | DEAH-box helicase domain of the chromodomain helicase DNA binding protein 9; ... |
780-880 | 8.83e-10 | ||||||||||
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 9; Chromodomain-helicase-DNA-binding protein 9 (CHD9) acts as a transcriptional coactivator for PPARA and possibly other nuclear receptors. It is proposed to be a ATP-dependent chromatin remodeling protein. CHD9 has DNA-dependent ATPase activity and binds to A/T-rich DNA. It also associates with A/T-rich regulatory regions in promoters of genes that participate in the differentiation of progenitors during osteogenesis. CHD9 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350819 [Multi-domain] Cd Length: 222 Bit Score: 60.40 E-value: 8.83e-10
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| DEXHc_SMARCA1 | cd18065 | DEAH-box helicase domain of SMARCA1; SWI/SNF related, matrix associated, actin dependent ... |
555-882 | 2.02e-09 | ||||||||||
DEAH-box helicase domain of SMARCA1; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1 (SMARCA1, also called SNF2L) is a component of NURF (nucleosome-remodeling factor) and CERF (CECR2-containing-remodeling factor) complexes which promote the perturbation of chromatin structure in an ATP-dependent manner. SMARCA1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350823 [Multi-domain] Cd Length: 233 Bit Score: 59.26 E-value: 2.02e-09
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| DEXHc_CHD2 | cd18054 | DEAH-box helicase domain of the chromodomain helicase DNA binding protein 2; ... |
556-880 | 2.97e-09 | ||||||||||
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 2; Chromodomain-helicase-DNA-binding protein 2 (CHD2) is a DNA-binding helicase that specifically binds to the promoter of target genes, leading to chromatin remodeling, possibly by promoting deposition of histone H3.3. It is involved in myogenesis via interaction with MYOD1; it binds to myogenic gene regulatory sequences and mediates incorporation of histone H3.3 prior to the onset of myogenic gene expression, promoting their expression. CHD2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350812 [Multi-domain] Cd Length: 237 Bit Score: 58.86 E-value: 2.97e-09
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| DEXHc_ATRX | cd18068 | DEXH-box helicase domain of ATRX; Transcriptional regulator ATRX (also called alpha ... |
790-860 | 4.21e-09 | ||||||||||
DEXH-box helicase domain of ATRX; Transcriptional regulator ATRX (also called alpha thalassemia/mental retardation syndrome X-linked and X-linked nuclear protein or XNP) is involved in transcriptional regulation and chromatin remodeling. Mutations in humans cause mental retardation, X-linked, syndromic, with hypotonic facies 1 (MRXSHF1) and alpha-thalassemia myelodysplasia syndrome (ATMDS). ATRX is part of the a DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350826 [Multi-domain] Cd Length: 246 Bit Score: 58.75 E-value: 4.21e-09
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| RING-HC_RNF5-like | cd16534 | RING finger, HC subclass, found in RING finger protein RNF5, RNF185 and similar proteins; RNF5 ... |
985-1022 | 1.01e-08 | ||||||||||
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: 52.30 E-value: 1.01e-08
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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 ... |
983-1029 | 1.21e-08 | ||||||||||
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: 52.56 E-value: 1.21e-08
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| RING | smart00184 | Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and ... |
986-1023 | 1.69e-08 | ||||||||||
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: 51.36 E-value: 1.69e-08
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| DEXHc_CHD1_2 | cd17993 | DEXH-box helicase domain of the chromodomain helicase DNA binding proteins 1 and 2, and ... |
557-880 | 3.58e-08 | ||||||||||
DEXH-box helicase domain of the chromodomain helicase DNA binding proteins 1 and 2, and similar proteins; Chromodomain-helicase-DNA-binding protein 1 (CHD1) is an ATP-dependent chromatin-remodeling factor which functions as the substrate recognition component of the transcription regulatory histone acetylation (HAT) complex SAGA. It regulates polymerase II transcription and is also required for efficient transcription by RNA polymerase I, and more specifically the polymerase I transcription termination step. It is not only involved in transcription-related chromatin-remodeling, but is also required to maintain a specific chromatin configuration across the genome. CHD1 is also associated with histone deacetylase (HDAC) activity. Chromodomain-helicase-DNA-binding protein 2 (CHD2) is a DNA-binding helicase that specifically binds to the promoter of target genes, leading to chromatin remodeling, possibly by promoting deposition of histone H3.3. It is involved in myogenesis via interaction with MYOD1; it binds to myogenic gene regulatory sequences and mediates incorporation of histone H3.3 prior to the onset of myogenic gene expression, promoting their expression. Both are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350751 [Multi-domain] Cd Length: 218 Bit Score: 55.44 E-value: 3.58e-08
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| RING-HC_RNF138 | cd16544 | RING finger, HC subclass, found in RING finger protein 138 (RNF138) and similar proteins; ... |
986-1029 | 4.93e-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: 50.48 E-value: 4.93e-08
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| RING-HC | cd16449 | HC subclass of RING (RING-HC) finger and its variants; The RING finger is a specialized type ... |
985-1023 | 6.85e-08 | ||||||||||
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: 49.79 E-value: 6.85e-08
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| RING-HC_HLTF | cd16509 | RING finger, HC subclass, found in helicase-like transcription factor (HLTF) and similar ... |
986-1035 | 1.39e-07 | ||||||||||
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: 49.23 E-value: 1.39e-07
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| RING-HC_BRCA1 | cd16498 | RING finger, HC subclass, found in breast cancer type 1 susceptibility protein (BRCA1) and ... |
986-1042 | 6.37e-07 | ||||||||||
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: 48.83 E-value: 6.37e-07
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| RING-HC_RNF213 | cd16561 | RING finger, HC subclass, found in RING finger protein 213 (RNF213) and similar proteins; ... |
986-1023 | 1.06e-06 | ||||||||||
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: 46.50 E-value: 1.06e-06
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| DEXHc_RAD54A | cd18067 | DEXH-box helicase domain of RAD54A; DNA repair and recombination protein RAD54A, also known as ... |
557-880 | 1.13e-06 | ||||||||||
DEXH-box helicase domain of RAD54A; DNA repair and recombination protein RAD54A, also known as RAD54L or RAD54, plays a role in homologous recombination related repair of DNA double-strand breaks. RAD54A is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350825 [Multi-domain] Cd Length: 243 Bit Score: 51.32 E-value: 1.13e-06
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| RING-HC_AtRMA-like | cd16745 | RING finger, HC subclass, found in Arabidopsis thaliana RING membrane-anchor proteins (AtRMAs) ... |
986-1022 | 1.16e-06 | ||||||||||
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: 46.32 E-value: 1.16e-06
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| DEXHc_CHD1 | cd18053 | DEAH-box helicase domain of the chromodomain helicase DNA binding protein 1; ... |
782-880 | 2.12e-06 | ||||||||||
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 1; Chromodomain-helicase-DNA-binding protein 1 (CHD1) is an ATP-dependent chromatin-remodeling factor which functions as substrate recognition component of the transcription regulatory histone acetylation (HAT) complex SAGA. It regulates polymerase II transcription and is also required for efficient transcription by RNA polymerase I, and more specifically the polymerase I transcription termination step. It is not only involved in transcription-related chromatin-remodeling, but also required to maintain a specific chromatin configuration across the genome. CHD1 is also associated with histone deacetylase (HDAC) activity. It is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350811 [Multi-domain] Cd Length: 237 Bit Score: 50.43 E-value: 2.12e-06
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| DEXHc_CHD4 | cd18056 | DEAH-box helicase domain of the chromodomain helicase DNA binding protein 4; ... |
782-880 | 3.76e-06 | ||||||||||
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 4; Chromodomain-helicase-DNA-binding protein 4 (CHD4) is a component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin by deacetylating histones. CHD4 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350814 [Multi-domain] Cd Length: 232 Bit Score: 49.68 E-value: 3.76e-06
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| RING-HC_Cbl-c | cd16710 | RING finger, HC subclass, found in E3 ubiquitin-protein ligase Cbl-c and similar proteins; ... |
980-1029 | 4.00e-06 | ||||||||||
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: 45.46 E-value: 4.00e-06
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| RING-HC_RNF185 | cd16744 | RING finger, HC subclass, found in RING finger protein 185 (RNF185) and similar proteins; ... |
986-1022 | 5.75e-06 | ||||||||||
RING finger, HC subclass, found in RING finger protein 185 (RNF185) and similar proteins; RNF185 is an E3 ubiquitin-protein ligase of endoplasmic reticulum-associated degradation (ERAD) that targets cystic fibrosis transmembrane conductance regulator (CFTR). It controls the degradation of CFTR and CFTR F508del allele in a RING- and proteasome-dependent manner, but does not control that of other classical ERAD model substrates. It also negatively regulates osteogenic differentiation by targeting dishevelled2 (Dvl2), a key mediator of the Wnt signaling pathway, for degradation. Moreover, RNF185 regulates selective mitochondrial autophagy through interaction with the Bcl-2 family protein BNIP1. It also plays an important role in cell adhesion and migration through the modulation of cell migration by ubiquitinating paxillin. RNF185 contains a C3HC4-type RING-HC finger. Pssm-ID: 438402 [Multi-domain] Cd Length: 57 Bit Score: 44.92 E-value: 5.75e-06
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| zf-RING_UBOX | pfam13445 | RING-type zinc-finger; This zinc-finger is a typical RING-type of plant ubiquitin ligases. |
986-1022 | 6.06e-06 | ||||||||||
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: 44.31 E-value: 6.06e-06
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| DEXHc_CHD3 | cd18055 | DEAH-box helicase domain of the chromodomain helicase DNA binding protein 3; ... |
782-880 | 6.35e-06 | ||||||||||
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 3; Chromodomain-helicase-DNA-binding protein 3 (CHD3) is a component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin by deacetylating histones. It is required for anchoring centrosomal pericentrin in both interphase and mitosis, for spindle organization and centrosome integrity. CHD3 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350813 [Multi-domain] Cd Length: 232 Bit Score: 48.85 E-value: 6.35e-06
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| RING-HC_CHFR | cd16503 | RING finger, HC subclass, found in checkpoint with forkhead and RING finger domains protein ... |
985-1036 | 7.17e-06 | ||||||||||
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: 44.28 E-value: 7.17e-06
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| DEXHc_CHD5 | cd18057 | DEAH-box helicase domain of the chromodomain helicase DNA binding protein 5; ... |
782-880 | 1.14e-05 | ||||||||||
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 5; Chromodomain-helicase-DNA-binding protein 5 (CHD5) is a chromatin-remodeling protein that binds DNA through histones and regulates gene transcription. It is thought to specifically recognize and bind trimethylated 'Lys-27' (H3K27me3) and non-methylated 'Lys-4' of histone H3 and plays a role in the development of the nervous system by activating the expression of genes promoting neuron terminal differentiation. In parallel, it may also positively regulate the trimethylation of histone H3 at 'Lys-27' thereby specifically repressing genes that promote the differentiation into non-neuronal cell lineages. As a tumor suppressor, it regulates the expression of genes involved in cell proliferation and differentiation. In spermatogenesis, it probably regulates histone hyperacetylation and the replacement of histones by transition proteins in chromatin, a crucial step in the condensation of spermatid chromatin and the production of functional spermatozoa. CHD5 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350815 [Multi-domain] Cd Length: 232 Bit Score: 48.14 E-value: 1.14e-05
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| zf-C3HC4_2 | pfam13923 | Zinc finger, C3HC4 type (RING finger); |
986-1022 | 1.33e-05 | ||||||||||
Zinc finger, C3HC4 type (RING finger); Pssm-ID: 404756 [Multi-domain] Cd Length: 40 Bit Score: 43.19 E-value: 1.33e-05
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| RING-HC_ScRAD18-like | cd23148 | RING finger, HC subclass, found in Saccharomyces cerevisiae radiation sensitivity protein 18 ... |
986-1035 | 1.35e-05 | ||||||||||
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: 43.68 E-value: 1.35e-05
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| RING-HC_RNF125 | cd16542 | RING finger, HC subclass, found in RING finger protein 125 (RNF125); RNF125, also known as ... |
986-1030 | 1.41e-05 | ||||||||||
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: 43.33 E-value: 1.41e-05
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| DEXHc_CHD3_4_5 | cd17994 | DEAH-box helicase domain of the chromodomain helicase DNA binding proteins 3, 4 and 5; ... |
782-880 | 1.77e-05 | ||||||||||
DEAH-box helicase domain of the chromodomain helicase DNA binding proteins 3, 4 and 5; Chromodomain-helicase-DNA-binding protein 3 (CHD3) is a component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin by deacetylating histones. It is required for anchoring centrosomal pericentrin in both interphase and mitosis, for spindle organization and centrosome integrity. Chromodomain-helicase-DNA-binding protein 4 (CHD4) is a component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin by deacetylating histones. Chromodomain-helicase-DNA-binding protein 5 (CHD5) is a chromatin-remodeling protein that binds DNA through histones and regulates gene transcription. It is thought to specifically recognize and bind trimethylated 'Lys-27' (H3K27me3) and non-methylated 'Lys-4' of histone H3 and plays a role in the development of the nervous system by activating the expression of genes promoting neuron terminal differentiation. In parallel, it may also positively regulate the trimethylation of histone H3 at 'Lys-27' thereby specifically repressing genes that promote the differentiation into non-neuronal cell lineages. As a tumor suppressor, it regulates the expression of genes involved in cell proliferation and differentiation. In spermatogenesis, it probably regulates histone hyperacetylation and the replacement of histones by transition proteins in chromatin, a crucial step in the condensation of spermatid chromatin and the production of functional spermatozoa. CHD3, CHD4, and CHD5 are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350752 [Multi-domain] Cd Length: 196 Bit Score: 47.05 E-value: 1.77e-05
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| RING-H2 | cd16448 | H2 subclass of RING (RING-H2) fingers and its variants; The RING finger is a specialized type ... |
986-1027 | 1.94e-05 | ||||||||||
H2 subclass of RING (RING-H2) fingers 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 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). This family corresponds to the H2 subclass of RING (RING-H2) finger proteins that are characterized by containing C3H2C3-type canonical RING-H2 fingers or noncanonical RING-H2 finger variants, including C4HC3- (RING-CH alias RINGv), C3H3C2-, C3H2C2D-, C3DHC3-, and C4HC2H-type modified RING-H2 fingers. The canonical RING-H2 finger has been defined as C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-H-X2-C-X(4-48)-C-X2-C, X is any amino acid and the number of X residues varies in different fingers. It binds two Zn ions in a unique "cross-brace" arrangement, which distinguishes it from tandem zinc fingers and other similar motifs. RING-H2 finger 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 serves as a scaffold 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: 438112 [Multi-domain] Cd Length: 43 Bit Score: 42.77 E-value: 1.94e-05
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| RING-HC_TRIM77_C-IV | cd16543 | RING finger, HC subclass, found in tripartite motif-containing protein 77 (TRIM77) and similar ... |
985-1022 | 3.12e-05 | ||||||||||
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: 42.76 E-value: 3.12e-05
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| RING-HC_COP1 | cd16504 | RING finger, HC subclass, found in constitutive photomorphogenesis protein 1 (COP1) and ... |
985-1031 | 3.27e-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: 42.23 E-value: 3.27e-05
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| RING-HC_EHV1-like | cd23130 | RING finger, HC subclass, found in Equid alphaherpesvirus 1 (Equine herpesvirus 1/EHV-1) ... |
985-1031 | 3.61e-05 | ||||||||||
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: 42.34 E-value: 3.61e-05
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| DEXHc_ARIP4 | cd18069 | DEXH-box helicase domain of ARIP4; Androgen receptor-interacting protein 4 (ARIP4, also called ... |
790-858 | 4.02e-05 | ||||||||||
DEXH-box helicase domain of ARIP4; Androgen receptor-interacting protein 4 (ARIP4, also called RAD54 like 2 or RAD54L2 ) modulates androgen receptor (AR)-dependent transactivation in a promoter-dependent manner. ARIP4 is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350827 [Multi-domain] Cd Length: 227 Bit Score: 46.35 E-value: 4.02e-05
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| mRING-HC-C3HC3D_TRAF6 | cd16643 | Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) ... |
986-1035 | 4.04e-05 | ||||||||||
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: 42.37 E-value: 4.04e-05
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| DEXQc_bact_SNF2 | cd18013 | DEXQ-box helicase domain of bacterial SNF2 family proteins; Proteins belonging to the SNF2 ... |
787-841 | 4.09e-05 | ||||||||||
DEXQ-box helicase domain of bacterial SNF2 family proteins; Proteins belonging to the SNF2 family of DNA dependent ATPases are important members of the chromatin remodeling complexes that are implicated in epigenetic control of gene expression. The Snf2 family comprise a large group of ATP-hydrolyzing proteins that are ubiquitous in eukaryotes, but also present in eubacteria and archaea. The bacterial SNF2 present in this family are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350771 [Multi-domain] Cd Length: 218 Bit Score: 46.19 E-value: 4.09e-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 ... |
985-1022 | 4.35e-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: 41.83 E-value: 4.35e-05
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| RING-HC_RNF5 | cd16743 | RING finger, HC subclass, found in RING finger protein 5 (RNF5) and similar proteins; RNF5, ... |
986-1022 | 4.57e-05 | ||||||||||
RING finger, HC subclass, found in RING finger protein 5 (RNF5) and similar proteins; RNF5, also known as protein G16 or Ram1, is an E3 ubiquitin-protein ligase anchored to the outer membrane of the endoplasmic reticulum (ER). It 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. It also regulates the turnover of specific G protein-coupled receptors by ubiquitinating JNK-associated membrane protein (JAMP) and preventing proteasome recruitment. RNF5 limits basal levels of autophagy and influences susceptibility to bacterial infection through the regulation of ATG4B stability. It is also involved in the degradation of Pendrin, a transmembrane chloride/anion exchanger highly expressed in thyroid, kidney, and inner ear. RNF5 plays an important role in cell adhesion and migration. It can modulate cell migration by ubiquitinating paxillin. Furthermore, RNF5 interacts with virus-induced signaling adaptor (VISA) at mitochondria in a viral infection-dependent manner, and further targets VISA at K362 and K461 for K48-linked ubiquitination and degradation after viral infection. It also negatively regulates virus-triggered signaling by targeting MITA, also known as STING, for ubiquitination and degradation at the mitochondria. In addition, RNF5 determines breast cancer response to ER stress-inducing chemotherapies through the regulation of the L-glutamine carrier proteins SLC1A5 and SLC38A2 (SLC1A5/38A2). It also has been implicated in muscle organization and in recognition and processing of misfolded proteins. RNF5 contains a C3HC4-type RING-HC finger. Pssm-ID: 438401 [Multi-domain] Cd Length: 54 Bit Score: 42.18 E-value: 4.57e-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 ... |
986-1022 | 5.46e-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: 41.72 E-value: 5.46e-05
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| DEXHc_RAD54B | cd18066 | DEXH-box helicase domain of RAD54B; DNA repair and recombination protein RAD54B, also known as ... |
790-861 | 5.99e-05 | ||||||||||
DEXH-box helicase domain of RAD54B; DNA repair and recombination protein RAD54B, also known as RDH54, binds to double-stranded DNA, displays ATPase activity in the presence of DNA, and may have a role in meiotic and mitotic recombination. RAD54B is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350824 [Multi-domain] Cd Length: 235 Bit Score: 45.99 E-value: 5.99e-05
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| SPL-RING_NSE2 | cd16651 | SPL-RING finger found in E3 SUMO-protein ligase NSE2 and similar proteins; NSE2, also known as ... |
985-1035 | 6.60e-05 | ||||||||||
SPL-RING finger found in E3 SUMO-protein ligase NSE2 and similar proteins; NSE2, also known as MMS21 homolog (MMS21) or non-structural maintenance of chromosomes element 2 homolog (Non-SMC element 2 homolog, NSMCE2), is an autosumoylating small ubiquitin-like modifier (SUMO) ligase required for the response to DNA damage. It regulates sumoylation and nuclear-to-cytoplasmic translocation of skeletal and heart muscle-specific variant of the alpha subunit of nascent polypeptide associated complex (skNAC)-Smyd1 in myogenesis. It is also required for resisting extrinsically induced genotoxic stress. Moreover, NSE2 together with its partner proteins SMC6 and SMC5 form a tight subcomplex of the structural maintenance of chromosomes SMC5-6 complex, which includes another two subcomplexes, NSE1-NSE3-NSE4 and NSE5-NSE6. SMC6 and NSE3 are sumoylated in an NSE2-dependent manner, but SMC5 and NSE1 are not. NSE2-dependent E3 SUMO ligase activity is required for efficient DNA repair, but not for SMC5-6 complex stability. NSE2 contains a RING variant known as a Siz/PIAS (protein inhibitor of activated signal transducer and activator of transcription)-like RING (SPL-RING) finger that is likely shared by the SP-RING type SUMO E3 ligases, such as PIAS family proteins. The SPL-RING finger is a variant of the RING finger, which lacks the second, fifth, and sixth zinc-binding residues of the consensus C3H2C3-/C3HC4-type RING fingers. It harbors only one Zn binding site and is required for the sumoylating activity. Pssm-ID: 438313 [Multi-domain] Cd Length: 67 Bit Score: 42.25 E-value: 6.60e-05
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| RING-HC_ScPSH1-like | cd16568 | RING finger, HC subclass, found in Saccharomyces cerevisiae POB3/SPT16 histone-associated ... |
982-1031 | 1.34e-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: 40.82 E-value: 1.34e-04
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| RING-HC_Cbl-like | cd16502 | RING finger, HC subclass, found in Casitas B-lineage lymphoma (Cbl) proteins; The Cbl adaptor ... |
985-1023 | 1.40e-04 | ||||||||||
RING finger, HC subclass, found in Casitas B-lineage lymphoma (Cbl) proteins; The Cbl adaptor protein family contains a small class of RING-type E3 ubiquitin ligases with oncogenic activity, which is represented by three mammalian members, c-Cbl, Cbl-b and Cbl-c, as well as two invertebrate Cbl-family proteins, D-Cbl in Drosophila and Sli-1 in C. elegans. Cbl proteins function as potent negative regulators of various signaling cascades in a wide range of cell types. They play roles in ubiquitinating activated tyrosine kinases and targeting them for degradation. D-Cbl associates with the Drosophila epidermal growth factor receptor (EGFR) and overexpression of D-Cbl in the eye of Drosophila embryos inhibits EGFR-dependent photoreceptor cell development. Sli-1 is a negative regulator of the Let-23 receptor tyrosine kinase, an EGFR homolog, in vulva development. Cbl proteins in this subfamily consist of a highly conserved N-terminal half that includes 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) and a C3HC4-type RING-HC finger, both of which are required for Cbl-mediated downregulation of RTKs, and a divergent C-terminal region. Pssm-ID: 438165 [Multi-domain] Cd Length: 43 Bit Score: 40.41 E-value: 1.40e-04
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| RING-HC_RNF20-like | cd16704 | RING finger, HC subclass, found in RING finger protein RNF20, RNF40, and similar proteins; ... |
986-1027 | 1.54e-04 | ||||||||||
RING finger, HC subclass, found in RING finger protein RNF20, RNF40, and similar proteins; RNF20, also known as BRE1A, and RNF40, also known as BRE1B, are E3 ubiquitin-protein ligases that work together to form a heterodimeric 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. RNF20 regulates the cell cycle and differentiation of neural precursor cells (NPCs) and links histone H2B ubiquitylation with inflammation and inflammation-associated cancer. RNF40, also known as 95 kDa retinoblastoma-associated protein (RBP95), was identified as a novel leucine zipper retinoblastoma protein (pRb)-associated protein that may function as a regulation factor in RNA polymerase II-mediated transcription and/or transcriptional processing. All subfamily members contain a C3HC4-type RING-HC finger at its C-terminus. Pssm-ID: 438364 [Multi-domain] Cd Length: 65 Bit Score: 40.90 E-value: 1.54e-04
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| zf-C3HC4_3 | pfam13920 | Zinc finger, C3HC4 type (RING finger); |
985-1023 | 1.61e-04 | ||||||||||
Zinc finger, C3HC4 type (RING finger); Pssm-ID: 464042 [Multi-domain] Cd Length: 50 Bit Score: 40.44 E-value: 1.61e-04
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| DEXHc_SMARCA2 | cd18063 | DEXH-box helicase domain of SMARCA2; SWI/SNF related, matrix associated, actin dependent ... |
782-882 | 1.66e-04 | ||||||||||
DEXH-box helicase domain of SMARCA2; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2 (SMARCA2, also known as brahma homolog) is a component of the BAF complex. SMARCA2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350821 [Multi-domain] Cd Length: 251 Bit Score: 44.67 E-value: 1.66e-04
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| RING-HC_PRT1-like | cd23132 | RING finger, HC subclass, found in Arabidopsis thaliana proteolysis 1 protein (PRT1) and ... |
986-1022 | 1.70e-04 | ||||||||||
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: 40.48 E-value: 1.70e-04
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| DEXHc_SMARCA4 | cd18062 | DEXH-box helicase domain of SMARCA4; SWI/SNF related, matrix associated, actin dependent ... |
782-882 | 2.01e-04 | ||||||||||
DEXH-box helicase domain of SMARCA4; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4 (SMARCA4, also known as transcription activator BRG1) is a component of the CREST-BRG1 complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. Mutation of SMARCA4 (BRG1), the ATPase of BAF (mSWI/SNF) and PBAF complexes, contributes to a range of malignancies and neurologic disorders. SMARCA4 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350820 [Multi-domain] Cd Length: 251 Bit Score: 44.65 E-value: 2.01e-04
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| RING-HC_Cbl-b | cd16709 | RING finger, HC subclass, found in E3 ubiquitin-protein ligase Cbl-b and similar proteins; ... |
981-1031 | 2.01e-04 | ||||||||||
RING finger, HC subclass, found in E3 ubiquitin-protein ligase Cbl-b and similar proteins; Cbl-b, also known as Casitas B-lineage lymphoma proto-oncogene b, RING finger protein 56 (RNF56), SH3-binding protein Cbl-b, or signal transduction protein Cbl-b, has been identified as a regulator of antigen-specific, T cell-intrinsic, peripheral immune tolerance, a state also known as clonal anergy. It may inhibit activation of the p85 subunit of phosphoinositide 3-kinase (PI3K), protein kinase C-theta (PKC-theta), and phospholipase C-gamma1 (PLC-gamma1) and negatively regulates T-cell receptor-induced transcription factor nuclear factor kappaB (NF-kappaB) activation. In addition, Cbl-b may target multiple signaling molecules involved in transforming growth factor (TGF)-beta-mediated transactivation pathways. Cbl-b contains a tyrosine-kinase-binding domain (TKB, also known as the phosphotyrosine binding PTB domain, is composed of a four helix-bundle, a Ca2+ binding EF-hand and a highly variant SH2 domain), a proline rich domain, a nuclear localization signal, a C3HC4-type RING-HC finger and an ubiquitin-associated (UBA) domain. Pssm-ID: 438369 [Multi-domain] Cd Length: 76 Bit Score: 41.20 E-value: 2.01e-04
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| RING-HC_TRIM39_C-IV | cd16601 | RING finger, HC subclass, found in tripartite motif-containing protein 39 (TRIM39) and similar ... |
984-1022 | 2.21e-04 | ||||||||||
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: 39.78 E-value: 2.21e-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, ... |
985-1025 | 2.49e-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: 39.69 E-value: 2.49e-04
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| zf-C3HC4 | pfam00097 | Zinc finger, C3HC4 type (RING finger); The C3HC4 type zinc-finger (RING finger) is a ... |
986-1022 | 2.71e-04 | ||||||||||
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: 39.65 E-value: 2.71e-04
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| mRING-HC-C3HC3D_TRAF7 | cd16644 | Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) ... |
985-1022 | 2.96e-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: 39.64 E-value: 2.96e-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; ... |
986-1026 | 3.30e-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: 39.32 E-value: 3.30e-04
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| RING-HC_XBAT35-like | cd23129 | RING finger, HC subclass, found in Arabidopsis thaliana protein XB3 homolog 5 (XBAT35) and ... |
986-1032 | 4.22e-04 | ||||||||||
RING finger, HC subclass, found in Arabidopsis thaliana protein XB3 homolog 5 (XBAT35) and similar proteins; XBAT35, also known as ankyrin repeat domain and RING finger-containing protein XBAT35, or RING-type E3 ubiquitin transferase XBAT35, has no E3 ubiquitin-protein ligase activity observed when associated with the E2 enzyme UBC8 in vitro. It contains a typical C3HC4-type RING-HC finger. Pssm-ID: 438491 [Multi-domain] Cd Length: 54 Bit Score: 39.55 E-value: 4.22e-04
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| RING-HC_ARI6-like | cd23141 | RING finger, HC subclass, found in Arabidopsis thaliana protein ariadne homolog 6 (ARI6) and ... |
986-1009 | 4.39e-04 | ||||||||||
RING finger, HC subclass, found in Arabidopsis thaliana protein ariadne homolog 6 (ARI6) and similar proteins; This subfamily includes ARI6 and ARI11. They might act as E3 ubiquitin-protein ligases, or as part of E3 complexes, which accept ubiquitin from specific E2 ubiquitin-conjugating enzymes and then transfer it to substrates. Members of this subfamily contain a typical C3HC4-type RING-HC finger. Pssm-ID: 438503 [Multi-domain] Cd Length: 62 Bit Score: 39.78 E-value: 4.39e-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 ... |
985-1022 | 4.65e-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: 39.36 E-value: 4.65e-04
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| RING-HC_RNF4 | cd16533 | RING finger, HC subclass, found in RING finger protein 4 (RNF4) and similar proteins; RNF4, ... |
986-1031 | 4.74e-04 | ||||||||||
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: 39.49 E-value: 4.74e-04
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| RING-HC_Topors | cd16574 | RING finger, HC subclass, found in topoisomerase I-binding arginine/serine-rich protein ... |
986-1029 | 4.98e-04 | ||||||||||
RING finger, HC subclass, found in topoisomerase I-binding arginine/serine-rich protein (Topors) and similar proteins; Topors, also known as topoisomerase I-binding RING finger protein, tumor suppressor p53- binding protein 3, or p53-binding protein 3 (p53BP3), is a ubiquitously expressed nuclear E3 ubiquitin-protein ligase that can ligate both ubiquitin and small ubiquitin-like modifier (SUMO) to substrate proteins in the nucleus. It contains an N-terminal C3HC4-type RING-HC finger which ligates ubiquitin to its target proteins including DNA topoisomerase I, p53, NKX3.1, H2AX, and the AAV-2 Rep78/68 proteins. As a RING-dependent E3 ubiquitin ligase, Topors works with the E2 enzymes UbcH5a, UbcH5c, and UbcH6, but not with UbcH7, CDC34, or UbcH2b. Topors acts as a tumor suppressor in various malignancies. It regulates p53 modification, suggesting it may be responsible for astrocyte elevated gene-1 (AEG-1, also known as metadherin, or LYRIC) ubiquitin modification. Plk1-mediated phosphorylation of Topors inhibits Topors-mediated sumoylation of p53, whereas p53 ubiquitination is enhanced, leading to p53 degradation. It also functions as a negative regulator of the prostate tumor suppressor NKX3.1. Moreover, Topors is associated with promyelocytic leukemia nuclear bodies, and may be involved in the cellular response to camptothecin. It also plays a key role in the turnover of H2AX protein, discriminating the type of DNA damaging stress. Furthermore, Topors is a cilia-centrosomal protein associated with autosomal dominant retinal degeneration. Mutations in TOPORS cause autosomal dominant retinitis pigmentosa (adRP). Pssm-ID: 438236 [Multi-domain] Cd Length: 47 Bit Score: 39.19 E-value: 4.98e-04
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| RING-HC_Cbl | cd16708 | RING finger, HC subclass, found in E3 ubiquitin-protein ligase Cbl and similar proteins; Cbl, ... |
981-1031 | 5.32e-04 | ||||||||||
RING finger, HC subclass, found in E3 ubiquitin-protein ligase Cbl and similar proteins; Cbl, also known as Casitas B-lineage lymphoma proto-oncogene, proto-oncogene c-Cbl, RING finger protein 55 (RNF55), or signal transduction protein Cbl, is a multi-domain protein that acts as a key negative regulator of various receptor and non-receptor tyrosine kinase signaling. 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 proline-rich domain, a C3HC4-type RING-HC finger, and an ubiquitin-associated (UBA) domain. TKB is responsible for the interactions with many tyrosine kinases, such as the colony-stimulating factor-1 (CSF-1) receptor, Syk/ZAP-70, and Src-family of protein tyrosine kinases. The proline-rich domain can recruit proteins with a SH3 domain. Moreover, Cbl functions as an E3 ubiquitin ligase that can bind ubiquitin-conjugating enzymes (E2s) through the RING-HC finger. Pssm-ID: 438368 [Multi-domain] Cd Length: 77 Bit Score: 40.07 E-value: 5.32e-04
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| PEX10 | COG5574 | RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, ... |
986-1022 | 5.44e-04 | ||||||||||
RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]; Pssm-ID: 227861 [Multi-domain] Cd Length: 271 Bit Score: 43.34 E-value: 5.44e-04
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| RING-HC_RNF40 | cd16815 | RING finger, HC subclass, found in RING finger protein 40 (RNF40); RNF40, also known as BRE1B ... |
974-1027 | 5.61e-04 | ||||||||||
RING finger, HC subclass, found in RING finger protein 40 (RNF40); RNF40, also known as BRE1B or 95 kDa retinoblastoma-associated protein (RBP95), was identified as a novel leucine zipper retinoblastoma protein (pRb)-associated protein that may function as a regulation factor in RNA polymerase II-mediated transcription and/or transcriptional processing. RNF40 also functions as an E3 ubiquitin-protein ligase that forms a heterodimeric complex with BRE1B, also known as RNF40, to 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. It cooperates with SUPT16H to induce dynamic changes in chromatin structure during DSB repair. RNF40 contains a C3HC4-type RING-HC finger at the C-terminus. Pssm-ID: 438464 [Multi-domain] Cd Length: 78 Bit Score: 40.01 E-value: 5.61e-04
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| RING-HC_TRIM25_C-IV | cd16597 | RING finger, HC subclass, found in tripartite motif-containing protein TRIM25 and similar ... |
985-1022 | 7.18e-04 | ||||||||||
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: 39.22 E-value: 7.18e-04
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| RING_Ubox | cd00162 | RING finger (Really Interesting New Gene) domain and U-box domain superfamily; The RING finger ... |
986-1023 | 8.50e-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: 8.50e-04
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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 ... |
986-1010 | 9.66e-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: 38.43 E-value: 9.66e-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 ... |
986-1028 | 1.08e-03 | ||||||||||
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: 38.60 E-value: 1.08e-03
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| RING-HC_RNFT1-like | cd16532 | RING finger, HC subclass, found in RING finger and transmembrane domain-containing protein ... |
984-1012 | 1.12e-03 | ||||||||||
RING finger, HC subclass, found in RING finger and transmembrane domain-containing protein RNFT1, RNFT2, and similar proteins; Both RNFT1 and RNFT2 are multi-pass membrane proteins containing a C3HC4-type RING-HC finger. Their biological roles remain unclear. Pssm-ID: 438194 [Multi-domain] Cd Length: 41 Bit Score: 37.67 E-value: 1.12e-03
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| RING-HC_RNF113A_B | cd16539 | RING finger, HC subclass, found in RING finger proteins RNF113A, RNF113B, and similar proteins; ... |
986-1013 | 1.28e-03 | ||||||||||
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: 37.96 E-value: 1.28e-03
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| RING-H2_Rapsyn | cd16478 | RING finger, H2 subclass, found in 43 kDa receptor-associated protein of the synapse (Rapsyn) ... |
986-1027 | 1.40e-03 | ||||||||||
RING finger, H2 subclass, found in 43 kDa receptor-associated protein of the synapse (Rapsyn) and similar proteins; Rapsyn, also known as acetylcholine receptor (AChR)-associated 43 kDa protein or RING finger protein 205 (RNF205), is a 43 kDa postsynaptic protein that plays an essential role in the clustering and maintenance of AChR in the postsynaptic membrane of the motor endplate. AChRs enable the transport of rapsyn from the Golgi complex to the plasma membrane through a molecule-specific interaction. Rapsyn also mediates subsynaptic anchoring of protein kinase A (PKA) type I in close proximity to the postsynaptic membrane, which is essential for synapse maintenance. Its mutations in humans cause endplate AChR deficiency and myasthenic syndrome. Rapsyn contains an N-terminal myristoylation signal required for membrane association, seven tetratricopeptide repeats (TPRs) that subserve rapsyn self-association, a coiled-coil domain responsible for the binding of determinants within the long cytoplasmic loop of each AChR subunit, a C3H2C3-type RING-H2 finger that binds to the cytoplasmic domain of beta-dystroglycan and to S-NRAP and links rapsyn to the subsynaptic cytoskeleton, and a serine phosphorylation site. Pssm-ID: 438141 [Multi-domain] Cd Length: 48 Bit Score: 37.82 E-value: 1.40e-03
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| zf-C3HC4_4 | pfam15227 | zinc finger of C3HC4-type, RING; This is a family of primate-specific Ret finger protein-like ... |
986-1022 | 1.55e-03 | ||||||||||
zinc finger of C3HC4-type, RING; This is a family of primate-specific Ret finger protein-like (RFPL) zinc-fingers of the C3HC4 type. Ret finger protein-like proteins are primate-specific target genes of Pax6, a key transcription factor for pancreas, eye and neocortex development. This domain is likely to be DNA-binding. This zinc-finger domain together with the RDM domain, pfam11002, forms a large zinc-finger structure of the RING/U-Box superfamily. RING-containing proteins are known to exert an E3 ubiquitin protein ligase activity with the zinc-finger structure being mandatory for binding to the E2 ubiquitin-conjugating enzyme. Pssm-ID: 464570 [Multi-domain] Cd Length: 42 Bit Score: 37.41 E-value: 1.55e-03
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| RING-HC_RNF39 | cd16592 | RING finger, HC subclass, found in RING finger protein 39 (RNF39) and similar proteins; RNF39, ... |
983-1013 | 1.71e-03 | ||||||||||
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: 37.81 E-value: 1.71e-03
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| RING-HC_RBR_HHARI | cd16626 | RING finger, HC subclass, found in human homolog of Drosophila ariadne (HHARI) and similar ... |
985-1028 | 1.74e-03 | ||||||||||
RING finger, HC subclass, found in human homolog of Drosophila ariadne (HHARI) and similar proteins; This subfamily includes Drosophila melanogaster protein ariadne-1 (ARI-1), and its eukaryotic homologs, such as HHARI. ARI-1 is a widely expressed Drosophila RING-finger protein that localizes mainly in the cytoplasm and is required for neural development. It interacts with a novel ubiquitin-conjugating enzyme, UbcD10. HHARI, also known as H7-AP2, monocyte protein 6 (MOP-6), protein ariadne-1 homolog, Ariadne RBR E3 ubiquitin protein ligase 1 (ARIH1), ariadne-1 (ARI-1), UbcH7-binding protein, UbcM4-interacting protein, or ubiquitin-conjugating enzyme E2-binding protein 1, is an RBR-type E3 ubiquitin-protein ligase highly expressed in nuclei, where it is co-localized with nuclear bodies including Cajal, PML, and Lewy bodies. It interacts with the E2 conjugating enzymes UbcH7, UbcH8, UbcM4, and UbcD10 in human, mouse, and fly, and modulates the ubiquitylation of substrate proteins including single-minded 2 (SIM2) and translation initiation factor 4E homologous protein (4EHP). It functions as a potent mediator of DNA damage-induced translation arrest, which protects stem and cancer cells against genotoxic stress by initiating a 4EHP-mediated mRNA translation arrest. HHARI contains an RBR domain that was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been corrected as RING-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR (RING1-BRcat-Rcat) domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase function to facilitate the ubiquitination reaction. This model corresponds to the RING domain, a C3HC4-type RING-HC finger required for RBR-mediated ubiquitination. Pssm-ID: 438288 Cd Length: 59 Bit Score: 37.71 E-value: 1.74e-03
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| RING-HC_RNF141 | cd16545 | RING finger, HC subclass, found in RING finger protein 141 (RNF141) and similar proteins; ... |
986-1022 | 1.82e-03 | ||||||||||
RING finger, HC subclass, found in RING finger protein 141 (RNF141) and similar proteins; RNF141, also known as zinc finger protein 230 (ZNF230), is a RING finger protein present primarily in the nuclei of spermatogonia, the acrosome, and the tail of spermatozoa. It may have a broad function during early development of vertebrates. It plays an important role in spermatogenesis, including spermatogenic cell proliferation and sperm maturation, as well as motility and fertilization. It also exhibits DNA binding activity. RNF141/ZNF230 gene mutations may be associated with azoospermia. RNF141 contains a C3HC4-type RING finger domain that may function as an activator module in transcription. Pssm-ID: 438207 [Multi-domain] Cd Length: 40 Bit Score: 37.07 E-value: 1.82e-03
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| RING-HC_RNF20 | cd16814 | RING finger, HC subclass, found in RING finger protein 20 (RNF20); RNF20, also known as BRE1A ... |
975-1025 | 1.86e-03 | ||||||||||
RING finger, HC subclass, found in RING finger protein 20 (RNF20); RNF20, also known as BRE1A or BRE1, is an E3 ubiquitin-protein ligase that forms a heterodimeric complex together with BRE1B, also known as RNF40, to 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. It regulates the cell cycle and differentiation of neural precursor cells (NPCs), and links histone H2B ubiquitylation with inflammation and inflammation-associated cancer. Moreover, RNF20 promotes the polyubiquitination and proteasome-dependent degradation of transcription factor activator protein 2alpha (AP-2alpha), a negative regulator of adipogenesis by repressing the transcription of CCAAT/enhancer binding protein (C/EBPalpha) gene. Furthermore, RNF20 functions as an additional chromatin regulator that is necessary for mixed-lineage leukemia (MLL)-fusion-mediated leukemogenesis. It also inhibits TFIIS-facilitated transcriptional elongation to suppress pro-oncogenic gene expression. TFIIS is a factor capable of relieving stalled RNA polymerase II. RNF20 contains a C3HC4-type RING-HC finger at its C-terminus. Pssm-ID: 438463 [Multi-domain] Cd Length: 75 Bit Score: 38.48 E-value: 1.86e-03
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| RING-HC_TRIM21_C-IV | cd16596 | RING finger, HC subclass, found in tripartite motif-containing protein TRIM21 and similar ... |
986-1022 | 2.00e-03 | ||||||||||
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: 38.34 E-value: 2.00e-03
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| RING-HC_TRIM58_C-IV | cd16606 | RING finger, HC subclass, found in tripartite motif-containing protein TRIM58 and similar ... |
984-1012 | 2.58e-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: 37.15 E-value: 2.58e-03
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| RING-HC_RNFT1 | cd16741 | RING finger, HC subclass, found in RING finger and transmembrane domain-containing protein 1 ... |
971-1010 | 3.00e-03 | ||||||||||
RING finger, HC subclass, found in RING finger and transmembrane domain-containing protein 1 (RNFT1); RNFT1, also known as protein PTD016, is a multi-pass membrane protein containing a C3HC4-type RING-HC finger. Its biological role remains unclear. Pssm-ID: 438399 [Multi-domain] Cd Length: 58 Bit Score: 37.17 E-value: 3.00e-03
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| RING-HC_TRIM40-C-V | cd16583 | RING finger, HC subclass, found in tripartite motif-containing protein 40 (TRIM40) and similar ... |
985-1010 | 3.34e-03 | ||||||||||
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: 37.12 E-value: 3.34e-03
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| RING-HC_dBre1-like | cd16705 | RING finger, HC subclass, found in Drosophila melanogaster Bre1 (dBre1) and similar proteins; ... |
986-1026 | 3.51e-03 | ||||||||||
RING finger, HC subclass, found in Drosophila melanogaster Bre1 (dBre1) and similar proteins; dBre1 is the functional homolog of yeast Bre1, an E3 ubiquitin ligase required for the monoubiquitination of histone H2B and, indirectly, for H3K4 methylation. dBre1 acts as a nuclear component required for the expression of Notch target genes in Drosophila development. dBre1 contains a C3HC4-type RING-HC finger at its C-terminus. Pssm-ID: 438365 [Multi-domain] Cd Length: 69 Bit Score: 37.25 E-value: 3.51e-03
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| vRING-HC-C4C4_RBBP6 | cd16620 | Variant RING finger, HC subclass (C4C4-type), found in retinoblastoma-binding protein 6 (RBBP6) ... |
985-1026 | 3.82e-03 | ||||||||||
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: 36.61 E-value: 3.82e-03
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| mRING_PEX12 | cd16451 | Modified RING finger found in peroxin-12 (PEX12) and similar proteins; PEX12, also known as ... |
984-1022 | 4.25e-03 | ||||||||||
Modified RING finger found in peroxin-12 (PEX12) and similar proteins; PEX12, also known as peroxisome assembly protein 12 or peroxisome assembly factor 3 (PAF-3), is a RING finger domain-containing integral membrane peroxin required for protein import into peroxisomes. Mutations in human PEX12 result in the peroxisome deficiency Zellweger syndrome of complementation group III (CG-III), a lethal neurological disorder. PEX12 also functions as an E3-ubiquitin ligase that facilitates the PEX4-dependent monoubiquitination of PEX5, a key player in peroxisomal matrix protein import, to control PEX5 receptor recycling or degradation. PEX12 contains a modified RING finger that lacks the third, fourth, and eighth zinc-binding residues of the consensus RING finger motif, suggesting PEX12 may only bind one zinc ion. Pssm-ID: 438115 [Multi-domain] Cd Length: 54 Bit Score: 36.45 E-value: 4.25e-03
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| RING-HC_TRIM17_C-IV | cd16595 | RING finger, HC subclass, found in tripartite motif-containing protein TRIM17 and similar ... |
984-1010 | 4.70e-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: 36.89 E-value: 4.70e-03
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| RING-HC_AtBRCA1-like | cd23147 | RING finger, HC subclass, found in Arabidopsis thaliana protein BREAST CANCER SUSCEPTIBILITY 1 ... |
986-1022 | 5.28e-03 | ||||||||||
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: 36.29 E-value: 5.28e-03
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| RING-HC_TRIM41-like_C-IV | cd16602 | RING finger, HC subclass, found in tripartite motif-containing proteins TRIM41, TRIM52 and ... |
984-1010 | 7.38e-03 | ||||||||||
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: 36.06 E-value: 7.38e-03
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| RING-HC_RNF123 | cd16541 | RING finger, HC subclass, found in RING finger protein 123 (RNF123) and similar proteins; ... |
986-1028 | 7.58e-03 | ||||||||||
RING finger, HC subclass, found in RING finger protein 123 (RNF123) and similar proteins; RNF123, also known as Kip1 ubiquitination-promoting complex protein 1 (KPC1), is an E3 ubiquitin-protein ligase that mediates ubiquitination and proteasomal processing of the nuclear factor-kappaB 1 (NF-kappaB1) precursor p105 to the p50 active subunit that restricts tumor growth. It also regulates degradation of heterochromatin protein 1alpha (HP1alpha) and 1beta (HP1beta) in lamin A/C knock-down cells. Moreover, RNF123, together with Kip1 ubiquitylation-promoting complex 2 (KPC2), forms the Kip1 ubiquitination-promoting complex (KPC), acting as a cytoplasmic ubiquitin ligase that regulates degradation of the cyclin-dependent kinase inhibitor p27 (Kip1) at the G1 phase of the cell cycle. RNF123 may also function as a clinically relevant, peripheral state marker of depression. RNF123 contains a C3HC4-type RING-HC finger at the C-terminus. Pssm-ID: 438203 [Multi-domain] Cd Length: 44 Bit Score: 35.74 E-value: 7.58e-03
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| RING-HC_TRIM26_C-IV | cd16598 | RING finger, HC subclass, found in tripartite motif-containing protein 26 (TRIM26) and similar ... |
986-1022 | 7.65e-03 | ||||||||||
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: 36.30 E-value: 7.65e-03
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| RING-HC_RAG1 | cd16530 | RING finger, HC subclass, found in recombination activating gene-1 (RAG-1) and similar ... |
986-1022 | 7.74e-03 | ||||||||||
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: 35.49 E-value: 7.74e-03
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| RING-HC_PEX2 | cd16526 | RING finger, HC subclass, found in peroxin-2 (PEX2) and similar proteins; PEX2, also known as ... |
986-1029 | 7.77e-03 | ||||||||||
RING finger, HC subclass, found in peroxin-2 (PEX2) and similar proteins; PEX2, also known as peroxisome biogenesis factor 2, 35 kDa peroxisomal membrane protein, peroxisomal membrane protein 3, peroxisome assembly factor 1 (PAF-1), or RING finger protein 72 (RNF72), is an integral peroxisomal membrane protein with two transmembrane regions and a C3HC4-type RING-HC finger within its cytoplasmically exposed C-terminus. It may be involved in the biogenesis of peroxisomes, as well as in peroxisomal matrix protein import. Mutations in the PEX2 gene are the primary defect in a subset of patients with Zellweger syndrome and related peroxisome biogenesis disorders. Moreover, PEX2 functions as an E3-ubiquitin ligase that mediates the UBC4-dependent polyubiquitination of PEX5, a key player in peroxisomal matrix protein import, to control PEX5 receptor recycling or degradation. Pssm-ID: 438189 [Multi-domain] Cd Length: 49 Bit Score: 35.82 E-value: 7.77e-03
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| RING-H2_RNF103 | cd16473 | RING finger, H2 subclass, found in RING finger protein 103 (RNF103) and similar proteins; ... |
1001-1028 | 8.67e-03 | ||||||||||
RING finger, H2 subclass, found in RING finger protein 103 (RNF103) and similar proteins; RNF103, also known as KF-1 or zinc finger protein 103 homolog (Zfp-103), is an endoplasmic reticulum (ER)-resident E3 ubiquitin-protein ligase that is widely expressed in many different organs, including brain, heart, kidney, spleen, and lung. It is involved in the ER-associated degradation (ERAD) pathway by interacting with components of the ERAD pathway, including Derlin-1 and VCP. RNF103 contains several hydrophobic regions at its N-terminal and middle regions, as well as a C-terminal C3H2C3-type RING-H2 finger. Pssm-ID: 438136 [Multi-domain] Cd Length: 55 Bit Score: 35.71 E-value: 8.67e-03
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| mRING-HC-C3HC3D_Nrdp1 | cd16634 | Modified RING finger, HC subclass (C3HC3D-type), found in neuregulin receptor degradation ... |
985-1015 | 8.71e-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: 35.48 E-value: 8.71e-03
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| mRING-C3HGC3_RFWD3 | cd16450 | Modified RING finger, C3HGC3-type, found in RING finger and WD repeat domain-containing ... |
985-1035 | 9.25e-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: 36.05 E-value: 9.25e-03
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