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Conserved domains on  [gi|568930705|ref|XP_006538670|]
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ubiquitin carboxyl-terminal hydrolase 48 isoform X9 [Mus musculus]

Protein Classification

ubiquitin family protein( domain architecture ID 10110368)

ubiquitin family protein belongs to an diverse class of protein modifier and gene expression regulatory proteins that participate in a number of cellular processes

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Ubl_USP48 cd01795
ubiquitin-like (Ubl) domain found in ubiquitin-specific-processing protease 48 (USP48) and ...
 432-527 4.88e-41

ubiquitin-like (Ubl) domain found in ubiquitin-specific-processing protease 48 (USP48) and similar proteins; USP48, also termed USP31, or deubiquitinating enzyme 48, or ubiquitin thioesterase 48, or ubiquitin carboxyl-terminal hydrolase 48, belongs to the ubiquitin specific protease (USP) family that is one of at least seven deubiquitylating enzyme (DUB) families capable of deconjugating ubiquitin (Ub)and ubiquitin-like (Ubl) adducts. While the USP proteins have a conserved catalytic core domain, USP48 differs in its domain architecture. It contains an N-terminal USP domain, three DUSP (domain present in ubiquitin-specific protease) domains, and a C-terminal Ubl domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions. USP48 is a deubiquitinating enzyme that interacts with TNF receptor-associated factor 2 (TRAF2) and has been implicated in activation of nuclear factor-kappaB (NF-kappaB). Moreover, as a nuclear deubiquitinase regulated by casein kinase 2 (CK2), USP48 controls the ubiquitin/proteasome-system (UPS)-dependent turnover of activated NF-kappaB/RelA in the nucleus together with the COP9 signalosome, suggesting a role of USP48 in a timely control of immune responses.


:

Pssm-ID: 340493 [Multi-domain]  Cd Length: 99  Bit Score: 142.81  E-value: 4.88e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568930705 432 RKVRGE-KALLVSANQTLKELKIQIMHAFSVAPFDQNLSIDGKILNDDCATLGTLGVIPESVILLKADEPIADYAAMD-- 508
Cdd:cd01795    1 RRVRGErKSLTVSSTTTLKELKLQIMEKFSVAPFDQHLYFNGRELTDDSATLADLGILPGDVLYLKVDEPPDDPDDADea 80

                         90
                 ....*....|....*....
gi 568930705 509 DVMQVCMPEEGFKGTGLLG 527
Cdd:cd01795   81 DVSRARVPEEGFKGTALLG 99
 
Name Accession Description Interval E-value
Ubl_USP48 cd01795
ubiquitin-like (Ubl) domain found in ubiquitin-specific-processing protease 48 (USP48) and ...
 432-527 4.88e-41

ubiquitin-like (Ubl) domain found in ubiquitin-specific-processing protease 48 (USP48) and similar proteins; USP48, also termed USP31, or deubiquitinating enzyme 48, or ubiquitin thioesterase 48, or ubiquitin carboxyl-terminal hydrolase 48, belongs to the ubiquitin specific protease (USP) family that is one of at least seven deubiquitylating enzyme (DUB) families capable of deconjugating ubiquitin (Ub)and ubiquitin-like (Ubl) adducts. While the USP proteins have a conserved catalytic core domain, USP48 differs in its domain architecture. It contains an N-terminal USP domain, three DUSP (domain present in ubiquitin-specific protease) domains, and a C-terminal Ubl domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions. USP48 is a deubiquitinating enzyme that interacts with TNF receptor-associated factor 2 (TRAF2) and has been implicated in activation of nuclear factor-kappaB (NF-kappaB). Moreover, as a nuclear deubiquitinase regulated by casein kinase 2 (CK2), USP48 controls the ubiquitin/proteasome-system (UPS)-dependent turnover of activated NF-kappaB/RelA in the nucleus together with the COP9 signalosome, suggesting a role of USP48 in a timely control of immune responses.


Pssm-ID: 340493 [Multi-domain]  Cd Length: 99  Bit Score: 142.81  E-value: 4.88e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568930705 432 RKVRGE-KALLVSANQTLKELKIQIMHAFSVAPFDQNLSIDGKILNDDCATLGTLGVIPESVILLKADEPIADYAAMD-- 508
Cdd:cd01795    1 RRVRGErKSLTVSSTTTLKELKLQIMEKFSVAPFDQHLYFNGRELTDDSATLADLGILPGDVLYLKVDEPPDDPDDADea 80

                         90
                 ....*....|....*....
gi 568930705 509 DVMQVCMPEEGFKGTGLLG 527
Cdd:cd01795   81 DVSRARVPEEGFKGTALLG 99
UBQ smart00213
Ubiquitin homologues; Ubiquitin-mediated proteolysis is involved in the regulated turnover of ...
 437-495 5.87e-06

Ubiquitin homologues; Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression


Pssm-ID: 214563 [Multi-domain]  Cd Length: 72  Bit Score: 44.17  E-value: 5.87e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 568930705   437 EKALLVSANQTLKELKIQIMHAFSVAPFDQNLSIDGKILNDDCaTLGTLGVIPESVILL 495
Cdd:smart00213  12 TITLEVKPSDTVSELKEKIAELTGIPPEQQRLIYKGKVLEDDR-TLADYGIQDGSTIHL 69
ubiquitin pfam00240
Ubiquitin family; This family contains a number of ubiquitin-like proteins: SUMO (smt3 homolog) ...
 442-495 5.58e-04

Ubiquitin family; This family contains a number of ubiquitin-like proteins: SUMO (smt3 homolog), Nedd8, Elongin B, Rub1, and Parkin. A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites.


Pssm-ID: 459726 [Multi-domain]  Cd Length: 72  Bit Score: 38.69  E-value: 5.58e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 568930705  442 VSANQTLKELKIQIMHAFSVAPFDQNLSIDGKILNDDcATLGTLGVIPESVILL 495
Cdd:pfam00240  15 VDPTDTVLELKEKIAEKEGVPPEQQRLIYSGKVLEDD-QTLGEYGIEDGSTIHL 67
 
Name Accession Description Interval E-value
Ubl_USP48 cd01795
ubiquitin-like (Ubl) domain found in ubiquitin-specific-processing protease 48 (USP48) and ...
 432-527 4.88e-41

ubiquitin-like (Ubl) domain found in ubiquitin-specific-processing protease 48 (USP48) and similar proteins; USP48, also termed USP31, or deubiquitinating enzyme 48, or ubiquitin thioesterase 48, or ubiquitin carboxyl-terminal hydrolase 48, belongs to the ubiquitin specific protease (USP) family that is one of at least seven deubiquitylating enzyme (DUB) families capable of deconjugating ubiquitin (Ub)and ubiquitin-like (Ubl) adducts. While the USP proteins have a conserved catalytic core domain, USP48 differs in its domain architecture. It contains an N-terminal USP domain, three DUSP (domain present in ubiquitin-specific protease) domains, and a C-terminal Ubl domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions. USP48 is a deubiquitinating enzyme that interacts with TNF receptor-associated factor 2 (TRAF2) and has been implicated in activation of nuclear factor-kappaB (NF-kappaB). Moreover, as a nuclear deubiquitinase regulated by casein kinase 2 (CK2), USP48 controls the ubiquitin/proteasome-system (UPS)-dependent turnover of activated NF-kappaB/RelA in the nucleus together with the COP9 signalosome, suggesting a role of USP48 in a timely control of immune responses.


Pssm-ID: 340493 [Multi-domain]  Cd Length: 99  Bit Score: 142.81  E-value: 4.88e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568930705 432 RKVRGE-KALLVSANQTLKELKIQIMHAFSVAPFDQNLSIDGKILNDDCATLGTLGVIPESVILLKADEPIADYAAMD-- 508
Cdd:cd01795    1 RRVRGErKSLTVSSTTTLKELKLQIMEKFSVAPFDQHLYFNGRELTDDSATLADLGILPGDVLYLKVDEPPDDPDDADea 80

                         90
                 ....*....|....*....
gi 568930705 509 DVMQVCMPEEGFKGTGLLG 527
Cdd:cd01795   81 DVSRARVPEEGFKGTALLG 99
Ubl_ubiquitin_like cd17039
ubiquitin-like (Ubl) domain found in ubiquitin and ubiquitin-like Ubl proteins; Ubiquitin-like ...
 442-495 5.48e-07

ubiquitin-like (Ubl) domain found in ubiquitin and ubiquitin-like Ubl proteins; Ubiquitin-like (Ubl) proteins have a similar ubiquitin (Ub) beta-grasp fold and attach to other proteins in a Ubl manner but with biochemically distinct roles. Ub and Ubl proteins conjugate and deconjugate via ligases and peptidases to covalently modify target polypeptides. Some Ubl domains have adaptor roles in Ub-signaling by mediating protein-protein interaction. Prokaryotic sulfur carrier proteins are Ub-related proteins that can be activated in an ATP-dependent manner. Polyubiquitination signals for a diverse set of cellular events via different isopeptide linkages formed between the C terminus of one ubiquitin (Ub) and the epsilon-amine of K6, K11, K27, K29, K33, K48, or K63 of a second Ub. One of these seven lysine residues (K27, Ub numbering) is conserved in this Ubl_ubiquitin_like family. K27-linked Ub chains are versatile and can be recognized by several downstream receptor proteins. K27 has roles beyond chain linkage, such as in Ubl NEDD8 (which contains many of the same lysines (K6, K11, K27, K33, K48) as Ub) where K27 has a role (other than conjugation) in the mechanism of protein neddylation.


Pssm-ID: 340559 [Multi-domain]  Cd Length: 68  Bit Score: 46.82  E-value: 5.48e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 568930705 442 VSANQTLKELKIQIMHAFSVAPFDQNLSIDGKILNDDCaTLGTLGVIPESVILL 495
Cdd:cd17039   15 VDPDDTVADLKEKIEEKTGIPVEQQRLIYNGKELKDDK-TLSDYGIKDGSTIHL 67
UBQ smart00213
Ubiquitin homologues; Ubiquitin-mediated proteolysis is involved in the regulated turnover of ...
 437-495 5.87e-06

Ubiquitin homologues; Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression


Pssm-ID: 214563 [Multi-domain]  Cd Length: 72  Bit Score: 44.17  E-value: 5.87e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 568930705   437 EKALLVSANQTLKELKIQIMHAFSVAPFDQNLSIDGKILNDDCaTLGTLGVIPESVILL 495
Cdd:smart00213  12 TITLEVKPSDTVSELKEKIAELTGIPPEQQRLIYKGKVLEDDR-TLADYGIQDGSTIHL 69
ubiquitin pfam00240
Ubiquitin family; This family contains a number of ubiquitin-like proteins: SUMO (smt3 homolog) ...
 442-495 5.58e-04

Ubiquitin family; This family contains a number of ubiquitin-like proteins: SUMO (smt3 homolog), Nedd8, Elongin B, Rub1, and Parkin. A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites.


Pssm-ID: 459726 [Multi-domain]  Cd Length: 72  Bit Score: 38.69  E-value: 5.58e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 568930705  442 VSANQTLKELKIQIMHAFSVAPFDQNLSIDGKILNDDcATLGTLGVIPESVILL 495
Cdd:pfam00240  15 VDPTDTVLELKEKIAEKEGVPPEQQRLIYSGKVLEDD-QTLGEYGIEDGSTIHL 67
Ubl_AtNPL4_like cd17055
ubiquitin-like (Ubl) domain found in Arabidopsis thaliana NPL4-like proteins NPL4-1, NPL4-2, ...
 430-487 2.95e-03

ubiquitin-like (Ubl) domain found in Arabidopsis thaliana NPL4-like proteins NPL4-1, NPL4-2, and similar proteins; The family includes a group of uncharacterized plant ubiquitin-like (Ubl) domain-containing proteins, including Arabidopsis thaliana NPL4-like protein 1 and NPL4-like protein 2.


Pssm-ID: 340575  Cd Length: 73  Bit Score: 36.42  E-value: 2.95e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568930705 430 RHRKvrGEKALLVSANQTLKELKIQIMHAFSVAPFDQNLSIDGK---ILNDDCATLGTLGV 487
Cdd:cd17055    6 RSRD--GTERVEVPDDATVGDLKEKIAEQLSVPVSDQTLSLDPGpdlLTAKSSATLSQLGL 64
Ubl_Ddi1_like cd01796
ubiquitin-like (Ubl) domain found in the eukaryotic Ddi1 family; The eukaryotic Ddi1 family, ...
 442-496 5.70e-03

ubiquitin-like (Ubl) domain found in the eukaryotic Ddi1 family; The eukaryotic Ddi1 family, including yeast aspartyl protease DNA-damage inducible 1 (Ddi1) and Ddi1-like proteins from vertebrates and other eukaryotes, has been characterized by containing an N-terminal ubiquitin-like (Ubl) domain and a conserved retroviral aspartyl-protease-like domain (RVP) that is important in cell-cycle control. Yeast Ddi1 and many family members also contain a C-terminal ubiquitin-association (UBA) domain, however, Ddi1-like proteins from all vertebrates lack the UBA domain. Ddi1, also termed v-SNARE-master 1 (Vsm1), is an ubiquitin receptor involved in the cell cycle and late secretory pathway in Saccharomyces cerevisiae. It functions as an UBA-Ubl shuttle protein that is required for the proteasome to enable ubiquitin-dependent degradation of its ligands. For instance, Ddi1 plays an essential role in the final stages of proteasomal degradation of Ho endonuclease and of its cognate FBP, Ufo1. Moreover, Ddi1 and its associated protein Rad23p play a cooperative role as negative regulators in yeast PHO pathway. This family also includes mammalian regulatory solute carrier protein family 1 member 1 (RSC1A1), also termed transporter regulator RS1 (RS1), which mediates transcriptional and post-transcriptional regulation of Na(+)-D-glucose cotransporter SGLT1. Ddi1-like proteins play a significant role in cell cycle control, growth control, and trafficking in yeast and may play a crucial role in embryogenesis in higher eukaryotes.


Pssm-ID: 340494 [Multi-domain]  Cd Length: 73  Bit Score: 35.61  E-value: 5.70e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 568930705 442 VSANQTLKELKIQIMHAFSVAPFDQNLSIDGKILNDDCATLGTLGVIPESVILLK 496
Cdd:cd01796   18 VSPDMTLEDLKALCEAETGIPAAEQVLLHNGQPLTDDKKTLEALGLKDGDLLLLR 72
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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