UV excision repair protein RAD23 [Caenorhabditis elegans]
Protein Classification
RAD23 family protein( domain architecture ID 1002550)
RAD23 family protein similar to Schizosaccharomyces pombe UV excision repair protein rhp23 that is involved in postreplication repair of UV-damaged DNA
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||||
| rad23 super family | cl36702 | UV excision repair protein Rad23; All proteins in this family for which functions are known ... |
3-319 | 1.32e-67 | ||||||
UV excision repair protein Rad23; All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] The actual alignment was detected with superfamily member TIGR00601: Pssm-ID: 273167 [Multi-domain] Cd Length: 378 Bit Score: 216.30 E-value: 1.32e-67
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| Name | Accession | Description | Interval | E-value | ||||||
| rad23 | TIGR00601 | UV excision repair protein Rad23; All proteins in this family for which functions are known ... |
3-319 | 1.32e-67 | ||||||
UV excision repair protein Rad23; All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] Pssm-ID: 273167 [Multi-domain] Cd Length: 378 Bit Score: 216.30 E-value: 1.32e-67
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| Ubl_Rad23 | cd01805 | ubiquitin-like (Ubl) domain found in the Rad23 protein family; The Rad23 family includes the ... |
3-75 | 5.46e-24 | ||||||
ubiquitin-like (Ubl) domain found in the Rad23 protein family; The Rad23 family includes the yeast nucleotide excision repair (NER) proteins, Rad23p (in Saccharomyces cerevisiae) and Rhp23p (in Schizosaccharomyces pombe), their mammalian orthologs HR23A and HR23B, and putative DNA repair proteins from plants. Rad23 proteins play dual roles in DNA repair as well as in proteosomal degradation. They have affinity for both the proteasome and ubiquitinylated proteins and participate in translocating polyubiquitinated proteins to the proteasome. Rad23 proteins carry an ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, and two ubiquitin-associated (UBA) domains, as well as a xeroderma pigmentosum group C (XPC) protein-binding domain. The Ubl domain is responsible for the binding to proteasome. The UBA domains are important for binding of ubiquitin (Ub) or multi-ubiquitinated substrates, which suggests Rad23 proteins might be involved in certain pathways of Ub metabolism. Both the Ubl domain and the XPC-binding domain are necessary for efficient NER function of Rad23 proteins. Pssm-ID: 340503 [Multi-domain] Cd Length: 72 Bit Score: 93.01 E-value: 5.46e-24
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| XPC-binding | pfam09280 | XPC-binding domain; Members of this family adopt a structure consisting of four alpha helices, ... |
196-248 | 2.40e-18 | ||||||
XPC-binding domain; Members of this family adopt a structure consisting of four alpha helices, arranged in an array. They bind specifically and directly to the xeroderma pigmentosum group C protein (XPC) to initiate nucleotide excision repair. Pssm-ID: 462740 Cd Length: 57 Bit Score: 77.54 E-value: 2.40e-18
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| UBQ | smart00213 | Ubiquitin homologues; Ubiquitin-mediated proteolysis is involved in the regulated turnover of ... |
3-76 | 2.00e-13 | ||||||
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: 64.59 E-value: 2.00e-13
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| Name | Accession | Description | Interval | E-value | ||||||
| rad23 | TIGR00601 | UV excision repair protein Rad23; All proteins in this family for which functions are known ... |
3-319 | 1.32e-67 | ||||||
UV excision repair protein Rad23; All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] Pssm-ID: 273167 [Multi-domain] Cd Length: 378 Bit Score: 216.30 E-value: 1.32e-67
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| Ubl_Rad23 | cd01805 | ubiquitin-like (Ubl) domain found in the Rad23 protein family; The Rad23 family includes the ... |
3-75 | 5.46e-24 | ||||||
ubiquitin-like (Ubl) domain found in the Rad23 protein family; The Rad23 family includes the yeast nucleotide excision repair (NER) proteins, Rad23p (in Saccharomyces cerevisiae) and Rhp23p (in Schizosaccharomyces pombe), their mammalian orthologs HR23A and HR23B, and putative DNA repair proteins from plants. Rad23 proteins play dual roles in DNA repair as well as in proteosomal degradation. They have affinity for both the proteasome and ubiquitinylated proteins and participate in translocating polyubiquitinated proteins to the proteasome. Rad23 proteins carry an ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, and two ubiquitin-associated (UBA) domains, as well as a xeroderma pigmentosum group C (XPC) protein-binding domain. The Ubl domain is responsible for the binding to proteasome. The UBA domains are important for binding of ubiquitin (Ub) or multi-ubiquitinated substrates, which suggests Rad23 proteins might be involved in certain pathways of Ub metabolism. Both the Ubl domain and the XPC-binding domain are necessary for efficient NER function of Rad23 proteins. Pssm-ID: 340503 [Multi-domain] Cd Length: 72 Bit Score: 93.01 E-value: 5.46e-24
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| XPC-binding | pfam09280 | XPC-binding domain; Members of this family adopt a structure consisting of four alpha helices, ... |
196-248 | 2.40e-18 | ||||||
XPC-binding domain; Members of this family adopt a structure consisting of four alpha helices, arranged in an array. They bind specifically and directly to the xeroderma pigmentosum group C protein (XPC) to initiate nucleotide excision repair. Pssm-ID: 462740 Cd Length: 57 Bit Score: 77.54 E-value: 2.40e-18
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| ubiquitin | pfam00240 | Ubiquitin family; This family contains a number of ubiquitin-like proteins: SUMO (smt3 homolog) ... |
5-78 | 5.26e-16 | ||||||
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: 71.43 E-value: 5.26e-16
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| UBA1_Rad23_like | cd14280 | UBA1 domain of Rad23 proteins found in eukaryotes; The Rad23 family includes the yeast ... |
128-166 | 1.68e-14 | ||||||
UBA1 domain of Rad23 proteins found in eukaryotes; The Rad23 family includes the yeast nucleotide excision repair (NER) proteins, Rad23p (in Saccharomyces cerevisiae) and Rhp23p (in Schizosaccharomyces pombe), their mammalian orthologs HR23A and HR23B, and putative DNA repair proteins from plants. Rad23 proteins play dual roles in DNA repair as well as in proteosomal degradation. They have affinity for both the proteasome and ubiquitinylated proteins and participate in translocating polyubiquitinated proteins to the proteasome. Rad23 proteins carry a ubiquitin-like (UBL) and two ubiquitin-associated (UBA) domains, as well as a xeroderma pigmentosum group C (XPC) protein-binding domain. UBL domain is responsible for the binding to proteasome. UBA domains are important for binding of ubiquitin (Ub) or multi-ubiquitinated substrates which suggests Rad23 proteins might be involved in certain pathways of ubiquitin metabolism. Both UBL domain and XPC-binding domain are necessary for efficient NER function of Rad23 proteins. This model corresponds to the UBA1 domain. Pssm-ID: 270466 Cd Length: 39 Bit Score: 66.48 E-value: 1.68e-14
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| UBQ | smart00213 | Ubiquitin homologues; Ubiquitin-mediated proteolysis is involved in the regulated turnover of ... |
3-76 | 2.00e-13 | ||||||
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: 64.59 E-value: 2.00e-13
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| Ubl_HR23B | cd16126 | ubiquitin-like (Ubl) domain found in UV excision repair protein RAD23 homolog B (HR23B); HR23B, ... |
3-79 | 2.44e-12 | ||||||
ubiquitin-like (Ubl) domain found in UV excision repair protein RAD23 homolog B (HR23B); HR23B, also termed xeroderma pigmentosum group C (XPC) repair-complementing complex 58 kDa protein (p58), is tightly complexed with XPC protein to form the XPC-HR23B complex. Although it displays a high affinity for both single- and double-stranded DNA, the XPC-HR23B complex functions as a global genome repair (GGR)-specific repair factor that is specifically involved in global genome but not transcription-coupled nucleotide excision repair (NER). HR23B also interacts specifically with S5a subunit of the human 26S proteasome, and plays an important role in shuttling ubiquitinated cargo proteins to the proteasome. HR23B contains an N-terminal ubiquitin-like (Ubl) domain that binds proteasomes and two C-terminal ubiquitin-associated (UBA) domains that bind ubiquitin or multi-ubiquitinated substrates. In addition, it has a XPC protein-binding domain that might be necessary for its efficient NER function. Pssm-ID: 340543 Cd Length: 78 Bit Score: 61.67 E-value: 2.44e-12
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| Ubl_HR23A | cd17126 | ubiquitin-like (Ubl) domain found in UV excision repair protein RAD23 homolog A (HR23A); HR23A, ... |
3-77 | 5.03e-12 | ||||||
ubiquitin-like (Ubl) domain found in UV excision repair protein RAD23 homolog A (HR23A); HR23A, also termed RAD23A, is a DNA repair protein that binds to 19S subunit of the 26S proteasome and shuttles ubiquitinated proteins to the proteasome for degradation, which is required for efficient nucleotide excision repair (NER), a primary mechanism for removing UV-induced DNA lesions. HR23A also plays a critical role in the interaction of HIV-1 viral protein R (Vpr) with the proteasome, especially facilitating Vpr to promote protein poly-ubiquitination. HR23A contains an N-terminal ubiquitin-like (Ubl) domain that binds proteasomes and two C-terminal ubiquitin-associated (UBA) domains that bind ubiquitin or multi-ubiquitinated substrates. In addition, it has a XPC protein-binding domain that might be necessary for its efficient NER function. Pssm-ID: 340646 Cd Length: 76 Bit Score: 60.84 E-value: 5.03e-12
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| UBA1_Rhp23p_like | cd14378 | UBA1 domain of Schizosaccharomyces pombe UV excision repair protein Rhp23p and its homologs; ... |
127-169 | 4.10e-11 | ||||||
UBA1 domain of Schizosaccharomyces pombe UV excision repair protein Rhp23p and its homologs; The subfamily contains several fungal multi-ubiquitin receptors, including Schizosaccharomyces pombe Rhp23p and Saccharomyces cerevisiae Rad23p, both of which are orthologs of human HR23A. They play roles in nucleotide excision repair (NER) and in cell cycle regulation. They also function as shuttle proteins transporting ubiquitinated substrates destined for degradation from the E3 ligase to the 26S proteasome. For instance, S. pombe Rhp23p forms a complex with Rhp41p to recognize photolesions and help initiate DNA repair, and it also protects ubiquitin chains against disassembly by deubiquitinating enzymes. Like human HR23A, members in this subfamily interact with the proteasome through their N-terminal ubiquitin-like domain (UBL), and with ubiquitin (Ub), or multi-ubiquitinated substrates, through their two ubiquitin-associated domains (UBA), termed internal UBA1 and C-terminal UBA2. In addition, they contain a xeroderma pigmentosum group C (XPC) protein-binding domain that might be necessary for its efficient NER function. This model corresponds to the UBA1 domain. Pssm-ID: 270561 Cd Length: 47 Bit Score: 57.47 E-value: 4.10e-11
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| UBA1_HR23B | cd14426 | UBA1 domain of UV excision repair protein RAD23 homolog B (HR23B) found in vertebrates; HR23B, ... |
125-169 | 6.88e-11 | ||||||
UBA1 domain of UV excision repair protein RAD23 homolog B (HR23B) found in vertebrates; HR23B, also called xeroderma pigmentosum group C (XPC) repair-complementing complex 58 kDa protein (p58), is tightly complexed with XPC protein to form the XPC-HR23B complex. Although it displays a high affinity for both single- and double-stranded DNA, the XPC-HR23B complex functions as a global genome repair (GGR)-specific repair factor that is specifically involved in global genome but not transcription-coupled nucleotide excision repair (NER). HR23B also interacts specifically with S5a subunit of the human 26 S proteasome, and plays an important role in shuttling ubiquitinated cargo proteins to the proteasome. HR23B contains an N-terminal ubiquitin-like (UBL) domain that binds proteasomes and two C-terminal ubiquitin-associated (UBA) domains that bind ubiquitin or multi-ubiquitinated substrates. In addition, it has a XPC protein-binding domain that might be necessary for its efficient NER function. This model corresponds to the UBA1 domain. Pssm-ID: 270609 Cd Length: 46 Bit Score: 56.68 E-value: 6.88e-11
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| UBA1_Rad23 | cd14377 | UBA1 domain of Rad23 proteins found in metazoa; The family includes mammalian orthologs of ... |
128-167 | 2.54e-10 | ||||||
UBA1 domain of Rad23 proteins found in metazoa; The family includes mammalian orthologs of yeast nucleotide excision repair (NER) proteins, Rad23p (in Saccharomyces cerevisiae) and Rhp23p (in Schizosaccharomyces pombe). Rad23 proteins play dual roles in DNA repair as well as in proteosomal degradation. They have affinity for both the proteasome and ubiquitinylated proteins and participate in translocating polyubiquitinated proteins to the proteasome. Rad23 proteins carry a ubiquitin-like (UBL) and two ubiquitin-associated (UBA) domains, as well as a xeroderma pigmentosum group C (XPC) protein-binding domain. UBL domain is responsible for the binding to proteasome. UBA domains are important for binding of ubiquitin (Ub) or multi-ubiquitinated substrates which suggests Rad23 proteins might be involved in certain pathways of ubiquitin metabolism. Both UBL domain and XPC-binding domain are necessary for efficient NER function of Rad23 proteins. This model corresponds to the UBA1 domain. Pssm-ID: 270560 Cd Length: 40 Bit Score: 54.71 E-value: 2.54e-10
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| Ubl_ubiquitin_like | cd17039 | ubiquitin-like (Ubl) domain found in ubiquitin and ubiquitin-like Ubl proteins; Ubiquitin-like ... |
5-73 | 1.93e-09 | ||||||
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: 52.98 E-value: 1.93e-09
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| UBA2_Rad23 | cd14380 | UBA2 domain of Rad23 proteins found in metazoa; The family includes mammalian orthologs of ... |
278-318 | 3.61e-09 | ||||||
UBA2 domain of Rad23 proteins found in metazoa; The family includes mammalian orthologs of yeast nucleotide excision repair (NER) proteins, Rad23p (in Saccharomyces cerevisiae) and Rhp23p (in Schizosaccharomyces pombe). Rad23 proteins play dual roles in DNA repair as well as in proteosomal degradation. They have affinity for both the proteasome and ubiquitinylated proteins and participate in translocating polyubiquitinated proteins to the proteasome. Rad23 proteins carry a ubiquitin-like (UBL) and two ubiquitin-associated (UBA) domains, as well as a xeroderma pigmentosum group C (XPC) protein-binding domain. UBL domain is responsible for the binding to proteasome. UBA domains are important for binding of ubiquitin (Ub) or multi-ubiquitinated substrates which suggests Rad23 proteins might be involved in certain pathways of ubiquitin metabolism. Both UBL domain and XPC-binding domain are necessary for efficient NER function of Rad23 proteins. This model corresponds to the UBA2 domain. Pssm-ID: 270563 Cd Length: 39 Bit Score: 51.76 E-value: 3.61e-09
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| UBA2_Rad23_like | cd14281 | UBA2 domain of Rad23 proteins found in eukaryotes; The Rad23 family includes the yeast ... |
278-317 | 5.27e-08 | ||||||
UBA2 domain of Rad23 proteins found in eukaryotes; The Rad23 family includes the yeast nucleotide excision repair (NER) proteins, Rad23p (in Saccharomyces cerevisiae) and Rhp23p (in Schizosaccharomyces pombe), their mammalian orthologs HR23A and HR23B, and putative DNA repair proteins from plants. Rad23 proteins play dual roles in DNA repair as well as in proteosomal degradation. They have affinity for both the proteasome and ubiquitinylated proteins and participate in translocating polyubiquitinated proteins to the proteasome. Rad23 proteins carry a ubiquitin-like (UBL) and two ubiquitin-associated (UBA) domains, as well as a xeroderma pigmentosum group C (XPC) protein-binding domain. UBL domain is responsible for the binding to proteasome. UBA domains are important for binding of ubiquitin (Ub) or multi-ubiquitinated substrates which suggests Rad23 proteins might be involved in certain pathways of ubiquitin metabolism. Both UBL domain and XPC-binding domain are necessary for efficient NER function of Rad23 proteins. This model corresponds to the UBA2 domain. Pssm-ID: 270467 Cd Length: 38 Bit Score: 48.28 E-value: 5.27e-08
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| UBA2_HR23A | cd14427 | UBA2 domain of UV excision repair protein RAD23 homolog A (HR23A) found in vertebrates; HR23A, ... |
278-318 | 6.47e-08 | ||||||
UBA2 domain of UV excision repair protein RAD23 homolog A (HR23A) found in vertebrates; HR23A, also called Rad23A, is a DNA repair protein that binds to 19S subunit of the 26S proteasome and shuttles ubiquitinated proteins to the proteasome for degradation which is required for efficient nucleotide excision repair (NER), a primary mechanism for removing UV-induced DNA lesions. HR23A also plays a critical role in the interaction of HIV-1 viral protein R (Vpr) with proteasome, especially facilitating Vpr to promote protein poly-ubiquitination. HR23A contains an N-terminal ubiquitin-like (UBL) domain that binds proteasomes and two C-terminal ubiquitin-associated (UBA) domains that bind ubiquitin or multi-ubiquitinated substrates. In addition, it has a XPC protein-binding domain that might be necessary for its efficient NER function. This model corresponds to the UBA2 domain. Pssm-ID: 270610 Cd Length: 41 Bit Score: 48.06 E-value: 6.47e-08
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| Ubl_Dsk2p_like | cd16106 | ubiquitin-like (Ubl) domain found in Saccharomyces cerevisiae proteasome interacting protein ... |
3-56 | 9.35e-08 | ||||||
ubiquitin-like (Ubl) domain found in Saccharomyces cerevisiae proteasome interacting protein Dsk2p and similar proteins; The family contains several fungal multiubiquitin receptors, including Saccharomyces cerevisiae Dsk2p and Schizosaccharomyces pombe Dph1p, both of which have been characterized as shuttle proteins transporting ubiquitinated substrates destined for degradation from the E3 ligase to the 26S proteasome. They interact with the proteasome through their N-terminal ubiquitin-like domain (Ubl) and with ubiquitin (Ub) through their C-terminal Ub-associated domain (UBA). S. cerevisiae Dsk2p is a nuclear-enriched protein that may involve in the ubiquitin-proteasome proteolytic pathway through interacting with K48-linked polyubiquitin and the proteasome. Moreover, it has been implicated in spindle pole duplication through assisting in Cdc31 assembly into the new spindle pole body (SPB). S. pombe Dph1p is an ubiquitin (Ub0 receptor working in concert with the class V myosin, Myo52, to target the degradation of the S. pombe CLIP-170 homolog, Tip1. It also can protect Ub chains against disassembly by deubiquitinating enzymes. Pssm-ID: 340523 [Multi-domain] Cd Length: 73 Bit Score: 48.40 E-value: 9.35e-08
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| UBA1_Rad23_plant | cd14379 | UBA1 domain of putative DNA repair proteins Rad23 found in plant; The radiation sensitive 23 ... |
130-169 | 1.33e-07 | ||||||
UBA1 domain of putative DNA repair proteins Rad23 found in plant; The radiation sensitive 23 (Rad23) subfamily consists of four isoforms of putative DNA repair proteins from Arabidopsis thaliana and similar proteins from other plants. The nuclear-enriched Rad23 proteins function in the cell cycle, morphology, and fertility of plants through their delivery of ubiquitin (Ub)/26S proteasome system (UPS) substrates to the 26S proteasome. Rad23 proteins contain an N-terminal ubiquitin-like (UBL) domain that associates with the 26S proteasome Ub receptor RPN10, and two C-terminal ubiquitin-associated (UBA) domains that bind Ub conjugates. This model corresponds to the UBA1 domain. Pssm-ID: 270562 Cd Length: 50 Bit Score: 47.61 E-value: 1.33e-07
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| UBA | smart00165 | Ubiquitin associated domain; Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 ... |
130-165 | 4.14e-07 | ||||||
Ubiquitin associated domain; Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin. Pssm-ID: 197551 [Multi-domain] Cd Length: 37 Bit Score: 45.56 E-value: 4.14e-07
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| UBA | pfam00627 | UBA/TS-N domain; This small domain is composed of three alpha helices. This family includes ... |
128-164 | 5.46e-07 | ||||||
UBA/TS-N domain; This small domain is composed of three alpha helices. This family includes the previously defined UBA and TS-N domains. The UBA-domain (ubiquitin associated domain) is a novel sequence motif found in several proteins having connections to ubiquitin and the ubiquitination pathway. The structure of the UBA domain consists of a compact three helix bundle. This domain is found at the N terminus of EF-TS hence the name TS-N. The structure of EF-TS is known and this domain is implicated in its interaction with EF-TU. The domain has been found in non EF-TS proteins such as alpha-NAC and MJ0280. Pssm-ID: 395502 [Multi-domain] Cd Length: 37 Bit Score: 45.51 E-value: 5.46e-07
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| UBA1_HR23A | cd14425 | UBA1 domain of UV excision repair protein RAD23 homolog A (HR23A) found in vertebrates; HR23A, ... |
128-167 | 1.75e-06 | ||||||
UBA1 domain of UV excision repair protein RAD23 homolog A (HR23A) found in vertebrates; HR23A, also called Rad23A, is a DNA repair protein that binds to 19S subunit of the 26S proteasome and shuttles ubiquitinated proteins to the proteasome for degradation which is required for efficient nucleotide excision repair (NER), a primary mechanism for removing UV-induced DNA lesions. HR23A also plays a critical role in the interaction of HIV-1 viral protein R (Vpr) with proteasome, especially facilitating Vpr to promote protein poly-ubiquitination. HR23A contains an N-terminal ubiquitin-like (UBL) domain that binds proteasomes and two C-terminal ubiquitin-associated (UBA) domains that bind ubiquitin or multi-ubiquitinated substrates. In addition, it has a XPC protein-binding domain that might be necessary for its efficient NER function. This model corresponds to the UBA1 domain. Pssm-ID: 270608 Cd Length: 40 Bit Score: 43.96 E-value: 1.75e-06
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| UBA2_HR23B | cd14428 | UBA2 domain of UV excision repair protein RAD23 homolog B (HR23B) found in vertebrates; HR23B, ... |
278-323 | 3.76e-06 | ||||||
UBA2 domain of UV excision repair protein RAD23 homolog B (HR23B) found in vertebrates; HR23B, also called xeroderma pigmentosum group C (XPC) repair-complementing complex 58 kDa protein (p58), is tightly complexed with XPC protein to form the XPC-HR23B complex. Although it displays a high affinity for both single- and double-stranded DNA, the XPC-HR23B complex functions as a global genome repair (GGR)-specific repair factor that is specifically involved in global genome but not transcription-coupled nucleotide excision repair (NER). HR23B also interacts specifically with S5a subunit of the human 26 S proteasome, and plays an important role in shuttling ubiquitinated cargo proteins to the proteasome. HR23B contains an N-terminal ubiquitin-like (UBL) domain that binds proteasomes and two C-terminal ubiquitin-associated (UBA) domains that bind ubiquitin or multi-ubiquitinated substrates. In addition, it has a XPC protein-binding domain that might be necessary for its efficient NER function. This model corresponds to the UBA2 domain. Pssm-ID: 270611 Cd Length: 45 Bit Score: 43.17 E-value: 3.76e-06
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| UBA2_RAD23_plant | cd14382 | UBA2 domain of putative DNA repair proteins RAD23 found in plant; The radiation sensitive 23 ... |
275-319 | 4.84e-06 | ||||||
UBA2 domain of putative DNA repair proteins RAD23 found in plant; The radiation sensitive 23 (RAD23) subfamily consists of four isoforms of putative DNA repair proteins from Arabidopsis thaliana and similar proteins from other plants. The nuclear-enriched RAD23 proteins function in the cell cycle, morphology, and fertility of plants through their delivery of ubiquitin (Ub)/26S proteasome system (UPS) substrates to the 26S proteasome. RAD23 proteins contain an N-terminal ubiquitin-like (UBL) domain that associates with the 26S proteasome Ub receptor RPN10, and two C-terminal ubiquitin-associated (UBA) domains that bind Ub conjugates. This model corresponds to the UBA2 domain. Pssm-ID: 270565 [Multi-domain] Cd Length: 43 Bit Score: 43.00 E-value: 4.84e-06
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| UBA2_Rhp23p_like | cd14381 | UBA2 domain of Schizosaccharomyces pombe UV excision repair protein Rhp23p and its fungal ... |
278-319 | 1.38e-05 | ||||||
UBA2 domain of Schizosaccharomyces pombe UV excision repair protein Rhp23p and its fungal homologs; The subfamily contains several fungal multiubiquitin receptors, including Schizosaccharomyces pombe Rhp23p and Saccharomyces cerevisiae Rad23p, both of which are orthologs of human HR23A. They play roles in nucleotide excision repair (NER) and in cell cycle regulation. They also function as shuttle proteins transporting ubiquitinated substrates destined for degradation from the E3 ligase to the 26S proteasome. For instance, S. pombe Rhp23p forms a complex with Rhp41p to recognize photolesions and help initiate DNA repair, and it also protects ubiquitin chains against disassembly by deubiquitinating enzymes. Like human HR23A, members in this subfamily interact with the proteasome through their N-terminal ubiquitin-like domain (UBL), and with ubiquitin (Ub), or multi-ubiquitinated substrates, through their two ubiquitin-associated domains (UBA), termed internal UBA1 and C-terminal UBA2. In addition, they contain a xeroderma pigmentosum group C (XPC) protein-binding domain that might be necessary for its efficient NER function. This model corresponds to the UBA2 domain. Pssm-ID: 270564 Cd Length: 40 Bit Score: 41.74 E-value: 1.38e-05
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| UBA2_UBP5 | cd14386 | UBA2 domain found in ubiquitin carboxyl-terminal hydrolase 5 (UBP5); UBP5, also called ... |
130-171 | 2.02e-05 | ||||||
UBA2 domain found in ubiquitin carboxyl-terminal hydrolase 5 (UBP5); UBP5, also called deubiquitinating enzyme 5, Isopeptidase T (IsoT), ubiquitin thioesterase 5, or ubiquitin-specific-processing protease 5, is a deubiquitinating enzyme largely responsible for the disassembly of the majority of unanchored polyubiquitin in the cell. Zinc is required for its catalytic activity. UBP5 contains four ubiquitin (Ub)-binding sites including an N-terminal zinc finger (ZnF) domain, a catalytic ubiquitin-specific processing protease (UBP) domain (catalytic C-box and H-box), and two ubiquitin-associated (UBA) domains. ZnF domain binds the proximal ubiquitin. UBP domain forms the active site. UBA domains are involved in binding linear or K48-linked polyubiquitin. This model corresponds to the UBA2 domain. Pssm-ID: 270569 [Multi-domain] Cd Length: 43 Bit Score: 41.16 E-value: 2.02e-05
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| UBA1_NUB1_like | cd14291 | UBA1 domain found in NEDD8 ultimate buster 1 (NUB1) and similar proteins; NUB1, also called ... |
130-164 | 1.42e-04 | ||||||
UBA1 domain found in NEDD8 ultimate buster 1 (NUB1) and similar proteins; NUB1, also called negative regulator of ubiquitin-like proteins 1, renal carcinoma antigen NY-REN-18, or protein BS4, is a NEDD8-interacting protein that can be induced by interferon. It functions as a strong post-transcriptional down-regulator of the NEDD8 expression and plays critical roles in regulating many biological events, such as cell growth, NF-kappaB signaling, and biological responses to hypoxia. NUB1 can also interact with aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1) which may function in the regulation of cell cycle progression. NUB1 contains three ubiquitin-associated domains (UBA), a bipartite nuclear localization signal (NLS) and a PEST motif. This model corresponds to UBA1 domain. Pssm-ID: 270477 [Multi-domain] Cd Length: 36 Bit Score: 38.58 E-value: 1.42e-04
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| STI1 | smart00727 | Heat shock chaperonin-binding motif; |
194-237 | 6.04e-04 | ||||||
Heat shock chaperonin-binding motif; Pssm-ID: 128966 Cd Length: 41 Bit Score: 36.86 E-value: 6.04e-04
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| Ubl_Ddi1_like | cd01796 | ubiquitin-like (Ubl) domain found in the eukaryotic Ddi1 family; The eukaryotic Ddi1 family, ... |
1-59 | 6.66e-04 | ||||||
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: 37.54 E-value: 6.66e-04
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| Ubl2_FAT10 | cd17053 | ubiquitin-like (Ubl) domain 2 found in leukocyte antigen F (HLA-F) adjacent transcript 10 ... |
3-64 | 8.43e-04 | ||||||
ubiquitin-like (Ubl) domain 2 found in leukocyte antigen F (HLA-F) adjacent transcript 10 (FAT10) and similar proteins; FAT10, also termed ubiquitin D (UBD), or diubiquitin, is a cytokine-inducible ubiquitin-like (Ubl) modifer that is highly expressed in the thymus, and targets substrates covalently for 26S proteasomal degradation. It is also associated with cancer development, antigen processing and antimicrobial defense, chromosomal stability and cell cycle regulation. FAT10 is presented on immune cells and under the inflammatory conditions, is synergistically induced by interferon gamma (IFNgamma) and tumor necrosis factor (TNFalpha) in the non-immune (liver parenchymal) cells. FAT10 contains two Ubl domains. The family corresponds to the second Ubl domain of FAT10. Some family members contain only one Ubl domain. Pssm-ID: 340573 Cd Length: 71 Bit Score: 37.33 E-value: 8.43e-04
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| UBA2_UBP13 | cd14387 | UBA2 domain found in ubiquitin carboxyl-terminal hydrolase 13 (UBP13); UBP13, also called ... |
130-164 | 1.24e-03 | ||||||
UBA2 domain found in ubiquitin carboxyl-terminal hydrolase 13 (UBP13); UBP13, also called deubiquitinating enzyme 13, Isopeptidase T-3 (isoT3), ubiquitin thioesterase 13, or ubiquitin-specific-processing protease 13 is an ortholog of UBP5 implicated in catalyzing hydrolysis of various ubiquitin (Ub)-chains. It contains a zinc finger (ZnF) domain, a catalytic ubiquitin-specific processing protease (UBP) domain (catalytic C-box and H-box), and two ubiquitin-associated (UBA) domains. Due to the non-activating catalysis for K63-polyubiquitin chains, UBP13 may function differently from USP5 in cellular deubiquitination processes. Moreover, the zinc finger (ZnF) domain of USP13 cannot bind to Ub. Its tandem UBA domains can bind with different types of diUb but preferentially with K63-linked.USP13 can also regulate the protein level of CD3delta in cells via its UBA domains. This model corresponds to the UBA2 domain. Pssm-ID: 270570 Cd Length: 35 Bit Score: 35.81 E-value: 1.24e-03
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| UBA | pfam00627 | UBA/TS-N domain; This small domain is composed of three alpha helices. This family includes ... |
278-316 | 2.66e-03 | ||||||
UBA/TS-N domain; This small domain is composed of three alpha helices. This family includes the previously defined UBA and TS-N domains. The UBA-domain (ubiquitin associated domain) is a novel sequence motif found in several proteins having connections to ubiquitin and the ubiquitination pathway. The structure of the UBA domain consists of a compact three helix bundle. This domain is found at the N terminus of EF-TS hence the name TS-N. The structure of EF-TS is known and this domain is implicated in its interaction with EF-TU. The domain has been found in non EF-TS proteins such as alpha-NAC and MJ0280. Pssm-ID: 395502 [Multi-domain] Cd Length: 37 Bit Score: 35.11 E-value: 2.66e-03
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| Rad60-SLD_2 | pfam13881 | Ubiquitin-2 like Rad60 SUMO-like; |
24-74 | 3.73e-03 | ||||||
Ubiquitin-2 like Rad60 SUMO-like; Pssm-ID: 372780 Cd Length: 111 Bit Score: 36.52 E-value: 3.73e-03
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| Ubl_FUBI | cd01793 | ubiquitin-like (Ubl) domain found in ubiquitin-like protein FUBI and similar proteins; FUBI is ... |
16-66 | 4.73e-03 | ||||||
ubiquitin-like (Ubl) domain found in ubiquitin-like protein FUBI and similar proteins; FUBI is a pro-apoptotic regulatory gene FAU encoding ubiquitin-like protein with ribosomal protein S30 as a C-terminal extension. FUBI functions as a tumor suppressor protein that may be involved in the ATP-dependent proteolytic activity of ubiquitin. The N-terminal ubiquitin-like (Ubl) domain of FUBI has the beta-grasp Ubl fold, and it may act as a substitute or an inhibitor of ubiquitin or one of ubiquitin's close relatives UCRP, FAT10, and Nedd8. Pssm-ID: 340491 Cd Length: 74 Bit Score: 35.34 E-value: 4.73e-03
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| Ubl_HERP | cd01790 | ubiquitin-like (Ubl) domain found in homocysteine-inducible endoplasmic reticulum stress ... |
15-57 | 6.25e-03 | ||||||
ubiquitin-like (Ubl) domain found in homocysteine-inducible endoplasmic reticulum stress protein HERP; HERP is an endoplasmic reticulum (ER) integral membrane protein containing an N-terminal ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold. The Ubl domain is required for the degradation of HERP itself as well as for HERP-mediated anti-apoptotic effects. HERP is induced by the ER stress response pathway and is involved in improving the balance of folding capacity and protein loads in the ER. There are two types of HERP, HERP1 and HERP2, which are encoded by the HERPUD1 and HERPUD2 genes, respectively. Pssm-ID: 340488 Cd Length: 78 Bit Score: 34.92 E-value: 6.25e-03
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| UBA_cnDdi1_like | cd14310 | UBA domain found in Cryptococcus neoformans DNA-damage response protein Ddi1 and similar ... |
135-162 | 9.20e-03 | ||||||
UBA domain found in Cryptococcus neoformans DNA-damage response protein Ddi1 and similar proteins; The family includes some uncharacterized Ddi and similar proteins which show a high level of sequence similarity with yeast Ddi1. Ddi1, also called v-SNARE-master 1 (Vsm1), is a ubiquitin receptor involved in regulation of the cell cycle and late secretory pathway in yeast. It functions as a ubiquitin association domain (UBA)- ubiquitin-like-domain (UBL) shuttle protein that is required for the proteasome to enable ubiquitin-dependent degradation of its ligands. Ddi1 contains an N-terminal UBL domain and a C-terminal UBA domain. It also harbors a central retroviral aspartyl-protease-like domain (RVP) which may be important in cell-cycle control. At this point, Ddi1 may function proteolytically during regulated protein turnover in the cell. Pssm-ID: 270495 Cd Length: 30 Bit Score: 33.28 E-value: 9.20e-03
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| UBA | cd14270 | UBA domain found in proteins involved in ubiquitin-mediated proteolysis; The ... |
136-162 | 9.86e-03 | ||||||
UBA domain found in proteins involved in ubiquitin-mediated proteolysis; The ubiquitin-associated (UBA) domains are commonly occurring sequence motifs found in proteins involved in ubiquitin-mediated proteolysis. They contribute to ubiquitin (Ub) binding or ubiquitin-like (UbL) domain binding. However, some kinds of UBA domains can only the bind UbL domain, but not the Ub domain. UBA domains are normally comprised of compact three-helix bundles which contain a conserved GF/Y-loop. They can bind polyubiquitin with high affinity. They also bind monoubiquitin and other proteins. Most UBA domain-containing proteins have one UBA domain, but some harbor two or three UBA domains. Pssm-ID: 270456 [Multi-domain] Cd Length: 30 Bit Score: 33.09 E-value: 9.86e-03
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