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]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442614351    1 MIITIKNLQQQTFTIEFAPEKTVLELKKKIFEERGPE-YVAEKQKLIYAGVILTDDRTVGSYNVDEKKFIVVMLTRDSSS 79
Cdd:TIGR00601   1 MTLTFKTLQQQKFKIDMEPDETVKELKEKIEAEQGKDaYPVAQQKLIYSGKILSDDKTVKEYKIKEKDFVVVMVSKPKTG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442614351   80 SNRNQLSVKESNKLTSTDDSKQSMPCEEANHtnSPSSTNTEDSvlSRETRPLSSDELIGELAQASLQSRAESNLLMGDEY 159
Cdd:TIGR00601  81 TGKVAPPAATPTSAPTPTPSPPASPASGMSA--APASAVEEKS--PSEESATATAPESPSTSVPSSGSDAASTLVVGSER 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442614351  160 NQTVLSMVEMGYPREQVERAMAASYNNPERAVEYLINGIP-------AEEGTFYNRLNESTN----PSLIPSGPQPASAT 228
Cdd:TIGR00601 157 ETTIEEIMEMGYEREEVERALRAAFNNPDRAVEYLLTGIPedpeqpePVQQTAASTAAATTEtpqhGSVFEQAAQGGTEQ 236

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442614351  229 SAERSTeSNSDPFEFLRSQPQFLQMRSLIYQNPHLLHAVLQQIGQTNPALLQLISENQDAFLNMLNQPI-DRESESgatv 307
Cdd:TIGR00601 237 PATEAA-QGGNPLEFLRNQPQFQQLRQVVQQNPQLLPPLLQQIGQENPQLLQQISQHPEQFLQMLNEPVgELASES---- 311

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442614351  308 ppvsnaripstldnvDLFSpdlevatsaqrsaaGTSAAHQSGSAADNEdleqplgvstIRLNRQDKDAIERLKALGFPEA 387
Cdd:TIGR00601 312 ---------------DMEG--------------GVGAIAEAGLPQMNQ----------IQVTPEEKEAIERLCALGFDRG 352

                         410       420
                  ....*....|....*....|....*.
gi 442614351  388 LVLQAYFACEKNEEQAANFLLSSSFD 413
Cdd:TIGR00601 353 LVIQAYFACDKNEELAANYLLSQNFD 378

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]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442614351    1 MIITIKNLQQQTFTIEFAPEKTVLELKKKIFEERGPE-YVAEKQKLIYAGVILTDDRTVGSYNVDEKKFIVVMLTRDSSS 79
Cdd:TIGR00601   1 MTLTFKTLQQQKFKIDMEPDETVKELKEKIEAEQGKDaYPVAQQKLIYSGKILSDDKTVKEYKIKEKDFVVVMVSKPKTG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442614351   80 SNRNQLSVKESNKLTSTDDSKQSMPCEEANHtnSPSSTNTEDSvlSRETRPLSSDELIGELAQASLQSRAESNLLMGDEY 159
Cdd:TIGR00601  81 TGKVAPPAATPTSAPTPTPSPPASPASGMSA--APASAVEEKS--PSEESATATAPESPSTSVPSSGSDAASTLVVGSER 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442614351  160 NQTVLSMVEMGYPREQVERAMAASYNNPERAVEYLINGIP-------AEEGTFYNRLNESTN----PSLIPSGPQPASAT 228
Cdd:TIGR00601 157 ETTIEEIMEMGYEREEVERALRAAFNNPDRAVEYLLTGIPedpeqpePVQQTAASTAAATTEtpqhGSVFEQAAQGGTEQ 236

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442614351  229 SAERSTeSNSDPFEFLRSQPQFLQMRSLIYQNPHLLHAVLQQIGQTNPALLQLISENQDAFLNMLNQPI-DRESESgatv 307
Cdd:TIGR00601 237 PATEAA-QGGNPLEFLRNQPQFQQLRQVVQQNPQLLPPLLQQIGQENPQLLQQISQHPEQFLQMLNEPVgELASES---- 311

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442614351  308 ppvsnaripstldnvDLFSpdlevatsaqrsaaGTSAAHQSGSAADNEdleqplgvstIRLNRQDKDAIERLKALGFPEA 387
Cdd:TIGR00601 312 ---------------DMEG--------------GVGAIAEAGLPQMNQ----------IQVTPEEKEAIERLCALGFDRG 352

                         410       420
                  ....*....|....*....|....*.
gi 442614351  388 LVLQAYFACEKNEEQAANFLLSSSFD 413
Cdd:TIGR00601 353 LVIQAYFACDKNEELAANYLLSQNFD 378

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.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 442614351  241 FEFLRSQPQFLQMRSLIYQNPHLLHAVLQQIGQTNPALLQLISENQDAFLNMLNQPI 297
Cdd:pfam09280   1 LDFLRNNPQFQQLRQLVQQNPQLLQPLLQQLAQSNPQLAQLIQQNQEEFLQLLNEPG 57

ubiquitin; Provisional

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 442614351   1 MIITIKNLQQQTFTIEFAPEKTVLELKKKIFEERGPEyvAEKQKLIYAGVILTDDRTVGSYNV 63
Cdd:PTZ00044   1 MQILIKTLTGKKQSFNFEPDNTVQQVKMALQEKEGID--VKQIRLIYSGKQMSDDLKLSDYKV 61

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]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442614351    1 MIITIKNLQQQTFTIEFAPEKTVLELKKKIFEERGPE-YVAEKQKLIYAGVILTDDRTVGSYNVDEKKFIVVMLTRDSSS 79
Cdd:TIGR00601   1 MTLTFKTLQQQKFKIDMEPDETVKELKEKIEAEQGKDaYPVAQQKLIYSGKILSDDKTVKEYKIKEKDFVVVMVSKPKTG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442614351   80 SNRNQLSVKESNKLTSTDDSKQSMPCEEANHtnSPSSTNTEDSvlSRETRPLSSDELIGELAQASLQSRAESNLLMGDEY 159
Cdd:TIGR00601  81 TGKVAPPAATPTSAPTPTPSPPASPASGMSA--APASAVEEKS--PSEESATATAPESPSTSVPSSGSDAASTLVVGSER 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442614351  160 NQTVLSMVEMGYPREQVERAMAASYNNPERAVEYLINGIP-------AEEGTFYNRLNESTN----PSLIPSGPQPASAT 228
Cdd:TIGR00601 157 ETTIEEIMEMGYEREEVERALRAAFNNPDRAVEYLLTGIPedpeqpePVQQTAASTAAATTEtpqhGSVFEQAAQGGTEQ 236

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442614351  229 SAERSTeSNSDPFEFLRSQPQFLQMRSLIYQNPHLLHAVLQQIGQTNPALLQLISENQDAFLNMLNQPI-DRESESgatv 307
Cdd:TIGR00601 237 PATEAA-QGGNPLEFLRNQPQFQQLRQVVQQNPQLLPPLLQQIGQENPQLLQQISQHPEQFLQMLNEPVgELASES---- 311

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442614351  308 ppvsnaripstldnvDLFSpdlevatsaqrsaaGTSAAHQSGSAADNEdleqplgvstIRLNRQDKDAIERLKALGFPEA 387
Cdd:TIGR00601 312 ---------------DMEG--------------GVGAIAEAGLPQMNQ----------IQVTPEEKEAIERLCALGFDRG 352

                         410       420
                  ....*....|....*....|....*.
gi 442614351  388 LVLQAYFACEKNEEQAANFLLSSSFD 413
Cdd:TIGR00601 353 LVIQAYFACDKNEELAANYLLSQNFD 378

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.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 442614351  241 FEFLRSQPQFLQMRSLIYQNPHLLHAVLQQIGQTNPALLQLISENQDAFLNMLNQPI 297
Cdd:pfam09280   1 LDFLRNNPQFQQLRQLVQQNPQLLQPLLQQLAQSNPQLAQLIQQNQEEFLQLLNEPG 57

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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 442614351   1 MIITIKNLQQQTFTIEFAPEKTVLELKKKIFEERGPE-YVAEKQKLIYAGVILTDDRTVGSYNVDEKKFIVVMLTR 75
Cdd:cd17126    1 VTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDaFPVAGQKLIYAGKILSDDVPIRDYRIDEKNFVVVMVTK 76

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.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 442614351 371 QDKDAIERLKALGFPEALVLQAYFACEKNEEQAANFLLSSS 411
Cdd:cd14427    1 QEKEAIERLKALGFPESLVIQAYFACEKNENLAANFLLSQN 41

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.

                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 442614351 371 QDKDAIERLKALGFPEALVLQAYFACEKNEEQAANFLLS 409
Cdd:cd14380    1 EEREAIERLKALGFPEGLVIQAYFACDKNENLAANFLLS 39

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.

                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 442614351 158 EYNQTVLSMVEMGYPREQVERAMAASYNNPERAVEYLIN 196
Cdd:cd14280    1 ELEATINNIMSMGFEREQVVRALRAAFNNPDRAVEYLLS 39

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.

                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 442614351 371 QDKDAIERLKALGFPEALVLQAYFACEKNEEQAANFLL 408
Cdd:cd14281    1 EEREAIERLVALGFSRDQAIEAYLACDKNEELAANYLF 38

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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442614351   3 ITIKNLQQQTFTIEFAPEKTVLELKKKIFEERGPEyvAEKQKLIYAGVILTDDRTVGSYNVDEKKFIVVM 72
Cdd:cd17039    1 ITVKTLDGKTYTVEVDPDDTVADLKEKIEEKTGIP--VEQQRLIYNGKELKDDKTLSDYGIKDGSTIHLV 68

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.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 442614351 153 LLMGDEYNQTVLSMVEMG---YPREQVERAMAASYNNPERAVEYLINGIP 199
Cdd:cd14379    1 LVAGSSLEQTVQQIMDMGggsWDRDTVVRALRAAYNNPERAVEYLYSGIP 50

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.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 442614351 154 LMGDEYNQTVLSMVEMGYPREQVERAMAASYNNPERAVEYLINGIP 199
Cdd:cd14426    1 VTGQSYENMVTEIMSMGYEREQVIAALRASFNNPDRAVEYLLMGIP 46

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.

                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 442614351  158 EYNQTVLSMVEMGYPREQVERAMAASYNNPERAVEYL 194
Cdd:pfam00627   1 EDEEAIQRLVEMGFDREQVREALRATGNNVERAAEYL 37

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.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 442614351 158 EYNQTVLSMVEMGYPREQVERAMAASYNNPERAVEYLING 197
Cdd:cd14425    1 EYETMLTEIMSMGYERERVVAALRASYNNPHRAVEYLLTG 40

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.

                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 442614351  371 QDKDAIERLKALGFPEALVLQAYFACEKNEEQAANFL 407
Cdd:pfam00627   1 EDEEAIQRLVEMGFDREQVREALRATGNNVERAAEYL 37

ubiquitin-like (Ubl) domain found in ubiquitin; Ubiquitin is a protein modifier in eukaryotes that is involved in various cellular processes, including transcriptional regulation, cell cycle control, and DNA repair. Ubiquitination is comprised of a cascade of E1, E2 and E3 enzymes that results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. Ubiquitin-like (Ubl) proteins have similar ubiquitin beta-grasp fold and attach to other proteins in a Ubl manner but with biochemically distinct roles. Ubiquitin (Ub)and Ubl proteins conjugate and deconjugate via ligases and peptidases to covalently modify target polypeptides. Ub includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 442614351   1 MIITIKNLQQQTFTIEFAPEKTVLELKKKIFEERG-PeyvAEKQKLIYAGVILTDDRTVGSYNV 63
Cdd:cd01803    1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGiP---PDQQRLIFAGKQLEDGRTLSDYNI 61

UBA domain found in vacuolar protein sorting-associated protein 13D (VP13D) and similar proteins; VP13D is a chorea-acanthocytosis (CHAC)-similar protein encoded by gene VPS13D. it contains two putative domains, ubiquitin-associated (UBA) domain and lectin domain of ricin B chain profile (ricin-B-lectin), suggesting it may interact with, and be involved in the trafficking of, proteins modified with ubiquitin and/or carbohydrate molecules. Further investigation is required.

                         10        20        30
                 ....*....|....*....|....*....|
gi 442614351 166 MVEMGYPREQVERAMAASYNNPERAVEYLI 195
Cdd:cd14306    4 LMELGFPEEDCIRALRACGGNVEEAANWLL 33

ubiquitin-like (Ubl) domain found in splicing factor 3A 120kDa subunit (SF3a120) and similar proteins; Mammalian splicing factor SF3a consists of three subunits of 60, 66, and 120 kDa and functions early during pre-mRNA splicing by converting the U2 snRNP to its active form. The 120kDa subunit SF3a120, also termed splicing factor 3A subunit 1 (SF3A1), or spliceosome-associated protein 114 (SAP114), is the U2 snRNP-specific protein that is critical for spliceosome assembly and normal splicing events. During splicing, SF3a120, together with the U2 snRNP and other proteins, are recruited to the 3' splicing site to generate the splicing complex A after the recognition of the 3' splicing site. SF3a120 contains two N-terminal SWAP (suppressor-of-white-apricot) domains, referred to collectively as the SURP module, as well as a C-terminal ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 442614351   7 NLQQQTFTIEFAPEKTVLELKKKIFEERG-PeyvAEKQKLIY-AGVILTDDRTVGSYNVD 64
Cdd:cd01800   18 KLNGQVLELTLPLTDTISVLKEKIHEELGmP---ANKQKLQVeGGGFLKDSNSLAFYNLG 74

UBA2 domain found in Schizosaccharomyces pombe ubiquitin carboxyl-terminal hydrolase 14 (spUBP14) and similar proteins; spUBP14, also called deubiquitinating enzyme 14, UBA domain-containing protein 2, ubiquitin thioesterase 14, or ubiquitin-specific-processing protease 14, functions as a deubiquitinating enzyme that is involved in protein degradation in fission yeast. Members in this family contain two tandem ubiquitin-association (UBA) domains. This model corresponds to the UBA2 domain.

                         10        20        30
                 ....*....|....*....|....*....|.
gi 442614351 167 VEMGYPREQVERAMAASYNNPERAVEYLING 197
Cdd:cd14297    8 VDMGFTEAQARKALRKTNNNVERAVDWLFEG 38

ubiquitin; Provisional

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 442614351   1 MIITIKNLQQQTFTIEFAPEKTVLELKKKIFEERGPEyvAEKQKLIYAGVILTDDRTVGSYNV 63
Cdd:PTZ00044   1 MQILIKTLTGKKQSFNFEPDNTVQQVKMALQEKEGID--VKQIRLIYSGKQMSDDLKLSDYKV 61

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.

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gi 442614351 163 VLSMVEMGYPREQVERAMAASYNNPERAVE 192
Cdd:cd14270    1 LAQLVEMGFSREQARRALRATNGDVEAAVE 30

ubiquitin-like (Ubl) domain found in AN1-type zinc finger protein 4 (ZFAND4) and similar proteins; ZFAND4, also termed AN1-type zinc finger and ubiquitin domain-containing protein-like 1 (ANUBL1), may function as an oncogene that promotes proliferation and regulates relevant tumor suppressor genes in gastric cancer, suggesting a role in gastric cancer initiation and progression. ZFAND4contains an N-terminal ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions, as well as a C-terminal AN1-type zinc finger. Unlike ubiquitin polyproteins and most ubiquitin fusion proteins, the N-terminal Ubl domain of ZFAND4 does not undergo proteolytic processing.

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gi 442614351   1 MIITIKNLQQQTFTIEFAPEKTVLELKKKIFEERGpeYVAEKQKLIYAGVILTDDRTVGSYNVDE 65
Cdd:cd01802    1 MELFIETLTGTAFELRVSPFETVASVKAKIQRLEG--IPVSQQHLIWSGRELEDDYCLHDYNITD 63

Ubiquitin-2 like Rad60 SUMO-like; The small ubiquitin-related modifier SUMO-1 is a Ub/Ubl family member, and although SUMO-1 shares structural similarity to Ub, SUMO's cellular functions remain distinct insomuch as SUMO modification alters protein function through changes in activity, cellular localization, or by protecting substrates from ubiquitination. Rad60 family members contain functionally enigmatic, integral SUMO-like domains (SLDs). Despite their divergence from SUMO, each Rad60 SLD interacts with a subset of SUMO pathway enzymes: SLD2 specifically binds the SUMO E2 conjugating enzyme (Ubc9)), whereas SLD1 binds the SUMO E1 (Fub2, also called Uba2) activating and E3 (Pli1, also called Siz1 and Siz2) specificity enzymes. Structural analysis of PDB:2uyz reveals a mechanistic basis for the near-synonymous roles of Rad60 and SUMO in survival of genotoxic stress and suggest unprecedented DNA-damage-response functions for SLDs in regulating SUMOylation. The Rad60 branch of this family is also known as RENi (Rad60-Esc2-Nip45), and biologically it should be two distinct families SUMO and RENi (Rad60-Esc2-Nip45).

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gi 442614351    1 MIITIKNLQQQTFTIEFAPEKTVLELKKKIFEERGPEyVAEKQKLIYAGVILTDDRTVGSYNVDEKKFIVVML 73
Cdd:pfam11976   1 IKIILKGKDGKEVFIKVKPTTTVSKLINAYRKKRGIP-PSQQVRLIFDGERLDPNSTVEDLDIEDGDTIDVVI 72

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.

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gi 442614351 166 MVEMGYPREQVERAMAASYNNPERAVEYL 194
Cdd:cd14291    8 LMEMGFSEAEARLALRACNGNVERAVDYI 36

ubiquitin-like (Ubl) domain 1 found in interferon-stimulated gene 15 (ISG15) and similar proteins; ISG15, also termed interferon-induced 15 kDa protein, or interferon-induced 17 kDa protein (IP17), or ubiquitin cross-reactive protein (UCRP), is an antiviral interferon-induced ubiquitin-like protein (Ubl) that upon viral infection, modifies cellular and viral proteins by mechanisms similar to ubiquitination. Although ISG15 has properties similar to those of other Ubl molecules, it is a unique member of the Ubl superfamily, whose expression and conjugation to target proteins are tightly regulated by specific signaling pathways, indicating it may have specialized functions in the immune system. ISG15 contains two tandem Ubl domains with a beta-grasp Ubl fold. This family corresponds to the first Ubl domain.

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gi 442614351   1 MIITIKNLQQQTFTIEFAPEKTVLELKKKIFEERG-PEYvaeKQKLIY--AGVILTDDRTVGSYNVDEKKfiVVML 73
Cdd:cd01792    1 WDLTVKMLTGNEFQVSVSPSMTVSELKAQITQKIGvPAF---QQRLAVqpSGVELQDGVRLASQGLGPSS--TVLL 71

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.

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gi 442614351 166 MVEMGYPREQVERAMAASYNNPERAVEYL 194
Cdd:cd14387    7 LMSMGFPRNRAIEALKRTNNNLDRALDWL 35

ubiquitin-like (Ubl) domain found in heme-oxidized IRP2 ubiquitin ligase 1 (HOIL-1) and similar proteins; HOIL-1, also termed RBCK1, or HOIL-1L, or RanBP-type and C3HC4-type zinc finger-containing protein 1, HBV-associated factor 4, or Hepatitis B virus X-associated protein 4, or RING finger protein 54 (RNF54), or ubiquitin-conjugating enzyme 7-interacting protein 3, or UbcM4-interacting protein 28 (UIP28), together with E3 ubiquitin-protein ligase RNF31 (also known as HOIP) and SHANK-associated RH domain interacting protein (SHARPIN), forms the E3-ligase complex (also known as linear-ubiquitin-chain assembly complex LUBAC) that regulates NF-kappaB activity and apoptosis through conjugation of linear polyubiquitin chains to NF-kappaB essential modulator (also known as NEMO or IKBKG). HOIL-1 plays a crucial role in TNF-alpha-mediated NF-kappaB activation. It also functions as an ubiquitin-protein ligase E3 that interacts with not only PKCbeta but also PKCzeta. It can recognize heme-oxidized IRP2 (iron regulatory protein2) and is thought to affect the turnover of oxidatively damaged proteins. HOIL-1 contains an N-terminal ubiqutin-like (UBL) domain and an Npl4 zinc-finger (NZF) domain, which regulate the interaction with the LUBAC subunit RNF31 and ubiquitin, respectively. The NZF domain belongs to RanBP2-type zinc finger (zf-RanBP2) domain superfamily. In addition, HOIL-1 has a 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 use 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.

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gi 442614351  12 TFTIEFAPEKTVLELKKKIFEERG-PeyvAEKQKLIYAGVILTDDRTVGSYNV 63
Cdd:cd01799   18 PITLKVRPHTTIASLKRQIFLEYGfP---PSVQRWIIGKRLATDDETLLSYGI 67