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 3687502      1 MNLTFKNLQQQKFVIsDVSADTKISELKEKIQTQQ---NYEVERQKLIYSGRILADDKTVGEYNIKEQDFIVCMVSRPKT 77
Cdd:TIGR00601   1 MTLTFKTLQQQKFKI-DMEPDETVKELKEKIEAEQgkdAYPVAQQKLIYSGKILSDDKTVKEYKIKEKDFVVVMVSKPKT 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3687502     78 ST-------STPKSAASPAPNPPASVPEKKVEAPSSTVAESTSTTQTVAAAAPSNPDTTATSEAPIDANTLAVGAQRNVA 150
Cdd:TIGR00601  80 GTgkvappaATPTSAPTPTPSPPASPASGMSAAPASAVEEKSPSEESATATAPESPSTSVPSSGSDAASTLVVGSERETT 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3687502    151 VENMVEMGYERSEVERAMRAAFNNPDRAVEYLLTGIPEDILNRQReesaaalAAQQQQSEALAPTSTGQPANLFEQAALS 230
Cdd:TIGR00601 160 IEEIMEMGYEREEVERALRAAFNNPDRAVEYLLTGIPEDPEQPEP-------VQQTAASTAAATTETPQHGSVFEQAAQG 232

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3687502    231 ENENQEQPSNTvGDDPLGFLRSIPQFQQLRQIVQQNPQMLETILQQIGQGDPALAQAITQNPEAFLQLLAEGAE---GES 307
Cdd:TIGR00601 233 GTEQPATEAAQ-GGNPLEFLRNQPQFQQLRQVVQQNPQLLPPLLQQIGQENPQLLQQISQHPEQFLQMLNEPVGelaSES 311

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 3687502    308 ALPSG-----------GIQIQITQEESESIDRLCQLGFDRNIVIQAYLACDKNEELAANYLFEHGHE 363
Cdd:TIGR00601 312 DMEGGvgaiaeaglpqMNQIQVTPEEKEAIERLCALGFDRGLVIQAYFACDKNEELAANYLLSQNFD 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 3687502      1 MNLTFKNLQQQKFVIsDVSADTKISELKEKIQTQQ---NYEVERQKLIYSGRILADDKTVGEYNIKEQDFIVCMVSRPKT 77
Cdd:TIGR00601   1 MTLTFKTLQQQKFKI-DMEPDETVKELKEKIEAEQgkdAYPVAQQKLIYSGKILSDDKTVKEYKIKEKDFVVVMVSKPKT 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3687502     78 ST-------STPKSAASPAPNPPASVPEKKVEAPSSTVAESTSTTQTVAAAAPSNPDTTATSEAPIDANTLAVGAQRNVA 150
Cdd:TIGR00601  80 GTgkvappaATPTSAPTPTPSPPASPASGMSAAPASAVEEKSPSEESATATAPESPSTSVPSSGSDAASTLVVGSERETT 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3687502    151 VENMVEMGYERSEVERAMRAAFNNPDRAVEYLLTGIPEDILNRQReesaaalAAQQQQSEALAPTSTGQPANLFEQAALS 230
Cdd:TIGR00601 160 IEEIMEMGYEREEVERALRAAFNNPDRAVEYLLTGIPEDPEQPEP-------VQQTAASTAAATTETPQHGSVFEQAAQG 232

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3687502    231 ENENQEQPSNTvGDDPLGFLRSIPQFQQLRQIVQQNPQMLETILQQIGQGDPALAQAITQNPEAFLQLLAEGAE---GES 307
Cdd:TIGR00601 233 GTEQPATEAAQ-GGNPLEFLRNQPQFQQLRQVVQQNPQLLPPLLQQIGQENPQLLQQISQHPEQFLQMLNEPVGelaSES 311

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 3687502    308 ALPSG-----------GIQIQITQEESESIDRLCQLGFDRNIVIQAYLACDKNEELAANYLFEHGHE 363
Cdd:TIGR00601 312 DMEGGvgaiaeaglpqMNQIQVTPEEKEAIERLCALGFDRGLVIQAYFACDKNEELAANYLLSQNFD 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 3687502    247 LGFLRSIPQFQQLRQIVQQNPQMLETILQQIGQGDPALAQAITQNPEAFLQLLAEGA 303
Cdd:pfam09280   1 LDFLRNNPQFQQLRQLVQQNPQLLQPLLQQLAQSNPQLAQLIQQNQEEFLQLLNEPG 57

Ubiquitin [Posttranslational modification, protein turnover, chaperones];

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 3687502   17 DVSADTKISELKEKIQTQQNYEVERQKLIYSGRILADDKTVGEYNIKEQDFIV 69
Cdd:COG5272  16 EVEPNDTIEAVKAKIQDKEGIPPDQQRLIFAGKQLEDDRTLADYNIQKESTLH 68

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 3687502      1 MNLTFKNLQQQKFVIsDVSADTKISELKEKIQTQQ---NYEVERQKLIYSGRILADDKTVGEYNIKEQDFIVCMVSRPKT 77
Cdd:TIGR00601   1 MTLTFKTLQQQKFKI-DMEPDETVKELKEKIEAEQgkdAYPVAQQKLIYSGKILSDDKTVKEYKIKEKDFVVVMVSKPKT 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3687502     78 ST-------STPKSAASPAPNPPASVPEKKVEAPSSTVAESTSTTQTVAAAAPSNPDTTATSEAPIDANTLAVGAQRNVA 150
Cdd:TIGR00601  80 GTgkvappaATPTSAPTPTPSPPASPASGMSAAPASAVEEKSPSEESATATAPESPSTSVPSSGSDAASTLVVGSERETT 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3687502    151 VENMVEMGYERSEVERAMRAAFNNPDRAVEYLLTGIPEDILNRQReesaaalAAQQQQSEALAPTSTGQPANLFEQAALS 230
Cdd:TIGR00601 160 IEEIMEMGYEREEVERALRAAFNNPDRAVEYLLTGIPEDPEQPEP-------VQQTAASTAAATTETPQHGSVFEQAAQG 232

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3687502    231 ENENQEQPSNTvGDDPLGFLRSIPQFQQLRQIVQQNPQMLETILQQIGQGDPALAQAITQNPEAFLQLLAEGAE---GES 307
Cdd:TIGR00601 233 GTEQPATEAAQ-GGNPLEFLRNQPQFQQLRQVVQQNPQLLPPLLQQIGQENPQLLQQISQHPEQFLQMLNEPVGelaSES 311

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 3687502    308 ALPSG-----------GIQIQITQEESESIDRLCQLGFDRNIVIQAYLACDKNEELAANYLFEHGHE 363
Cdd:TIGR00601 312 DMEGGvgaiaeaglpqMNQIQVTPEEKEAIERLCALGFDRGLVIQAYFACDKNEELAANYLLSQNFD 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 3687502    247 LGFLRSIPQFQQLRQIVQQNPQMLETILQQIGQGDPALAQAITQNPEAFLQLLAEGA 303
Cdd:pfam09280   1 LDFLRNNPQFQQLRQLVQQNPQLLQPLLQQLAQSNPQLAQLIQQNQEEFLQLLNEPG 57

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.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 3687502      3 LTFKNLQQQKFVIsDVSADTKISELKEKIQTQQNYEVERQKLIYSGRILADDKTVGEYNIKEQDFIVCMVSRP 75
Cdd:pfam00240   1 ITVKTLDGKKITL-EVDPTDTVLELKEKIAEKEGVPPEQQRLIYSGKVLEDDQTLGEYGIEDGSTIHLVLRQR 72

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.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|
gi 3687502  321 EESESIDRLCQLGFDRNIVIQAYLACDKNEELAANYLFEH 360
Cdd:cd14381   1 EEDQAIDRLCELGFDRDLVIQAYLACDKNEEMAANFLFEN 40

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 3687502  321 EESESIDRLCQLGFDRNIVIQAYLACDKNEELAANYLF 358
Cdd:cd14281   1 EEREAIERLVALGFSRDQAIEAYLACDKNEELAANYLF 38

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.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 3687502    1 MNLTFKNLQQQKFVISdVSADTKISELKEKIQTQQNYEVERQKLIYSGRILADDKTVGEYNIKEqDFIVCMVSRP 75
Cdd:cd16106   1 IKVTVKCSNGKKFTVE-VEPDATVLELKELIAEKSDIPAEQQRLIYKGKILKDEETLSSYKIQD-GHTVHLVKGA 73

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.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 3687502    1 MNLTFKNLQQQKFVIsDVSADTKISELKEKIQTQQN---YEVERQKLIYSGRILADDKTVGEYNIKEQDFIVCMVSRPK 76
Cdd:cd16126   1 MQITLKTLQQQTFKI-DIDPEETVKALKEKIESEKGkdaFPVAGQKLIYAGKILNDDTALKEYKIDEKNFVVVMVTKPK 78

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 3687502    1 MNLTFKNLQQQKFVIsDVSADTKISELKEKIQTQQNYE---VERQKLIYSGRILADDKTVGEYNIKEQDFIVCMVSR 74
Cdd:cd17126   1 VTITLKTLQQQTFKI-RMEPDETVKVLKEKIEAEKGRDafpVAGQKLIYAGKILSDDVPIRDYRIDEKNFVVVMVTK 76

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 3687502  141 LAVGAQRNVAVENMVEMG---YERSEVERAMRAAFNNPDRAVEYLLTGIP 187
Cdd:cd14379   1 LVAGSSLEQTVQQIMDMGggsWDRDTVVRALRAAYNNPERAVEYLYSGIP 50

ubiquitin-like (Ubl) domain found in ubiquitin-like proteins UBL4A and similar proteins; UBL4A, also termed GdX, is a ubiquitously expressed ubiquitin-like (Ubl) protein that forms a complex with partner proteins and participates in the protein processing through endoplasmic reticulum (ER), acting as a chaperone. As a key component of the BCL2-associated athanogene 6 (BAG6) chaperone complex, UBL4A plays a role in mediating DNA damage signaling and cell death. UBL4A also regulates insulin-induced Akt plasma membrane translocation through promotion of Arp2/3-dependent actin branching. Moreover, UBL4A specifically stabilizes the TC45/STAT3 association and promotes dephosphorylation of STAT3 to repress tumorigenesis. UBL4B is testis-specific, and encoded by an X-derived retrogene Ubl4b, which is specifically expressed in post-meiotic germ cells in mammals. As a germ cell-specific cytoplasmic protein, UBL4B is not present in somatic cells. Moreover, UBL4B is present in elongated spermatids, but not in spermatocytes and round spermatids, suggesting its function is restricted to late spermiogenesis. The function of UBL4A may be compensated by either UBL4B or other Ubl proteins in normal conditions. Both UBL4A and UBL4B contain a conserved Ubl domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 3687502    1 MNLTFKNLQQQKFVIsDVSADTKISELKEKIQTQQNYEVERQKLIYSGRILADDKTVGEYNIKEQDFIVCMV 72
Cdd:cd01807   1 MLITVKILQGKECTI-EVSPTESVLTVKQLVAEQLNVPVSQQRLVFKGKTLADEHSLSDYSIGPGSKIHLVV 71

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 3687502  321 EESESIDRLCQLGFDRNIVIQAYLACDKNEELAANYLFEHG 361
Cdd:cd14427   1 QEKEAIERLKALGFPESLVIQAYFACEKNENLAANFLLSQN 41

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 3687502    150 AVENMVEMGYERSEVERAMRAAFNNPDRAVEYL 182
Cdd:pfam00627   5 AIQRLVEMGFDREQVREALRATGNNVERAAEYL 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 3687502  146 QRNVAVENMVEMGYERSEVERAMRAAFNNPDRAVEYLLTG 185
Cdd:cd14425   1 EYETMLTEIMSMGYERERVVAALRASYNNPHRAVEYLLTG 40

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.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3687502    1 MNLTFKNLQQQKFVISDVSADTKISELKEKIQTQQNYEVERQKLIYSGRILADD-KTVGEYNIKEQDFIV 69
Cdd:cd01796   1 MKLTVTTEDDDRLFSLEVSPDMTLEDLKALCEAETGIPAAEQVLLHNGQPLTDDkKTLEALGLKDGDLLL 70

Ubiquitin associated domain; Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.

                           10        20        30
                   ....*....|....*....|....*....|....
gi 3687502     150 AVENMVEMGYERSEVERAMRAAFNNPDRAVEYLL 183
Cdd:smart00165   4 KIDQLLEMGFSREEALKALRAANGNVERAAEYLL 37

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).

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 3687502      1 MNLTFKNLQQQKFVISdVSADTKISELKEKIQTQQNY-EVERQKLIYSGRILADDKTVGEYNIKEQDFI 68
Cdd:pfam11976   1 IKIILKGKDGKEVFIK-VKPTTTVSKLINAYRKKRGIpPSQQVRLIFDGERLDPNSTVEDLDIEDGDTI 68

ubiquitin-like (Ubl) domain found in ubiquitin-like domain-containing CTD phosphatase 1 (UBLCP1) and similar proteins; UBLCP1 is a 26S proteasome phosphatase that regulates nuclear proteasome activity. It is localized in the nucleus and it contains conserved ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, which directly interacts with the proteasome. Knockdown of UBLCP1 in cells promotes 26S proteasome assembly and selectively enhances nuclear proteasome activity. UBLCP1 may also play a role in the regulation of phosphorylation state of RNA polymerase II C-terminal domain, a key event during mRNA metabolism.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 3687502   11 QKFVISDVSADTkISELKEKIQTQQNYEVERQKLI---YSGRILADDKTVGEYNIK 63
Cdd:cd01813  10 KEYPVTVLSSDT-VLDLKQRIFELTGVLPKRQKLLglkVKGKPADDDVKLSSLKLK 64

ubiquitin-like (Ubl) domain found in ubiquitin domain-containing protein UBFD1 and similar proteins; UBFD1, also termed ubiquitin-binding protein homolog (UBPH), is a polyubiquitin binding protein containing a conserved ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions. It may play a role as nuclear factor-kappaB (NF-kappaB) regulator.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 3687502   11 QKFVISdVSADTKISELKEKIQTQQNYEVERQKLIYSGrILADDKTVGE 59
Cdd:cd17047  10 EKYDVK-FPLDSTIAELKEHIETLTGVPPAMQKLMYKG-LLKDDKTLRE 56

ubiquitin-like (Ubl) domain found in ubiquitin-like PHD and RING finger domain-containing protein 1(UHRF1); UHRF1, also termed inverted CCAAT box-binding protein of 90 kDa, or nuclear protein 95, or nuclear zinc finger protein Np95 (Np95), or RING finger protein 106, or transcription factor ICBP90, or E3 ubiquitin-protein ligase UHRF1, is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma, gastric cancer, esophageal squamous cell carcinoma, colorectal cancer, prostate cancer, and breast cancer. UHRF1 can acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumor suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21.Moreover, UHRF1-dependent repression of factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination ofTIP60. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF1 contains an N-terminal ubiquitin-like domain (Ubl), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET and RING finger associated (SRA) domain, and a C-terminal RING-finger domain. It specifically binds to hemimethylated DNA, double-stranded CpG dinucleotides, and recruits the maintenance methyltransferase DNMT1 to its hemimethylated DNA substrate through its SRA domain. UHRF1-dependent H3K23 ubiquitination has an essential role in maintenance DNA methylation and replication. The tandem Tudor domain directs UHRF1 binding to the heterochromatin mark histone H3K9me3 and the PHD finger targets UHRF1 to unmodified histone H3 in euchromatic regions. The RING-finger domain exhibits both autocatalytic E3 ubiquitin (Ub) ligase activity and activity against histone H3 and DNMT1.

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                ....*....|....*....|....*....|....*....|....*....|....*...
gi 3687502   15 ISDVSADTKISELKEKIQTQQNYEVERQKLIYSGRILADDKTVGEYNIKEQDFIVCMV 72
Cdd:cd17122  16 IDSLSKLTKVEELRQKIQELFGVEPERQRLFYRGKQMEDGHTLFDYSVGLNDIVQLLV 73

ubiquitin-like (Ubl) domain found in parkin and similar proteins; Parkin, also termed Parkinson juvenile disease protein 2, is a RBR-type E3 ubiquitin-protein ligase that is associated with recessive early onset Parkinson's disease (PD), and exerts a protective effect against dopamine-induced alpha-synuclein-dependent cell toxicity. Mutations in the parkin gene cause autosomal recessive juvenile parkinsonism. Parkin functions within a multiprotein E3 ubiquitin ligase complex, catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins, such as BCL2, SYT11, CCNE1, GPR37, RHOT1/MIRO1, MFN1, MFN2, STUB1, SNCAIP, SEPT5, TOMM20, USP30, ZNF746 and AIMP2. It mediates monoubiquitination as well as Lys-6-, Lys-11-, Lys-48- and Lys-63-linked polyubiquitination of substrates depending on the context. Parkin may enhance cell viability and protects dopaminergic neurons from oxidative stress-mediated death by regulating mitochondrial function. It also limits the production of reactive oxygen species (ROS), and regulates cyclin-E during neuronal apoptosis. Moreover, parkin displays a ubiquitin ligase-independent function in transcriptional repression of p53. Parkin contains an N-terminal ubiquitin-like (Ubl) domain and a C-terminal 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 3687502   17 DVSADTKISELKEKIQTQQNYEVERQKLIYSGRILADDKTVGEYNIKEQDfIVCMVSRPKTS 78
Cdd:cd01798  14 EVDSDWSILQLKEVVAKRQGVPPDQLRIIFAGKELSDDLTLQNCDLGQQS-IVHAVQGPKRK 74

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.

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                ....*....|....*....|....*....|....*....|....*....|....
gi 3687502   12 KFVISDVSADTKISELKEKIQTQQNYEVERQKLIYSGRILADDKTVGEYNIKEQ 65
Cdd:cd01803  11 KTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKE 64

ubiquitin-like (Ubl) domain found in ubiquitin domain-containing proteins UBTD1, UBTD2, and similar proteins; This family represents a group of ubiquitin-like (Ubl) domain-containing proteins evolutionarily conserved and found in metazoa, fungi, and plants. They may regulate the activity and/or specificity of E2 ubiquitin conjugating enzymes belonging to the UBE2D family. Members in this family contain an N-terminal ubiquitin binding domain (UBD) and a C-terminal Ubl domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions.

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                ....*....|....*....|....*....|....*....|....*....|.
gi 3687502   19 SADTkISELKEKIQTQQNYEVERQKLIYSGRILADDKTVGEYNIkEQDFIV 69
Cdd:cd01794  17 STDT-VLQAKRRLQALEGIEPSRQRWFFSGKLLTDKTRIEDAKI-PKGFVV 65

ubiquitin-like (Ubl) domain found in eukaryotic protein linking integrin-associated protein (IAP, also known as CD47) with cytoskeleton (PLIC) proteins; The PLIC proteins (or ubiquilins) family contains human homologs of the yeast ubiquitin-like (Ubl) Dsk2 protein, PLIC-1 (also termed ubiquilin-1), PLIC-2 (also termed ubiquilin-2, or Chap1), PLIC-3 (also termed ubiquilin-3) and PLIC-4 (also termed ubiquilin-4, ataxin-1 interacting ubiquitin-like protein, A1Up, connexin43-interacting protein of 75 kDa, or CIP75), and mouse PLIC proteins. They are ubiquitin (Ub)-binding adaptor proteins involved in all protein degradation pathways through delivering ubiquitinated substrates to proteasomes. They also promote autophagy-dependent cell survival during nutrient starvation. PLIC-1 regulates the function of the thrombospondin receptor CD47 and G protein signaling. It plays a role in TLR4-mediated signaling through interacting with the Toll/interleukin-1 receptor (TIR) domain of TLR4. It also inhibits the TLR3-Trif antiviral pathway by reducing the abundance of Trif. Moreover, PLIC-1 binds to gamma-aminobutyric acid receptors (GABAARs) and modulates the Ub-dependent, proteasomal degradation of GABAARs. Furthermore, PLIC-1 acts as a molecular chaperone regulating amyloid precursor protein (APP) biosynthesis, trafficking, and degradation by stimulating K63-linked polyubiquitination of lysine 688 in the APP intracellular domain. In addition, PLIC-1 is involved in the protein aggregation-stress pathway via associating with the Ub-interacting motif (UIM) proteins ataxin 3, HSJ1a, and epidermal growth factor substrate 15 (EPS15). PLIC-2 is a protein that binds the ATPase domain of the HSP70-like Stch protein. It functions as a negative regulator of G protein-coupled receptor (GPCR) endocytosis. It also involved in amyotrophic lateral sclerosis (ALS)-related dementia. PLIC-3 is encoded by UbiquilinN3, a testis-specific gene. It shows high sequence similarity with the Xenopus protein XDRP1, a nuclear phosphoprotein that binds to the N-terminus of cyclin A and inhibits Ca2+-induced degradation of cyclin A, but not cyclin B. PLIC-4 is an ubiquitin-like (Ubl) nuclear protein that interacts with ataxin-1 and further links ataxin-1 with the chaperone and Ub-proteasome pathways. It also binds to the non-ubiquitinated gap junction protein connexin43 (Cx43) and regulates the turnover of Cx43 through the proteasomal pathway. PLIC proteins contain an N-terminal Ubl domain that is responsible for the binding of Ub-interacting motifs (UIMs) expressed by proteasomes and endocytic adaptors, and C-terminal Ub-associated (UBA) domain that interacts with Ub chains present on proteins destined for proteasomal degradation. In addition, mammalian PLIC2 proteins have an extra collagen-like motif region, which is absent in other PLIC proteins and the yeast Dsk2 protein.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 3687502   18 VSADTKISELKEKIQTQQNYEVERQKLIYSGRILADDKTVGEYNIK 63
Cdd:cd01808  18 VPEDSSVKEFKEEISKKFKAPVEQLVLIFAGKILKDQDTLSQHGIK 63

Beta-grasp ubiquitin-like fold; Ubiquitin is a protein modifier that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair in eukaryotes. The ubiquitination process comprises 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 proteins have similar ubiquitin beta-grasp fold and attach to other proteins in a ubiquitin-like manner but with biochemically distinct roles. Ubiquitin and ubiquitin-like proteins conjugate and deconjugate via ligases and peptidases to covalently modify target polypeptides. Some other ubiquitin-like domains have adaptor roles in ubiquitin-signaling by mediating protein-protein interaction. In addition to Ubiquitin-like (Ubl) domain, Ras-associating (RA) domain, F0/F1 sub-domain of FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, TGS (ThrRS, GTPase and SpoT) domain, Ras-binding domain (RBD), Ubiquitin regulatory domain X (UBX), Dublecortin-like domain, and RING finger- and WD40-associated ubiquitin-like (RAWUL) domain have beta-grasp ubiquitin-like folds, and are included in this superfamily.

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                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 3687502    3 LTFKNLQQQKFVisdVSADTKISELKEKIQTQQNYEVERQKLIYSGRILADDKTVGEYNIKEQDFIVC 70
Cdd:cd00196   3 VETPSLKKIVVA---VPPSTTLRQVLEKVAKRIGLPPDVIRLLFNGQVLDDLMTAKQVGLEPGEELHF 67

ubiquitin-like (Ubl) domain found in NEDD8 ultimate buster 1 (NUB1) and similar proteins; NUB1, also termed negative regulator of ubiquitin-like proteins 1, or 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 a conserved ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, three ubiquitin-associated domains (UBA), a bipartite nuclear localization signal (NLS) and a PEST motif.

                        10        20        30
                ....*....|....*....|....*....|....*....
gi 3687502   25 SELKEKIQTQQNYEVERQKLIYSGRILADDKTVGEYNIK 63
Cdd:cd17062  30 SELREKIAEELGVPEDRIKLISNGKVLKDEKTLAEQGVK 68

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 3687502  151 VENMVEMGYERSEVERAMRAAFNNPDRAVEYLLTG 185
Cdd:cd14306   1 VAKLMELGFPEEDCIRALRACGGNVEEAANWLLEN 35

UBA domain found in yeast UBA domain-containing protein RUP1p and similar proteins; RUP1p is a ubiquitin-associated (UBA) domain-containing protein encoded by a nonessential yeast gene RUP1. It can mediate the association of Rsp5 and Ubp2. The N-terminal UBA domain is responsible for antagonizing Rsp5 function, as well as bridging the Rsp5-Ubp2 interaction. No other characterized functional domains or motifs are found in RUP1p.

                        10        20        30
                ....*....|....*....|....*....|....*...
gi 3687502  323 SESIDRLCQLGFDRNIVIQAYLACDKNEELAANYLFEH 360
Cdd:cd14307   1 EEAVASLLEMGIPREVAIEALRETNGDVEAAANYIFSN 38

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 3687502  326 IDRLCQLGFDRNIVIQAYLACDKNEELAANYLFEHG 361
Cdd:cd14306   1 VAKLMELGFPEEDCIRALRACGGNVEEAANWLLENA 36

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.

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                ....*....|....*....|....*....|....*....
gi 3687502  150 AVENMVEMGYERSEVERAMRAAFNNPDRAVEYLLTGIPE 188
Cdd:cd14386   5 AVAMLVSMGFTRDQAIKALKATDNNVERAADWIFSHPDE 43

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.

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                ....*....|....*....|....*....|....*.
gi 3687502  150 AVENMVEMGYERSEVERAMRAAFNNPDRAVEYLLTG 185
Cdd:cd14297   3 LVKQLVDMGFTEAQARKALRKTNNNVERAVDWLFEG 38

Ubiquitin-2 like Rad60 SUMO-like;

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 3687502     19 SADTKISELKEKIQTQQNYEVERQ-------KLIYSGRILADDKTVGEY 60
Cdd:pfam13881  21 SPATTVADLKEKVIAQWPKDKENGpktvndvKLINAGKILENNKTLGEC 69

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 3687502  324 ESIDRLCQLGFDRNIVIQAYLACDKNEELAANYL 357
Cdd:cd14387   2 ESIAILMSMGFPRNRAIEALKRTNNNLDRALDWL 35

ubiquitin-like (Ubl) domain found in Kip1 ubiquitination-promoting complex protein 2 (KPC2) and similar proteins; KPC2, also termed ubiquitin-associated domain-containing protein 1 or UBA domain containing 1 (UBAC1), or glialblastoma cell differentiation-related protein 1 (GBDR1), is one of two subunits of Kip1 ubiquitination-promoting complex (KPC), a novel E3 ubiquitin-protein ligase that also contains KPC1 subunit and regulates the ubiquitin-dependent degradation of the cyclin-dependent kinase (CDK) inhibitor p27 at G1 phase. KPC2 contains an ubiquitin-like (Ubl) domain and two ubiquitin-associated (UBA) domains.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 3687502   15 ISDVSADTKISELKEKI-------QTQQNYEVERQKLIY--SGRILADDKTVGEYNIKEQDFIVCMVSR 74
Cdd:cd17066  19 LEEVTEDTTIEKLKEKClkhcvhgSLEDPKTLTHHKLIHaaSERVLSDTKTVLEENLQDKDVLLLIKKR 87