Ubiquitin-like domain; This entry includes N-terminal ubiquitin-like domain from proteins such as NEDD8 ultimate buster protein.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1870786610  70 RGTGNDNYRTTGIATIEVFLPPRLKKD----RKNLLETRLHITGRELRSKIAETFGLQenYIKIVINKKQLQLGKTLEEQ 145
Cdd:pfam18037   1 RGKGNQTFRETGVATLELLLPRDQRKAtktrKKNYLETKLDVTGQELRSRIAETFGLQ--YIKLILNGKTLQLDKTLEEQ 78

                          90
                  ....*....|....*...
gi 1870786610 146 GVAHNVKAMVLELKQSEE 163
Cdd:pfam18037  79 GVKHNSKVMVLELSDSEE 96

UBA domain-like superfamily; The ubiquitin-associated (UBA) domain-like superfamily contains alpha-helical structural homology ubiquitin-binding domains, including UBA domains and coupling of ubiquitin conjugation to endoplasmic reticulum degradation (CUE) domains which share a common three-helical bundle architecture. 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 bind the 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. CUE domain containing proteins are characterized by an FP and a di-leucine-like sequence and bind to monoubiquitin with varying affinities. Some higher eukaryotic CUE domain proteins do not bind monoubiquitin efficiently, since they carry LP, rather than FP among CUE domains. This superfamily also includes many UBA-like domains found in AMP-activated protein kinase (AMPK) related kinases, the NXF family of mRNA nuclear export factors, elongation factor Ts (EF-Ts), nascent polypeptide-associated complex subunit alpha (NACA) and similar proteins. Although many UBA-like domains may have a conserved TG but not GF/Y-loop, they still show a high level of structural and sequence similarity with three-helical ubiquitin binding domains.

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1870786610 444 ENIDRLVYMGFDALVAEAALRVFRGNVQLAAQTLAH 479
Cdd:cd14293     1 EKLDQLVYMGFERDVAESALRLTGGDVQQATQLLLD 36

Ubiquitin-like domain; This entry includes N-terminal ubiquitin-like domain from proteins such as NEDD8 ultimate buster protein.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1870786610  70 RGTGNDNYRTTGIATIEVFLPPRLKKD----RKNLLETRLHITGRELRSKIAETFGLQenYIKIVINKKQLQLGKTLEEQ 145
Cdd:pfam18037   1 RGKGNQTFRETGVATLELLLPRDQRKAtktrKKNYLETKLDVTGQELRSRIAETFGLQ--YIKLILNGKTLQLDKTLEEQ 78

                          90
                  ....*....|....*...
gi 1870786610 146 GVAHNVKAMVLELKQSEE 163
Cdd:pfam18037  79 GVKHNSKVMVLELSDSEE 96

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.

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1870786610 376 DPSKVDNLLQLGFTAQEARLGLRACDGNVDHAATHI 411
Cdd:cd14291     1 DEDKLQQLMEMGFSEAEARLALRACNGNVERAVDYI 36

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

                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 1870786610  376 DPSKVDNLLQLGFTAQEARLGLRACDGNVDHAATHI 411
Cdd:smart00165   1 DEEKIDQLLEMGFSREEALKALRAANGNVERAAEYL 36

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

                           10        20        30
                   ....*....|....*....|....*....|....*
gi 1870786610  443 QENIDRLVYMGFDALVAEAALRVFRGNVQLAAQTL 477
Cdd:smart00165   2 EEKIDQLLEMGFSREEALKALRAANGNVERAAEYL 36

Ubiquitin-like domain; This entry includes N-terminal ubiquitin-like domain from proteins such as NEDD8 ultimate buster protein.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1870786610  70 RGTGNDNYRTTGIATIEVFLPPRLKKD----RKNLLETRLHITGRELRSKIAETFGLQenYIKIVINKKQLQLGKTLEEQ 145
Cdd:pfam18037   1 RGKGNQTFRETGVATLELLLPRDQRKAtktrKKNYLETKLDVTGQELRSRIAETFGLQ--YIKLILNGKTLQLDKTLEEQ 78

                          90
                  ....*....|....*...
gi 1870786610 146 GVAHNVKAMVLELKQSEE 163
Cdd:pfam18037  79 GVKHNSKVMVLELSDSEE 96

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.

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1870786610 376 DPSKVDNLLQLGFTAQEARLGLRACDGNVDHAATHI 411
Cdd:cd14291     1 DEDKLQQLMEMGFSEAEARLALRACNGNVERAVDYI 36

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1870786610  92 RLKKDRKNLLETRLHITGRELRSKIAETFGLQENYIKIVINKKQLQLGKTLEEQGVAHNVKAMVL 156
Cdd:cd17039     4 KTLDGKTYTVEVDPDDTVADLKEKIEEKTGIPVEQQRLIYNGKELKDDKTLSDYGIKDGSTIHLV 68

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 1870786610 375 IDPSKVDNLLQLGFTAQEARLGLRACDGNVDHAATHI 411
Cdd:pfam00627   1 EDEEAIQRLVEMGFDREQVREALRATGNNVERAAEYL 37

UBA domain found in Saccharomyces cerevisiae DNA-damage response protein Ddi1 and similar proteins; Ddi1, also called v-SNARE-master 1 (Vsm1), is a ubiquitin receptor involved in regulation of the cell cycle and late secretory pathway in Saccharomyces cerevisiae. 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. 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. 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. This family also includes mammalian regulatory solute carrier protein family 1 member 1 (RSC1A1), also called transporter regulator RS1 (RS1) which mediates transcriptional and post-transcriptional regulation of Na(+)-D-glucose cotransporter SGLT1.

                          10        20        30
                  ....*....|....*....|....*....|.
gi 1870786610 378 SKVDNLLQLGFTAQEARLGLRACDGNVDHAA 408
Cdd:cd14309     2 EKIAQLMDLGFSREEAIQALEATNGNVELAA 32

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.

                          10        20        30
                  ....*....|....*....|....*....|....
gi 1870786610 375 IDPSKVDNLLQLGFTAQEARLGLRACDGNVDHAA 408
Cdd:cd14386     1 VPEEAVAMLVSMGFTRDQAIKALKATDNNVERAA 34

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.

                          10        20
                  ....*....|....*....|....*....
gi 1870786610 380 VDNLLQLGFTAQEARLGLRACDGNVDHAA 408
Cdd:cd14270     1 LAQLVEMGFSREQARRALRATNGDVEAAV 29