UBA domain found in ubiquitin-associated protein 2 (UBAP-2) like proteins; The family contains some uncharacterized ubiquitin-associated proteins, including UBAP-2 and its homolog, UBAP2-like [UBP2L, also called protein NICE-4 (for newly identified cDNA from the epidermal differentiation complex EDC)], both of which contain an N-terminal ubiquitin-associated (UBA) domain along with a highly conserved, but function unknown domain (DUF3697).

                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 1890255180   15 FEAKVKQLMEVTGKNQDECIVALHDCNGDVNKAINILL 52
Cdd:cd14277      1 IQEKVKQVMELTGRSEDEAVVALHDCDNDVNRAINFLL 38

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1890255180  262 VPHSQASEANSFETSQQQGFGQALVFTNSQHNNQMAP---GTGSSTAVNSCSPQSLSSVLGSGFGELAPPKMANITSSQI 338
Cdd:pfam03154  148 IPSPQDNESDSDSSAQQQILQTQPPVLQAQSGAASPPsppPPGTTQAATAGPTPSAPSVPPQGSPATSQPPNQTQSTAAP 227

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1890255180  339 LDQLKA-------------PSLGQFTTTPSTQQNSTSHPTTTTSWDLKPPTSQS--SVLSHLDFKSQPEPSPVLSQLSQR 403
Cdd:pfam03154  228 HTLIQQtptlhpqrlpsphPPLQPMTQPPPPSQVSPQPLPQPSLHGQMPPMPHSlqTGPSHMQHPVPPQPFPLTPQSSQS 307

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1890255180  404 Q---------QHQSQAVTVPPPGLESFPSQAKLRESTPGDSPSTVNKLLQLPSTTIENISVSVHQPQPKHI------KLA 468
Cdd:pfam03154  308 QvppgpspaaPGQSQQRIHTPPSQSQLQSQQPPREQPLPPAPLSMPHIKPPPTTPIPQLPNPQSHKHPPHLsgpspfQMN 387

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1890255180  469 KRRIPPASKIPASAVEM--PGSADVTGLNVQFGALEFGSEPS----LSEFGSAPSSENSNQIPISLYSKSLSEPLNTSLS 542
Cdd:pfam03154  388 SNLPPPPALKPLSSLSThhPPSAHPPPLQLMPQSQQLPPPPAqppvLTQSQSLPPPAASHPPTSGLHQVPSQSPFPQHPF 467

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1890255180  543 MTSAVQNSTYTTSVitscsltssslNSASPVAMSSSYDQSSVHNRIPYQSPVSSSESAPGTIMNGHGGGRSQQTLDTPKT 622
Cdd:pfam03154  468 VPGGPPPITPPSGP-----------PTSTSSAMPGIQPPSSASVSSSGPVPAAVSCPLPPVQIKEEALDEAEEPESPPPP 536

                          410       420
                   ....*....|....*....|.
gi 1890255180  623 TGPPSALPSVSSLPSTTSCTA 643
Cdd:pfam03154  537 PRSPSPEPTVVNTPSHASQSA 557

UBA domain found in ubiquitin-associated protein 2 (UBAP-2) like proteins; The family contains some uncharacterized ubiquitin-associated proteins, including UBAP-2 and its homolog, UBAP2-like [UBP2L, also called protein NICE-4 (for newly identified cDNA from the epidermal differentiation complex EDC)], both of which contain an N-terminal ubiquitin-associated (UBA) domain along with a highly conserved, but function unknown domain (DUF3697).

                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 1890255180   15 FEAKVKQLMEVTGKNQDECIVALHDCNGDVNKAINILL 52
Cdd:cd14277      1 IQEKVKQVMELTGRSEDEAVVALHDCDNDVNRAINFLL 38

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

                            10        20        30
                    ....*....|....*....|....*....|....*..
gi 1890255180    16 EAKVKQLMEVtGKNQDECIVALHDCNGDVNKAINILL 52
Cdd:smart00165    2 EEKIDQLLEM-GFSREEALKALRAANGNVERAAEYLL 37

UBA domain found in ubiquitin-associated protein 2 (UBAP-2) like proteins; The family contains some uncharacterized ubiquitin-associated proteins, including UBAP-2 and its homolog, UBAP2-like [UBP2L, also called protein NICE-4 (for newly identified cDNA from the epidermal differentiation complex EDC)], both of which contain an N-terminal ubiquitin-associated (UBA) domain along with a highly conserved, but function unknown domain (DUF3697).

                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 1890255180   15 FEAKVKQLMEVTGKNQDECIVALHDCNGDVNKAINILL 52
Cdd:cd14277      1 IQEKVKQVMELTGRSEDEAVVALHDCDNDVNRAINFLL 38

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
                   ....*....|....*....|....*...
gi 1890255180   22 LMEVTGKNQDECIVALHDCNGDVNKAIN 49
Cdd:cd00194      1 LVDITGASQEEAQQALEACGGNLNIAAN 28

UBA domain found in Saccharomyces cerevisiae protein GTS1 (Gts1p) and similar proteins; Gts1p, also called protein LSR1, is encoded by a pleiotropic gene GTS1 in budding yeast. The formation of Gts1p-mediated protein aggregates may induce reactive oxygen species (ROS) production and apoptosis. Gts1p also plays an important role in the regulation of heat and other stress responses under glucose-limited or -depleted conditions in either batch or continuous culture. Gts1p contains an N-terminal zinc finger motif similar to that of GATA-transcription factors, a ubiquitin-associated (UBA) domain and a C-terminal glutamine-rich strand. The zinc finger is responsible for the binding to the glycolytic enzyme glyceraldehydes-3-phosphate dehydrogenase (GAPDH) which is required for the maintenance of the metabolic oscillations of budding yeast. The polyglutamine sequence is indispensable for the pleiotropy and nuclear localization of Gts1p. It is essential for the transcriptional activation, whereas Gts1p lacks DNA binding activity.

                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 1890255180   14 DFEAKVKQLMEVTGKNQDECIVALHDCNGDVNKAINILL 52
Cdd:cd14400      1 KYSRQLRFLKEMGFTNEDNNLEALSQANGNINRAIDILL 39

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 1890255180   16 EAKVKQLMEVtGKNQDECIVALHDCNGDVNKAINILL 52
Cdd:cd14309      1 EEKIAQLMDL-GFSREEAIQALEATNGNVELAASLLF 36

UBA domain found in plant ubiquitin-conjugating enzyme E2 27 and similar proteins; UBC27, also called ubiquitin carrier protein 27, functions as a class II ubiquitin-conjugating (UBC) enzyme (E2). E2, together with E1 (ubiquitin-activating enzyme UBA) and E3 (ubiquitin ligase), is required in the multi-step reaction of ubiquitin conjugation. Unlike other Arabidopsis UBCs, in addition to an N-terminal ubiquitin-conjugating enzyme E2 catalytic domain (UBCc), UBC27 has an additional C-terminal ubiquitin-associated domain (UBA).

                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 1890255180   16 EAKVKQLMEVtGKNQDECIVALHDCNGDVNKAINILL 52
Cdd:cd14312      1 EEKVQRLVEM-GFPRDQAVVALESAGGDENAALEKLL 36