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).

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                   ....*....|....*....|....*....|....*...
gi 2471932624   53 FEAKVKQLMEVTGKNQDECIVALHDCNGDVNKAINILL 90
Cdd:cd14277      1 IQEKVKQVMELTGRSEDEAVVALHDCDNDVNRAINFLL 38

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 2471932624   53 FEAKVKQLMEVTGKNQDECIVALHDCNGDVNKAINILL 90
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 2471932624    54 EAKVKQLMEVtGKNQDECIVALHDCNGDVNKAINILL 90
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 2471932624   53 FEAKVKQLMEVTGKNQDECIVALHDCNGDVNKAINILL 90
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 2471932624   60 LMEVTGKNQDECIVALHDCNGDVNKAIN 87
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.

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                   ....*....|....*....|....*....|....*....
gi 2471932624   52 DFEAKVKQLMEVTGKNQDECIVALHDCNGDVNKAINILL 90
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 2471932624   54 EAKVKQLMEVtGKNQDECIVALHDCNGDVNKAINILL 90
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 2471932624   54 EAKVKQLMEVtGKNQDECIVALHDCNGDVNKAINILL 90
Cdd:cd14312      1 EEKVQRLVEM-GFPRDQAVVALESAGGDENAALEKLL 36