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.

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gi 1039737374 316 LRLQQLQHMGFPTEQAAVALAATGRVEGAVSLLVEGLVDTEALV 359
Cdd:cd14289     1 LRLQQLERMGFPTEKAVVALAATGRVEGAVSLLIGGQIGEETVV 44

UBA domain found in vertebrate rhomboid domain-containing protein 3 (RHBD3); RHBD3 is encoded by a novel chromosome 22 CpG island-associated gene (C22orf3) that is not expressed in a significant proportion of pituitary tumors. C22orf3 is also called pituitary tumor apoptosis gene (PTAG) or RHBDD3 which is located directly upstream of EWSR1. Although its biological function remains unclear, RHBD3 contains an N-terminal rhomboid domain and a C-terminal ubiquitin-associated (UBA) domain.

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gi 1039737374 316 LRLQQLQHMGFPTEQAAVALAATGRVEGAVSLLVEGLVDTEALV 359
Cdd:cd14289     1 LRLQQLERMGFPTEKAVVALAATGRVEGAVSLLIGGQIGEETVV 44

UBA domain found in vertebrate rhomboid domain-containing protein 3 (RHBD3); RHBD3 is encoded by a novel chromosome 22 CpG island-associated gene (C22orf3) that is not expressed in a significant proportion of pituitary tumors. C22orf3 is also called pituitary tumor apoptosis gene (PTAG) or RHBDD3 which is located directly upstream of EWSR1. Although its biological function remains unclear, RHBD3 contains an N-terminal rhomboid domain and a C-terminal ubiquitin-associated (UBA) domain.

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gi 1039737374 316 LRLQQLQHMGFPTEQAAVALAATGRVEGAVSLLVEGLVDTEALV 359
Cdd:cd14289     1 LRLQQLERMGFPTEKAVVALAATGRVEGAVSLLIGGQIGEETVV 44

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.

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gi 1039737374 313 VSSLRLQQLQHMGFPTEQAAVALAAT-GRVEGAVSLL 348
Cdd:pfam00627   1 EDEEAIQRLVEMGFDREQVREALRATgNNVERAAEYL 37

UBA domain found in plant PNGase/UBA or UBX (PUB) domain-containing proteins; This family includes some uncharacterized hypothetical proteins found in plants. Although their biological function remain unclear, all family members contain an N-terminal ubiquitin-associated (UBA) domain and a C-terminal PUB domain. UBA domain, along with UBL (ubiquitin-like) domain, has been implicated in proteasomal degradation by associating with substrates destined for degradation as well as with subunits of the proteasome, thus regulating protein turnover. PUB domain functions as a p97 (also known as valosin-containing protein or VCP) adaptor by interacting with the D1 and/or D2 ATPase domains. The type II AAA+ ATPase p97 is involved in a variety of cellular processes such as the deglycosylation of ERAD substrates, membrane fusion, transcription factor activation and cell cycle regulation through differential binding to specific adaptor proteins.

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gi 1039737374 318 LQQLQHMGFPTEQAAVALAATG--RVEGAVSLLVE 350
Cdd:cd14290     7 LKELEAMGFPRARAVRALHHTGntSVEAAVNWIVE 41