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        40
                  ....*....|....*....|....*....|....*....|....
gi 1831516897 128 EVNNEYLAHLLDLGFDEYTAVLALKRTNSAGVEQAVAWIVERSN 171
Cdd:cd14290     1 EVNADLLKELEAMGFPRARAVRALHHTGNTSVEAAVNWIVEHEN 44

Peptidyl-tRNA hydrolase PTH2; Peptidyl-tRNA hydrolases are enzymes that release tRNAs from peptidyl-tRNA during translation.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1831516897 202 KMVLVANMSLKMGTGKIAAQVGHATLGVYRQAMnsENGQNAIAAWTRHGQVKIVVKGQSTEQLMDLCKVAKDAGCYYYLV 281
Cdd:pfam01981   2 KQVLVVRTDLKMSKGKIAAQCAHAAVAAYEKAL--KPNPELLREWEREGQKKVVLKVPSEEELLELAEKAKSLGLPHALI 79

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1831516897 282 QDAGYTQIPAGSRTVLGIF-GTVEQVDSVTGGLKLL 316
Cdd:pfam01981  80 RDAGRTQIAPGTPTVLAIGpAPKELVDKITGHLKLL 115

peptidyl-tRNA hydrolase; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1831516897 203 MVLVANMSLKMGTGKIAAQVGHATLGVYRQAMNSENgqNAIAAWTRHGQVKIVVKGQSTEQLMDLCKVAKDAGCYYYLVQ 282
Cdd:PRK04322    1 QVIVVRTDLKMGKGKLAAQVAHAAVSAYEKADKSNR--EWLEEWLNEGQKKVVLKVNSEEELLELKEKAERLGLPTALIR 78

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1831516897 283 DAGYTQIPAGSRTVLGIF-GTVEQVDSVTGGLKLL 316
Cdd:PRK04322   79 DAGLTQLPPGTVTALGIGpAPEEKIDKITGDLKLL 113

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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1831516897 128 EVNNEYLAHLLDLGFDEYTAVLALKRTNSAGVEQAVAWIVERSN 171
Cdd:cd14290     1 EVNADLLKELEAMGFPRARAVRALHHTGNTSVEAAVNWIVEHEN 44

Peptidyl-tRNA hydrolase, type 2 (PTH2)_like . Peptidyl-tRNA hydrolase activity releases tRNA from the premature translation termination product peptidyl-tRNA. Two structurally different enzymes have been reported to encode such activity, Pth present in bacteria and eukaryotes and Pth2 present in archaea and eukaryotes.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1831516897 202 KMVLVANMSLKMGTGKIAAQVGHATLGVYRQAMNSENGQnaIAAWTRHGQVKIVVKGQSTEQLMDLCKVAKDAGCYYYLV 281
Cdd:cd02407     2 KMVIVVRNDLKMGKGKIAAQCAHAALAAYKKAMKDPPTL--LRAWELEGQKKVVLKVPSEEELLELAKKAKELGLPHSLI 79

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1831516897 282 QDAGYTQIPAGSRTVLGIF-GTVEQVDSVTGGLKLL 316
Cdd:cd02407    80 QDAGRTQIPPGTPTVLAIGpAPKEKVDKVTGHLKLL 115

Peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1831516897 202 KMVLVANMSLKMGTGKIAAQVGHATLGVYRQAMNSEngQNAIAAWTRHGQVKIVVKGQSTEQLMDLCKVAKDAGCYYYLV 281
Cdd:COG1990     4 KQVIVVRKDLKMSKGKLAAQVAHAAVSAALDALKKD--KEWFEEWKDEGQKKVVLKVNSEEELFELKEKAERLGLPTALI 81

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1831516897 282 QDAGYTQIPAGSRTVLGIF-GTVEQVDSVTGGLKLL 316
Cdd:COG1990    82 RDAGLTELEPGTVTCLGIGpAPEEKIDKITGDLKLL 117

peptidyl-tRNA hydrolase; This model describes an archaeal/eukaryotic form of peptidyl-tRNA hydrolase. Most bacterial forms are described by TIGR00447. [Protein synthesis, Other]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1831516897 202 KMVLVANMSLKMGTGKIAAQVGHATLGVYRQAMNSEngQNAIAAWTRHGQVKIVVKGQSTEQLMDLCKVAKDAGCYYYLV 281
Cdd:TIGR00283   2 KMVIVIRDDLGMGKGKIAAQVCHAAIIGFLKSKRKN--PSLRRKWLDEGQKKVVLKVNSLEELLEIYHKAESLGLVTGLI 79

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1831516897 282 QDAGYTQIPAGSRTVLGIfGTV--EQVDSVTGGLKLL 316
Cdd:TIGR00283  80 RDAGHTQIPPGTITAVGI-GPDedEKIDKITGDLKLL 115

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 1831516897 129 VNNEYLAHLLDLGFDEYTAVLALKRTNSaGVEQAVAWI 166
Cdd:pfam00627   1 EDEEAIQRLVEMGFDREQVREALRATGN-NVERAAEYL 37

UBA domain found in UBX domain-containing protein 1 (UBXN1) and similar proteins; UBXN1, also called SAPK substrate protein 1 (SAKS1) or UBA/UBX 33.3 kDa protein, is a widely expressed protein containing an N-terminal ubiquitin-associated (UBA) domain, a coiled-coil region, and a C-terminal ubiquitin-like (UBX) domain. It binds polyubiquitin and valosin-containing protein (VCP), and has been identified as a substrate for stress-activated protein kinases (SAPKs). Moreover, UBXN1 specifically binds to Homer2b. It may also interact with ubiquitin (Ub) and may be involved in the Ub-proteasome proteolytic pathways. In addition, UBXN1 can associate with autoubiquitinated BRCA1 tumor suppressor and inhibit its enzymatic function through its UBA domain.

                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1831516897 137 LLDLGFDEYTAVLALKRTNSAGVEQAVAWIVERSN 171
Cdd:cd14302     6 LIEMGFSRNRAEKALAKTGNQGVEAAMEWLLAHED 40

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 1831516897 134 LAHLLDLGFDEYTAVLALKRTNSaGVEQAVAWIVE 168
Cdd:cd14306     1 VAKLMELGFPEEDCIRALRACGG-NVEEAANWLLE 34

UBA1 domain found in Saccharomyces cerevisiae ubiquitin carboxyl-terminal hydrolase 14 (scUBP14) and similar proteins; scUBP14, also called deubiquitinating enzyme 14, glucose-induced degradation protein 6, ubiquitin thioesterase 14, or ubiquitin-specific-processing protease 14, is the yeast ortholog of human Isopeptidase T (USP5), a deubiquitinating enzyme known to bind the 29-linked polyubiquitin chains. scUBP14 has been identified as a K29-linked polyubiquitin binding protein as well. It is involved in K29-linked polyubiquitin metabolism by binding to the 29-linked Ub4 resin and serving as an internal positive control in budding yeast. Members in this family contain two tandem ubiquitin-association (UBA) domains. This model corresponds to the UBA1 domain.

                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1831516897 132 EYLAHLLDLGFDEYTAVLALKRTNSAGVEQAVAWIVE 168
Cdd:cd14296     2 EAVSQLMSMGFSENAAKRALYYTGNSSVEAAMNWLFE 38

UBA domain found in serine/threonine-protein kinase LATS and similar proteins; The LATS proteins family consists of two isoforms, LATS1 and LATS2, both of which are mammalian homologs of the Drosophila tumor suppressor gene lats/warts. LATS1, also called large tumor suppressor homolog 1, or WARTS protein kinase (warts), is a serine/threonine-protein kinase that highly conserved from fly to human. LATS2, also called kinase phosphorylated during mitosis protein, or large tumor suppressor homolog 2, or serine/threonine-protein kinase KPM, or Warts-like kinase, inhibits the G1/S transition and is essential for embryonic development, proliferation control and genomic integrity. LATS proteins contain an N-terminal ubiquitin-associated (UBA) domain and a C-terminal protein kinase domain.

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1831516897 131 NEYLAHLLDLGFDEYTAVLALKRTNSAGVEQAVAWI 166
Cdd:cd14322     1 NQMLQQLVAAGYSEEISMRALKKSGARTIEAAIEFI 36

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        30
                  ....*....|....*....|....*....|
gi 1831516897 134 LAHLLDLGFDEYTAVLALKRTNSaGVEQAV 163
Cdd:cd14270     1 LAQLVEMGFSREQARRALRATNG-DVEAAV 29