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Conserved domains on  [gi|18423499|ref|NP_568790|]
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Ubiquitin-associated/translation elongation factor EF1B protein [Arabidopsis thaliana]

Protein Classification

UBA domain-containing protein( domain architecture ID 229521)

ubiquitin-associated (UBA) domain-containing protein

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
UBA_like_SF super family cl21463
UBA domain-like superfamily; The ubiquitin-associated (UBA) domain-like superfamily contains ...
181-217 5.74e-07

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.


The actual alignment was detected with superfamily member cd14316:

Pssm-ID: 473871  Cd Length: 37  Bit Score: 44.83  E-value: 5.74e-07
                        10        20        30
                ....*....|....*....|....*....|....*..
gi 18423499 181 FANGFTAIREMGFPTNAVADALFMFENDTDKALAHLL 217
Cdd:cd14316   1 FLKLLNQLHELGFPEDKIKEALLKHNNDRDKALDELV 37
 
Name Accession Description Interval E-value
UBA2_UBAP1_like cd14316
UBA2 domain found in ubiquitin-associated protein 1 (UBAP-1) and similar proteins; UBAP-1, ...
181-217 5.74e-07

UBA2 domain found in ubiquitin-associated protein 1 (UBAP-1) and similar proteins; UBAP-1, also called nasopharyngeal carcinoma-associated gene 20 protein, is a ubiquitously expressed protein that may play an important role in the ubiquitin pathway and cell progression. It co-localizes with TDP-43 proteins in neuronal cytoplasmic inclusions and acts as a genetic risk factor for frontotemporal lobar degeneration (FTLD). Moreover, UBAP-1, together with VPS37A, forms an endosome-specific endosomal sorting complexes I required for transport (ESCRT-I) complex that displays a restricted cellular function, ubiquitin-dependent endosomal sorting and multivesicular body (MVB) biogenesis. UBAP-1 contains an N-terminal UBAP-1-MVB12-associated (UMA) domain, and two tandem ubiquitin-associated (UBA) domains that may be responsible for the binding of ubiquitin-conjugating enzymes. This model corresponds to UBA2 domain.


Pssm-ID: 270501  Cd Length: 37  Bit Score: 44.83  E-value: 5.74e-07
                        10        20        30
                ....*....|....*....|....*....|....*..
gi 18423499 181 FANGFTAIREMGFPTNAVADALFMFENDTDKALAHLL 217
Cdd:cd14316   1 FLKLLNQLHELGFPEDKIKEALLKHNNDRDKALDELV 37
 
Name Accession Description Interval E-value
UBA2_UBAP1_like cd14316
UBA2 domain found in ubiquitin-associated protein 1 (UBAP-1) and similar proteins; UBAP-1, ...
181-217 5.74e-07

UBA2 domain found in ubiquitin-associated protein 1 (UBAP-1) and similar proteins; UBAP-1, also called nasopharyngeal carcinoma-associated gene 20 protein, is a ubiquitously expressed protein that may play an important role in the ubiquitin pathway and cell progression. It co-localizes with TDP-43 proteins in neuronal cytoplasmic inclusions and acts as a genetic risk factor for frontotemporal lobar degeneration (FTLD). Moreover, UBAP-1, together with VPS37A, forms an endosome-specific endosomal sorting complexes I required for transport (ESCRT-I) complex that displays a restricted cellular function, ubiquitin-dependent endosomal sorting and multivesicular body (MVB) biogenesis. UBAP-1 contains an N-terminal UBAP-1-MVB12-associated (UMA) domain, and two tandem ubiquitin-associated (UBA) domains that may be responsible for the binding of ubiquitin-conjugating enzymes. This model corresponds to UBA2 domain.


Pssm-ID: 270501  Cd Length: 37  Bit Score: 44.83  E-value: 5.74e-07
                        10        20        30
                ....*....|....*....|....*....|....*..
gi 18423499 181 FANGFTAIREMGFPTNAVADALFMFENDTDKALAHLL 217
Cdd:cd14316   1 FLKLLNQLHELGFPEDKIKEALLKHNNDRDKALDELV 37
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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