Summary: UBA/TS-N domain
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UBA protein domain Edit Wikipedia article
elongation factor complex ef-tu/ef-ts from escherichia coli
In molecular biology, the protein domain UBA is short for ubiquitin-associated domains. Ubiquitin is a signal added to an incorrectly folded protein, which allows it to be degraded by the proteasome, and the amino acid constituents can be recycled. It is thought to be encoded for by STS-1 gene in humans.
This family of proteins is involved in a variety of additional cell processes, such as nucleotide excision repair (NER), spindle pole body duplication, and cell growth.
Protein degradation via the ubiquitin proteasome system (UPS) allows the cell to selectively negatively regulate intracellular proteins. Protein degradation helps to maintain protein quality control, signalling, and cell cycle progression. UBA has be proposed to limit ubiquitin chain elongation and to target polyubiquitinated proteins to the 26S proteasome for degradation.They have been identified in modular proteins involved in protein trafficking, DNA repair, proteasomal degradation, and cell cycle regulation. UBA bind to ubiquitin and aids all the cellular processes involved with ubiquitin; this includes:
- Antigen processing
- Biogenesis of organelles
- Cell cycle and division
- DNA transcription and DNA repair
- Differentiation and development
- Immune response and inflammation
- Neural and muscular degeneration
- Morphogenesis of neural networks
- Modulation of cell surface receptors, ion channels and the secretory pathway
- Response to stress and extracellular modulators
- Ribosome biogenesis
- Viral infection
The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle.
Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin.
More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors .
- Su V, Lau AF (2009). "Ubiquitin-like and ubiquitin-associated domain proteins: significance in proteasomal degradation.". Cell Mol Life Sci 66 (17): 2819–33. doi:10.1007/s00018-009-0048-9. PMC 2725189. PMID 19468686.
- Gomez TA, Kolawa N, Gee M, Sweredoski MJ, Deshaies RJ (2011). "Identification of a functional docking site in the Rpn1 LRR domain for the UBA-UBL domain protein Ddi1.". BMC Biol 9: 33. doi:10.1186/1741-7007-9-33. PMC 3126750. PMID 21627799.
- Tse MK, Hui SK, Yang Y, Yin ST, Hu HY, Zou B et al. (2011). "Structural analysis of the UBA domain of X-linked inhibitor of apoptosis protein reveals different surfaces for ubiquitin-binding and self-association.". PLoS ONE 6 (12): e28511. doi:10.1371/journal.pone.0028511. PMC 3240630. PMID 22194841.
- Li J, Chu H, Zhang Y, Mou T, Wu C, Zhang Q et al. (2012). "The rice HGW gene encodes a ubiquitin-associated (UBA) domain protein that regulates heading date and grain weight.". PLoS ONE 7 (3): e34231. doi:10.1371/journal.pone.0034231. PMC 3311617. PMID 22457828.
- Hofmann K, Bucher P (May 1996). "The UBA domain: a sequence motif present in multiple enzyme classes of the ubiquitination pathway". Trends Biochem. Sci. 21 (5): 172–3. doi:10.1016/S0968-0004(96)30015-7. PMID 8871400.
- Dieckmann T, Withers-Ward ES, Jarosinski MA, Liu CF, Chen IS, Feigon J (December 1998). "Structure of a human DNA repair protein UBA domain that interacts with HIV-1 Vpr". Nat. Struct. Biol. 5 (12): 1042–7. doi:10.1038/4220. PMID 9846873.
- Mueller TD, Feigon J (June 2002). "Solution structures of UBA domains reveal a conserved hydrophobic surface for protein-protein interactions". J. Mol. Biol. 319 (5): 1243–55. doi:10.1016/S0022-2836(02)00302-9. PMID 12079361.
UBA/TS-N domain Provide feedback
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 P70670 and MJ0280 Q57728 .
Dieckmann T, Withers-Ward ES, Jarosinski MA, Liu CF, Chen IS, Feigon J; , Nat Struct Biol 1998;5:1042-1047.: Structure of a human DNA repair protein UBA domain that interacts with HIV-1 Vpr. PUBMED:9846873 EPMC:9846873
Makarova KS, Aravind L, Galperin MY, Grishin NV, Tatusov RL, Wolf YI, Koonin EV; , Genome Res 1999;9:608-628.: Comparative genomics of the Archaea (Euryarchaeota): evolution of conserved protein families, the stable core, and the variable shell. PUBMED:10413400 EPMC:10413400
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR000449
UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases [PUBMED:8871400]. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle [PUBMED:9846873]. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin [PUBMED:12079361].
This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts.
More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [PUBMED:].
|Molecular function||protein binding (GO:0005515)|
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Curation and family details
|Seed source:||Bateman A|
|Number in seed:||141|
|Number in full:||9566|
|Average length of the domain:||37.30 aa|
|Average identity of full alignment:||34 %|
|Average coverage of the sequence by the domain:||8.50 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||26|
|Download:||download the raw HMM for this family|
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There are 6 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the UBA domain has been found. There are 104 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
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