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104  structures 4854  species 6  interactions 9566  sequences 206  architectures

Family: UBA (PF00627)

Summary: UBA/TS-N domain

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This is the Wikipedia entry entitled "UBA protein domain". More...

UBA protein domain Edit Wikipedia article

UBA
PDB 1efu EBI.jpg
elongation factor complex ef-tu/ef-ts from escherichia coli
Identifiers
Symbol UBA
Pfam PF00627
Pfam clan CL0214
InterPro IPR000449
PROSITE PDOC50030
SCOP 1efu
SUPERFAMILY 1efu
CDD cd00194

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.

Function[edit]

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.[1]

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.[2][3] UBA has be proposed to limit ubiquitin chain elongation and to target polyubiquitinated proteins to the 26S proteasome for degradation.[4]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:

Localisation[edit]

The ubiquitin-associated (UBA) protein domain is found to be localized in the cytoplasm and nucleus.[4]

Structure[edit]

UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues.[5]

Examples[edit]

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.[6]

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.[7]

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 .

References[edit]

  1. ^ 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. 
  2. ^ 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. 
  3. ^ 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. 
  4. ^ a b 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. 
  5. ^ 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. 
  6. ^ 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. 
  7. ^ 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. 

This article incorporates text from the public domain Pfam and InterPro IPR000449

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

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 [1]. 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 [2]. The domain has been found in non EF-TS proteins such as alpha-NAC P70670 and MJ0280 Q57728 [1].

Literature references

  1. 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

  2. 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

  3. Kawashima T, Berthet-Colominas C, Wulff M, Cusack S, Leberman R; , Nature 1996;379:511-518.: The structure of the Escherichia coli EF-Tu.EF-Ts complex at 2.5 A resolution. PUBMED:8596629 EPMC:8596629


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:].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan UBA (CL0214), which has the following description:

This superfamily includes domains related to the UBA domain. These domains are often involved in ubiquitin binding.

The clan contains the following 9 members:

CUE DMA DUF1296 RuvA_C TAP_C UBA UBA_2 UBA_3 UBA_4

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(141)
Full
(9566)
Representative proteomes NCBI
(7764)
Meta
(1831)
RP15
(1308)
RP35
(2242)
RP55
(3222)
RP75
(4154)
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Format an alignment

  Seed
(141)
Full
(9566)
Representative proteomes NCBI
(7764)
Meta
(1831)
RP15
(1308)
RP35
(2242)
RP55
(3222)
RP75
(4154)
Alignment:
Format:
Order:
Sequence:
Gaps:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(141)
Full
(9566)
Representative proteomes NCBI
(7764)
Meta
(1831)
RP15
(1308)
RP35
(2242)
RP55
(3222)
RP75
(4154)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Bateman A
Previous IDs: none
Type: Domain
Author: 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 information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.1 21.1
Trusted cut-off 21.1 21.1
Noise cut-off 21.0 21.0
Model length: 37
Family (HMM) version: 26
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 6 interactions for this family. More...

ubiquitin EF_TS UBA GTP_EFTU UQ_con Pkinase

Structures

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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