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15  structures 141  species 2  interactions 996  sequences 80  architectures

Family: WHEP-TRS (PF00458)

Summary: WHEP-TRS domain

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This is the Wikipedia entry entitled "WHEP-TRS protein domain". More...

WHEP-TRS protein domain Edit Wikipedia article

WHEP-TRS
PDB 1fyj EBI.jpg
Solution structure of multi-functional peptide motif-1 present in human glutamyl-prolyl tRNA synthetase (eprs).
Identifiers
Symbol WHEP-TRS
Pfam PF00458
InterPro IPR000738
PROSITE PDOC00614
SCOP 1gtr
SUPERFAMILY 1gtr

In molecular biology, the protein domain WHEP-TRS refers to helix-turn-helix domains. They are found in variable numbers in a particularly common protein, named, glutamyl-prolyl tRNA synthetase(EPRS). This protein domain has an important function in protein–protein interactions between synthetases. WHEP domains exhibit high-affinity interactions with tRNA, indicating a putative evolutionary relationship to facilitate tRNA binding to fused synthetases, thereby enhancing catalytic efficiency.[1]

Protein interactions

EPRS is a component of the interferon-gamma-activated inhibitor of translation (GAIT) complex, which interacts with stem-loop elements (GAIT elements) in mRNAs encoding proinflammatory proteins, for example, vascular endothelial growth factor-A (VEGFA). WHEP domains interact with the GAIT element in the 3′UTR of target mRNAs and with the regulatory protein NS1-associated protein-1 (NSAP1).[1]

Structure

A conserved domain of 46 amino acids, called WHEP-TRS has been shown[2] to exist in a number of higher eukaryote aminoacyl-transfer RNA synthetases. This domain is present one to six times in several enzymes. There are three copies in mammalian aminoacyl-tRNA synthetase in a region that separates the N-terminal glutamyl-tRNA synthetase domain from the C-terminal prolyl-tRNA synthetase domain, and six copies in the intercatalytic region of the Drosophila enzyme. The domain is found at the N-terminal extremity of the mammalian tryptophanyl- tRNA synthetase and histidyl-tRNA synthetase, and the mammalian, insect, nematode and plant glycyl- tRNA synthetases.[3]

References

  1. ^ a b Ray PS, Sullivan JC, Jia J, Francis J, Finnerty JR, Fox PL (2011). "Evolution of function of a fused metazoan tRNA synthetase.". Mol Biol Evol 28 (1): 437–47. doi:10.1093/molbev/msq246. PMC 3002251. PMID 20829344. 
  2. ^ Cerini C, Kerjan P, Astier M, Gratecos D, Mirande M, Sémériva M (December 1991). "A component of the multisynthetase complex is a multifunctional aminoacyl-tRNA synthetase". EMBO J. 10 (13): 4267–77. PMC 453179. PMID 1756734. 
  3. ^ Nada S, Chang PK, Dignam JD (April 1993). "Primary structure of the gene for glycyl-tRNA synthetase from Bombyx mori". J. Biol. Chem. 268 (11): 7660–7. PMID 8463296. 

This article incorporates text from the public domain Pfam and InterPro IPR000738

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External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000738

A conserved domain of 46 amino acids, called WHEP-TRS has been shown [PUBMED:1756734] to exist in a number of higher eukaryote aminoacyl-transfer RNA synthetases. This domain is present one to six times in the several enzymes. There are three copies in mammalian multifunctional aminoacyl-tRNA synthetase in a region that separates the N-terminal glutamyl-tRNA synthetase domain from the C-terminal prolyl-tRNA synthetase domain, and six copies in the intercatalytic region of the Drosophila enzyme. The domain is found at the N-terminal extremity of the mammalian tryptophanyl- tRNA synthetase and histidyl-tRNA synthetase, and the mammalian, insect, nematode and plant glycyl- tRNA synthetases [PUBMED:8463296]. The structure of a human WHEP-TRS domain has been solved and consists of two helices arranged in a helix-turn-helix [PUBMED:11123902]. The WHEP-TRS domain may play a role in the association of tRNA-synthetases into multienzyme complexes [PUBMED:9556618].

Gene Ontology

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Domain organisation

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

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Alignments

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(8)
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(175)
RP35
(232)
RP55
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RP75
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  Seed
(65)
Full
(996)
Representative proteomes NCBI
(981)
Meta
(8)
RP15
(175)
RP35
(232)
RP55
(425)
RP75
(582)
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  Seed
(65)
Full
(996)
Representative proteomes NCBI
(981)
Meta
(8)
RP15
(175)
RP35
(232)
RP55
(425)
RP75
(582)
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.

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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.

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Curation and family details

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Curation View help on the curation process

Seed source: Prosite
Previous IDs: none
Type: Family
Author: Finn RD
Number in seed: 65
Number in full: 996
Average length of the domain: 55.30 aa
Average identity of full alignment: 39 %
Average coverage of the sequence by the domain: 11.86 %

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 27.3 27.3
Trusted cut-off 27.3 27.5
Noise cut-off 27.2 27.2
Model length: 56
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 2 interactions for this family. More...

tRNA-synt_1b tRNA-synt_2b

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 WHEP-TRS domain has been found. There are 15 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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