!!

Powering down the Pfam website
On October 5th, we began redirecting traffic from Pfam (pfam.xfam.org) to InterPro (www.ebi.ac.uk/interpro). The Pfam website will remain available at pfam-legacy.xfam.org until January 2023, when it will be decommissioned. You can read more about the sunset period in our blog post.

Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
25  structures 756  species 0  interactions 5653  sequences 191  architectures

Family: WHEP-TRS (PF00458)

Summary: WHEP-TRS domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

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
SymbolWHEP-TRS
PfamPF00458
InterProIPR000738
PROSITEPDOC00614
SCOP21gtr / SCOPe / SUPFAM

Function

WHEP-TRS domains are helix-turn-helix domains. They are found in variable number in the glutamyl-prolyl tRNA synthetase(EPRS) proteins. They have 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.{{cite journal}}: CS1 maint: PMC format (link) CS1 maint: multiple names: authors list (link)
  2. ^ Cerini C, Kerjan P, Astier M, Gratecos D, Mirande M, Sémériva M (1991). "A component of the multisynthetase complex is a multifunctional aminoacyl-tRNA synthetase". EMBO J. 10 (13): 4267–77. PMC 453179. PMID 1756734. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  3. ^ Nada S, Chang PK, Dignam JD (1993). "Primary structure of the gene for glycyl-tRNA synthetase from Bombyx mori". J. Biol. Chem. 268 (11): 7660–7. PMID 8463296. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
This article incorporates text from the public domain Pfam and InterPro: IPR000738

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.

WHEP-TRS domain Provide feedback

No Pfam abstract.

Internal database links

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

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...

Loading domain graphics...

Pfam Clan

This family is a member of clan S15_NS1 (CL0600), which has the following description:

The clan contains the following 4 members:

Flu_B_NS1 Flu_NS1 Ribosomal_S15 WHEP-TRS

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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

View options

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
(158)
Full
(5653)
Representative proteomes UniProt
(9124)
RP15
(942)
RP35
(2015)
RP55
(4370)
RP75
(5744)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(158)
Full
(5653)
Representative proteomes UniProt
(9124)
RP15
(942)
RP35
(2015)
RP55
(4370)
RP75
(5744)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

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
(158)
Full
(5653)
Representative proteomes UniProt
(9124)
RP15
(942)
RP35
(2015)
RP55
(4370)
RP75
(5744)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

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: Prosite
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD
Number in seed: 158
Number in full: 5653
Average length of the domain: 52.3 aa
Average identity of full alignment: 42 %
Average coverage of the sequence by the domain: 10.64 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 32.5 32.5
Trusted cut-off 32.5 32.5
Noise cut-off 32.4 32.4
Model length: 53
Family (HMM) version: 23
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

Generate a FASTA-format file

Clear selection

This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

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 25 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 sequence.

Loading structure mapping...

AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A044V7D6 View 3D Structure Click here
A0A0G2JZI2 View 3D Structure Click here
A0A0J9Y825 View 3D Structure Click here
A0A0K0EAL6 View 3D Structure Click here
A0A0K0JKQ8 View 3D Structure Click here
A0A0N4UDS7 View 3D Structure Click here
A0A0R0EX16 View 3D Structure Click here
A0A158N7S1 View 3D Structure Click here
A0A3P7EDA8 View 3D Structure Click here
A0A3P7GDV2 View 3D Structure Click here
A0A3P7SWJ7 View 3D Structure Click here
A0A3Q0KEV1 View 3D Structure Click here
A0A5S6PRE1 View 3D Structure Click here
A1ZBE9 View 3D Structure Click here
D3Z941 View 3D Structure Click here
E9QI36 View 3D Structure Click here
F1QFL1 View 3D Structure Click here
F1QP23 View 3D Structure Click here
F1QUV7 View 3D Structure Click here
I1KZJ9 View 3D Structure Click here
O23627 View 3D Structure Click here
O43011 View 3D Structure Click here
P07178 View 3D Structure Click here
P07814 View 3D Structure Click here
P12081 View 3D Structure Click here
P17248 View 3D Structure Click here
P23381 View 3D Structure Click here
P23612 View 3D Structure Click here
P28668 View 3D Structure Click here
P32921 View 3D Structure Click here
P41250 View 3D Structure Click here
P56192 View 3D Structure Click here
Q04451 View 3D Structure Click here
Q10039 View 3D Structure Click here
Q22620 View 3D Structure Click here
Q23315 View 3D Structure Click here
Q2KI84 View 3D Structure Click here
Q2T9L8 View 3D Structure Click here
Q4QQV4 View 3D Structure Click here
Q5I0G4 View 3D Structure Click here