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48  structures 287  species 2  interactions 1706  sequences 40  architectures

Family: VHS (PF00790)

Summary: VHS domain

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

VHS protein domain Edit Wikipedia article

VHS
PDB 1dvp EBI.jpg
crystal structure of the vhs and fyve tandem domains of hrs, a protein involved in membrane trafficking and signal transduction
Identifiers
Symbol VHS
Pfam PF00790
Pfam clan CL0009
InterPro IPR002014
SMART VHS
SCOP 1elk
SUPERFAMILY 1elk

In molecular biology, the VHS protein domain is approximately 140 residues long. Its name is an acronym derived from its occurrence in VPS-27, Hrs and STAM. It is a domain commonly found in the N-terminus of many proteins.[1]

Function[edit]

VHS domains thought to be very important in vesicular trafficking, in particular, aiding membrane targeting and cargo recognition role.[1]

Structure[edit]

Resolution of the crystal structure of the VHS domain of Drosophila Hrs and human Tom1 revealed that it consists of eight helices arranged in a double-layer superhelix.[2] The existence of conserved patches of residues on the domain surface suggests that VHS domains may be involved in protein-protein recognition and docking. Overall, sequence similarity is low (approx 25%) amongst domain family members.

Classification[edit]

Based on regions surrounding the domain, VHS-proteins can be divided into 4 groups:[1]

  • STAM/EAST/Hbp which all share the domain composition VHS-SH3-ITAM and carry one or two ubiquitin-interacting motifs
  • VHS domain alone or in combination with domains other than those listed above The VHS domain is always found at the N- terminus of proteins suggesting that such topology is important for function. The domain is considered to have a general membrane targeting/cargo recognition role in vesicular trafficking.[3]

References[edit]

  1. ^ a b c Lohi O, Poussu A, Mao Y, Quiocho F, Lehto VP (2002). "VHS domain -- a longshoreman of vesicle lines.". FEBS Lett 513 (1): 19–23. PMID 11911875. 
  2. ^ Mao Y, Nickitenko A, Duan X, Lloyd TE, Wu MN, Bellen H, Quiocho FA (February 2000). "Crystal structure of the VHS and FYVE tandem domains of Hrs, a protein involved in membrane trafficking and signal transduction". Cell 100 (4): 447–56. doi:10.1016/S0092-8674(00)80680-7. PMID 10693761. 
  3. ^ Misra S, Beach BM, Hurley JH (September 2000). "Structure of the VHS domain of human Tom1 (target of myb 1): insights into interactions with proteins and membranes". Biochemistry 39 (37): 11282–90. doi:10.1021/bi0013546. PMID 10985773. 

This article incorporates text from the public domain Pfam and InterPro IPR002014

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VHS domain Provide feedback

Domain present in VPS-27, Hrs and STAM.

Literature references

  1. Mao Y, Nickitenko A, Duan X, Lloyd TE, Wu MN, Bellen H, Quiocho FA; , Cell 2000;100:447-456.: Crystal structure of the VHS and FYVE tandem domains of Hrs, a protein involved in membrane trafficking and signal transduction. PUBMED:10693761 EPMC:10693761

  2. Lohi O, Lehto VP; , FEBS Lett 1998;440:255-257.: VHS domain marks a group of proteins involved in endocytosis and vesicular trafficking. PUBMED:9872381 EPMC:9872381


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002014

The VHS domain is a ~140 residues long domain, whose name is derived from its occurrence in VPS-27, Hrs and STAM. Based on regions surrounding the domain, VHS-proteins can be divided into 4 groups [PUBMED:11911875]:

  • STAM/EAST/Hbp which all share the domain composition VHS-SH3-ITAM and carry one or two ubiquitin-interacting motifs
  • Proteins with a FYVE domain (INTERPRO) C-terminal to VHS which also carry one or two ubiquitin-interacting motifs
  • GGA proteins with a domain composition VHS-GAT (GGA and Tom1) homology domain
  • VHS domain alone or in combination with domains other than those listed above
The VHS domain is always found at the N- terminus of proteins suggesting that such topology is important for function. The domain is considered to have a general membrane targeting/cargo recognition role in vesicular trafficking [PUBMED:10985773].

Resolution of the crystal structure of the VHS domain of Drosophila Hrs and human Tom1 revealed that it consists of eight helices arranged in a double-layer superhelix [PUBMED:10693761]. The existence of conserved patches of residues on the domain surface suggests that VHS domains may be involved in protein-protein recognition and docking. Overall, sequence similarity is low (approx 25%) amongst domain family members.

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 ENTH_VHS (CL0009), which contains the following 3 members:

ANTH ENTH VHS

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
(15)
Full
(1706)
Representative proteomes NCBI
(1655)
Meta
(5)
RP15
(272)
RP35
(484)
RP55
(768)
RP75
(1025)
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Format an alignment

  Seed
(15)
Full
(1706)
Representative proteomes NCBI
(1655)
Meta
(5)
RP15
(272)
RP35
(484)
RP55
(768)
RP75
(1025)
Alignment:
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Order:
Sequence:
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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
(15)
Full
(1706)
Representative proteomes NCBI
(1655)
Meta
(5)
RP15
(272)
RP35
(484)
RP55
(768)
RP75
(1025)
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

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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.

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: Alignment kindly provided by SMART
Previous IDs: none
Type: Family
Author: SMART
Number in seed: 15
Number in full: 1706
Average length of the domain: 130.70 aa
Average identity of full alignment: 28 %
Average coverage of the sequence by the domain: 24.38 %

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 20.6 20.6
Trusted cut-off 20.6 20.6
Noise cut-off 20.5 20.5
Model length: 141
Family (HMM) version: 14
Download: download the raw HMM for this family

Species distribution

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Interactions

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

VHS FYVE

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 VHS domain has been found. There are 48 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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