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8  structures 94  species 0  interactions 739  sequences 21  architectures

Family: FYVE_2 (PF02318)

Summary: FYVE-type zinc finger

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 "FYVE domain". More...

FYVE domain Edit Wikipedia article

FYVE zinc finger
1joc.png
Early endosome antigen 1 (EEA1) dimer with lipids.[1]
Identifiers
Symbol FYVE
Pfam PF01363
InterPro IPR000306
PROSITE PDOC50178
SCOP 1vfy
SUPERFAMILY 1vfy
OPM superfamily 62
OPM protein 1vfy
CDD cd00065

In molecular biology the FYVE zinc finger domain is named after the four cysteine-rich proteins: Fab 1 (yeast orthologue of PIKfyve), YOTB, Vac 1 (vesicle transport protein), and EEA1, in which it has been found. FYVE domains bind Phosphatidylinositol 3-phosphate,[2] in a way dependent on its metal ion coordination and basic amino acids. The FYVE domain inserts into cell membranes in a pH dependent manner.[3] The FYVE domain has been connected to vacuolar protein sorting and endosome function.[4]

Structure

The FYVE domain is composed of two small beta hairpins (or zinc knuckles) followed by an alpha helix.[5] The FYVE finger binds two zinc ions. The FYVE finger has eight potential zinc coordinating cysteine positions and is characterized by having basic amino acids around the cysteines. Many members of this family also include two histidines in a sequence motif:

R+HHC+XCG, where + represents a charged residue and X any residue

The FYVE finger is structurally similar to the RING domain and the PHD finger.

Examples

The following is a list of human proteins containing this domain:

References

  1. ^ Dumas JJ, Merithew E, Sudharshan E, et al. (November 2001). "Multivalent endosome targeting by homodimeric EEA1". Mol. Cell 8 (5): 947–58. doi:10.1016/S1097-2765(01)00385-9. PMID 11741531. 
  2. ^ Gaullier JM, Simonsen A, D'Arrigo A, Bremnes B, Stenmark H, Aasland R (July 1998). "FYVE fingers bind PtdIns(3)P". Nature 394 (6692): 432–3. doi:10.1038/28767. PMID 9697764. 
  3. ^ He J, Vora M, Haney RM, et al. (September 2009). "Membrane insertion of the FYVE domain is modulated by pH". Proteins 76 (4): 852–60. doi:10.1002/prot.22392. PMC 2909462. PMID 19296456. 
  4. ^ Leevers SJ, Vanhaesebroeck B, Waterfield MD (April 1999). "Signalling through phosphoinositide 3-kinases: the lipids take centre stage". Curr. Opin. Cell Biol. 11 (2): 219–25. doi:10.1016/S0955-0674(99)80029-5. PMID 10209156. 
  5. ^ Misra S, Hurley JH (May 1999). "Crystal structure of a phosphatidylinositol 3-phosphate-specific membrane-targeting motif, the FYVE domain of Vps27p". Cell 97 (5): 657–66. doi:10.1016/S0092-8674(00)80776-X. PMID 10367894. 

Further reading

  • Stenmark H, Aasland R, Toh BH, D'Arrigo A (September 1996). "Endosomal localization of the autoantigen EEA1 is mediated by a zinc-binding FYVE finger". J. Biol. Chem. 271 (39): 24048–54. doi:10.1074/jbc.271.39.24048. PMID 8798641.  edit
  • Stenmark H, Aasland R (December 1999). "FYVE-finger proteins--effectors of an inositol lipid". J. Cell. Sci. 112 (Pt 23): 4175–83. PMID 10564636.  edit

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.

FYVE-type zinc finger Provide feedback

This FYVE-type zinc finger is found at the N-terminus of effector proteins including rabphilin-3A [1] and regulating synaptic membrane exocytosis protein 2 [2].

Literature references

  1. Ostermeier C, Brunger AT; , Cell 1999;96:363-374.: Structural basis of Rab effector specificity: crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A. PUBMED:10025402 EPMC:10025402

  2. Lu J, Machius M, Dulubova I, Dai H, Sudhof TC, Tomchick DR, Rizo J;, PLoS Biol. 2006;4:e192.: Structural basis for a Munc13-1 homodimer to Munc13-1/RIM heterodimer switch. PUBMED:16732694 EPMC:16732694


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003315

This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [PUBMED:10025402].

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 zf-FYVE-PHD (CL0390), which has the following description:

Superfamily contains a number of zinc-fingers, of the FYVE/PHD type, which are found in several groups of proteins including myelin-associated oligodendrocytic basic proteins (MOBP) Rabphilins, melanophilins, exophilins and myosin-VIIA and Rab-interacting protein families.

The clan contains the following 9 members:

FYVE FYVE_2 PHD PHD_2 RAG2_PHD zf-HC5HC2H zf-HC5HC2H_2 zf-PHD-like zf-piccolo

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...

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
(21)
Full
(739)
Representative proteomes NCBI
(696)
Meta
(0)
RP15
(57)
RP35
(84)
RP55
(185)
RP75
(344)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(21)
Full
(739)
Representative proteomes NCBI
(696)
Meta
(0)
RP15
(57)
RP35
(84)
RP55
(185)
RP75
(344)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(21)
Full
(739)
Representative proteomes NCBI
(696)
Meta
(0)
RP15
(57)
RP35
(84)
RP55
(185)
RP75
(344)
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.

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.

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: Jackhmmer:Q13875
Previous IDs: RPH3A_effector; RPH3A_effect_N;
Type: Family
Author: Mian N, Bateman A, Eberhardt R
Number in seed: 21
Number in full: 739
Average length of the domain: 106.60 aa
Average identity of full alignment: 29 %
Average coverage of the sequence by the domain: 14.78 %

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 27.0 27.0
Trusted cut-off 27.0 27.0
Noise cut-off 26.9 26.9
Model length: 118
Family (HMM) version: 11
Download: download the raw HMM for this family

Species distribution

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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 FYVE_2 domain has been found. There are 8 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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