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{
"metadata": {
"accession": "IPR003123",
"entry_id": null,
"type": "domain",
"go_terms": null,
"source_database": "interpro",
"member_databases": {
"profile": {
"PS51205": "VPS9 domain profile"
},
"smart": {
"SM00167": "Domain present in VPS9"
},
"pfam": {
"PF02204": "Vacuolar sorting protein 9 (VPS9) domain"
}
},
"integrated": null,
"hierarchy": {
"accession": "IPR003123",
"name": "VPS9 domain",
"type": "Domain",
"children": []
},
"name": {
"name": "VPS9 domain",
"short": "VPS9"
},
"description": [
{
"text": "<p>Rab proteins form a family of signal-transducing GTPases that cycle between\nactive GTP-bound and inactive GDP-bound forms. The Rab5 GTPase is an essential\nregulator of endocytosis and endosome biogenesis. Rab5 is activated by GDP-GTP\nexchange factors (GEFs) that contain a VPS9 domain and generate the Rab5-GTP\ncomplex [[cite:PUB00033760]].</p>",
"llm": false,
"checked": false,
"updated": false
},
{
"text": "<p>The VPS9 domain catalyzes nucleotide exchange on Rab5 or the yeast homologue VPS21. The domain has a length of ~140 residues and forms the central part of the yeast VPS9 (vacuolar protein sorting-associated) protein, which acts as a GEF for VPS21. Some domains which can occur in combination with the VPS9 domain are CUE, A20-type zinc finger, Ras-associating (RA), SH2, RCC1, DH, PH, rasGAP, MORN and ankyrin repeat.</p>\n\n<p>Structurally, the VPS9 domain adopts a layered fold of six α helices. Conserved residues from the fourth and sixth helices and the loops N-terminal to these helices form the surface that interacts with Rab5 and Rab21 [[cite:PUB00031605]].</p>\n\n<p>Some proteins known to contain a VPS9 domain:</p>\n\n<ul>\n\n<li>Fungal Vacuolar Protein Sorting-associated protein VPS9, a guanine nucleotide exchange factor for the Rab-like GTPase VPS21. VPS9 is needed for the transport of proteins from biosynthetic and endocytic pathways into the vacuole.</li>\n\n<li>Mammalian Rab5 GDP/GTP exchange factor or Rabex-5 (Rababtin-5 associated exchange factor for Rab5), catalyzes nucleotide exchange on RAB5A. Rabex-5 promotes endocytic membrane fusion and is involved in membrane trafficking of recycling endosomes.</li>\n\n<li>Mammalian Ras and Rab interactor 1 (RIN1), 2 (RIN2) and 3 (RIN3).</li>\n\n<li>Mammalian alsin or Amyotrophic Lateral Sclerosis protein 2 (ALS2). Different juvenile-onset forms of neurodegenerative diseases (ALS2, JPLS, IAHSP) are caused by mutations in the ALS2 gene, which result in truncated alsin lacking the C-terminal part of the VPS9 domain.</li>\n\n<li>Fruit fly protein sprint, which is a RIN homologue.</li>\n\n<li>Caenorhabditis elegans RME-6 protein, which is conserved among metazoans.</li>\n\n</ul>",
"llm": false,
"checked": false,
"updated": false
}
],
"wikipedia": null,
"literature": {
"PUB00033760": {
"PMID": 16330212,
"ISBN": null,
"volume": "16",
"issue": "1",
"year": 2006,
"title": "Vps9 domain-containing proteins: activators of Rab5 GTPases from yeast to neurons.",
"URL": null,
"raw_pages": "27-35",
"medline_journal": "Trends Cell Biol",
"ISO_journal": "Trends Cell Biol.",
"authors": [
"Carney DS",
"Davies BA",
"Horazdovsky BF."
],
"DOI_URL": "http://dx.doi.org/10.1016/j.tcb.2005.11.001"
},
"PUB00031605": {
"PMID": 15339665,
"ISBN": null,
"volume": "118",
"issue": "5",
"year": 2004,
"title": "Structure, exchange determinants, and family-wide rab specificity of the tandem helical bundle and Vps9 domains of Rabex-5.",
"URL": null,
"raw_pages": "607-17",
"medline_journal": "Cell",
"ISO_journal": "Cell",
"authors": [
"Delprato A",
"Merithew E",
"Lambright DG."
],
"DOI_URL": "http://dx.doi.org/10.1016/j.cell.2004.08.009"
}
},
"set_info": null,
"overlaps_with": [
{
"accession": "IPR037191",
"name": "VPS9 domain superfamily",
"type": "homologous_superfamily"
}
],
"counters": {
"subfamilies": 0,
"domain_architectures": 672,
"interactions": 1,
"matches": 24381,
"pathways": 20,
"proteins": 24379,
"proteomes": 3367,
"sets": 0,
"structural_models": {
"alphafold": 16643,
"bfvd": 0
},
"structures": 9,
"taxa": 9539
},
"entry_annotations": {
"alignment:seed": 43,
"alignment:full": 16061
},
"cross_references": {
"prositedoc": {
"displayName": "PROSITE Doc",
"description": "PROSITE is a database of protein families and domains.",
"rank": 18,
"accessions": [
{
"accession": "PDOC51205",
"url": "http://prosite.expasy.org/PDOC51205"
}
]
}
},
"is_llm": false,
"is_reviewed_llm": false,
"is_updated_llm": false,
"representative_structure": null
}
}
