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IPR003123 is a VPS9 domain.
<p>Rab proteins form a family of signal-transducing GTPases that cycle between active GTP-bound and inactive GDP-bound forms. The Rab5 GTPase is an essential regulator of endocytosis and endosome biogenesis. Rab5 is activated by GDP-GTP exchange factors (GEFs) that contain a VPS9 domain and generate the Rab5-GTP complex [[cite:PUB00033760]].</p> <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> <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> <p>Some proteins known to contain a VPS9 domain:</p> <ul> <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> <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> <li>Mammalian Ras and Rab interactor 1 (RIN1), 2 (RIN2) and 3 (RIN3).</li> <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> <li>Fruit fly protein sprint, which is a RIN homologue.</li> <li>Caenorhabditis elegans RME-6 protein, which is conserved among metazoans.</li> </ul>
This description is obtained from EB-eye REST.
| Transcript | Name | Description | Predicted domains | Domain count |
|---|---|---|---|---|
| – | Rab5 GDP/GTP exchange factor [Medicago truncatula] gi|357455969|ref|XP_003598265.1| | 7 | ||
| – | PREDICTED: vacuolar protein sorting-associated protein 9A-like [Glycine max] gi|356515841|ref|XP_003526606.1| | 8 | ||
| – | Vacuolar protein sorting-associated protein 9A; TAIR: AT3G19770.1 Vacuolar sorting protein 9 (VPS9) domain-containing protein; Swiss-Prot: sp|Q9LT31|VPS9A_ARATH Vacuolar protein sorting-associated protein 9A; TrEMBL-Plants: tr|I1KA37|I1KA37_SOYBN Uncharacterized protein; Found in the gene: LotjaGi1g1v0249600 | 13 | ||
| – | Vacuolar protein sorting-associated protein 9A; TAIR: AT3G19770.1 Vacuolar sorting protein 9 (VPS9) domain-containing protein; Swiss-Prot: sp|Q9LT31|VPS9A_ARATH Vacuolar protein sorting-associated protein 9A; TrEMBL-Plants: tr|G7J0B1|G7J0B1_MEDTR Vacuolar protein sorting-associated protein VPS9; Found in the gene: LotjaGi3g1v0330000 | 12 |
A list of co-occurring predicted domains within the L. japonicus gene space:
| Predicted domain | Source | Observations | Saturation (%) |
|---|---|---|---|
| SSF109993 | SUPERFAMILY | 1 | 25.00 |