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VAM6 Vam6p [ Saccharomyces cerevisiae S288C ]

Gene ID: 851482, updated on 18-Sep-2024

Summary

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Official Symbol
VAM6
Official Full Name
Vam6p
Primary source
SGD:S000002235
Locus tag
YDL077C
See related
AllianceGenome:SGD:S000002235; FungiDB:YDL077C; VEuPathDB:YDL077C
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Saccharomyces cerevisiae S288C (strain: S288C)
Lineage
Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
Also known as
CVT4; VPL18; VPL22; VPS39
Summary
Enables guanyl-nucleotide exchange factor activity and small GTPase binding activity. Contributes to phosphatidylinositol binding activity. Involved in several processes, including piecemeal microautophagy of the nucleus; positive regulation of TORC1 signaling; and vacuole fusion, non-autophagic. Located in fungal-type vacuole membrane and vacuole-mitochondrion membrane contact site. Part of HOPS complex. Orthologous to several human genes including TGFBRAP1 (transforming growth factor beta receptor associated protein 1). [provided by Alliance of Genome Resources, Apr 2022]
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Genomic context

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See VAM6 in Genome Data Viewer
Location:
chromosome: IV
Exon count:
1
Sequence:
Chromosome: IV; NC_001136.10 (316971..320120, complement)

Chromosome IV - NC_001136.10Genomic Context describing neighboring genes Neighboring gene putative serine/threonine protein kinase MRK1 Neighboring gene malate dehydrogenase MDH3 Neighboring gene Rxt3p Neighboring gene ribosomal 60S subunit protein L31A

Genomic regions, transcripts, and products

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Genomic Sequence:
NC_001136.10

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Subunit exchange among endolysosomal tethering complexes is linked to contact site formation at the vacuole. González Montoro A, et al. Mol Biol Cell, 2021 Dec 1. PMID 34668759, Free PMC Article
  2. Vps39 is required for ethanolamine-stimulated elevation in mitochondrial phosphatidylethanolamine. Iadarola DM, et al. Biochim Biophys Acta Mol Cell Biol Lipids, 2020 Jun. PMID 32058032, Free PMC Article
  3. The Vps39-like TRAP1 is an effector of Rab5 and likely the missing Vps3 subunit of human CORVET. Lachmann J, et al. Cell Logist, 2014 Oct-Dec. PMID 25750764, Free PMC Article
  4. Proteins needed for vesicle budding from the Golgi complex are also required for the docking step of homotypic vacuole fusion. Price A, et al. J Cell Biol, 2000 Mar 20. PMID 10725335, Free PMC Article
  5. Vam2/Vps41p and Vam6/Vps39p are components of a protein complex on the vacuolar membranes and involved in the vacuolar assembly in the yeast Saccharomyces cerevisiae. Nakamura N, et al. J Biol Chem, 1997 Apr 25. PMID 9111041

See all (130) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Subunit exchange among endolysosomal tethering complexes is linked to contact site formation at the vacuole.
    Title: Subunit exchange among endolysosomal tethering complexes is linked to contact site formation at the vacuole.
  2. Molecular species selectivity of lipid transport creates a mitochondrial sink for di-unsaturated phospholipids.
    Title: Molecular species selectivity of lipid transport creates a mitochondrial sink for di-unsaturated phospholipids.
  3. Vps39 is required for ethanolamine-stimulated elevation in mitochondrial phosphatidylethanolamine.
    Title: Vps39 is required for ethanolamine-stimulated elevation in mitochondrial phosphatidylethanolamine.
  4. uncover the general preprotein translocase of the outer membrane (TOM) subunit Tom40 as the direct binding partner of Vps39 on mitochondria
    Title: Vps39 Interacts with Tom40 to Establish One of Two Functionally Distinct Vacuole-Mitochondria Contact Sites.
  5. Vam6 controls TORC1(Tco89) function by activating the Gtr1 subunit of the EGO complex.
    Title: The Vam6 GEF controls TORC1 by activating the EGO complex.
Submit: New GeneRIF Correction

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Homology

Gene Ontology Provided by SGD

Function Evidence Code Pubs
enables guanyl-nucleotide exchange factor activity IDA
Inferred from Direct Assay
more info
 PubMed 
contributes_to phosphatidylinositol binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables small GTPase binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in autophagy IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in endosomal vesicle fusion IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in intracellular protein transport IEA
Inferred from Electronic Annotation
more info
  
involved_in piecemeal microautophagy of the nucleus IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of TORC1 signaling IGI
Inferred from Genetic Interaction
more info
 PubMed 
involved_in positive regulation of TORC1 signaling IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein transport IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of SNARE complex assembly IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in vacuole fusion, non-autophagic IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in vacuole fusion, non-autophagic IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in vacuole organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in vesicle tethering IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in vesicle-mediated transport IEA
Inferred from Electronic Annotation
more info
  
involved_in vesicle-mediated transport IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
part_of HOPS complex IPI
Inferred from Physical Interaction
more info
 PubMed 
located_in bounding membrane of organelle IEA
Inferred from Electronic Annotation
more info
  
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in fungal-type vacuole IDA
Inferred from Direct Assay
more info
 PubMed 
located_in fungal-type vacuole membrane HDA PubMed 
is_active_in fungal-type vacuole membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in fungal-type vacuole membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in membrane IEA
Inferred from Electronic Annotation
more info
  
located_in vacuolar membrane IEA
Inferred from Electronic Annotation
more info
  
located_in vacuole IEA
Inferred from Electronic Annotation
more info
  
located_in vacuole-mitochondrion membrane contact site IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
Vam6p
NP_010206.1
  • Guanine nucleotide exchange factor for the GTPase Gtr1p; subunit of the HOPS endocytic tethering complex; vacuole membrane protein; functions as a Rab GTPase effector, interacting with both GTP- and GDP-bound conformations of Ypt7p; facilitates tethering and promotes membrane fusion events at the late endosome and vacuole; required for both membrane and protein trafficking; component of vacuole-mitochondrion contacts (vCLAMPs) important for lipid transfer between organelles

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

  1. NC_001136.10 Reference assembly

    Range
    316971..320120 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001180136.1 → NP_010206.1  TPA: Vam6p [Saccharomyces cerevisiae S288C]

    See identical proteins and their annotated locations for NP_010206.1

    Status: REVIEWED

    UniProtKB/Swiss-Prot
    D6VRS2, Q07468
    UniProtKB/TrEMBL
    A6ZXQ1, B5VFJ1, N1P7Q2
    Conserved Domains (2) summary
    pfam10366
    Location:603 → 715
    Vps39_1; Vacuolar sorting protein 39 domain 1
    pfam10367
    Location:905 → 1016
    Vps39_2; Vacuolar sorting protein 39 domain 2
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q07468.1

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