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    VAM6 Vam6p [ Saccharomyces cerevisiae S288C ]

    Gene ID: 851482, updated on 7-Jul-2024

    Summary

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    Gene symbol
    VAM6
    Gene description
    Vam6p
    Primary source
    FungiDB:YDL077C
    Locus tag
    YDL077C
    See related
    SGD:S000002235; AllianceGenome:SGD:S000002235; 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
      A0A8H8UMK9, 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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