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    VPS53 Vps53p [ Saccharomyces cerevisiae S288C ]

    Gene ID: 853423, updated on 28-Oct-2024

    Summary

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    Official Symbol
    VPS53
    Official Full Name
    Vps53p
    Primary source
    SGD:S000003566
    Locus tag
    YJL029C
    See related
    AllianceGenome:SGD:S000003566; FungiDB:YJL029C; VEuPathDB:YJL029C
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Saccharomyces cerevisiae S288C (strain: S288C)
    Lineage
    Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
    Summary
    Involved in Golgi to vacuole transport; intracellular sphingolipid homeostasis; and retrograde transport, endosome to Golgi. Located in Golgi apparatus. Part of GARP complex. Used to study pontocerebellar hypoplasia type 2E. Human ortholog(s) of this gene implicated in pontocerebellar hypoplasia type 2E. Orthologous to human VPS53 (VPS53 subunit of GARP complex). [provided by Alliance of Genome Resources, Oct 2024]
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    Genomic context

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    See VPS53 in Genome Data Viewer
    Location:
    chromosome: X
    Exon count:
    1
    Sequence:
    Chromosome: X; NC_001142.9 (388385..390853, complement)

    Chromosome X - NC_001142.9Genomic Context describing neighboring genes Neighboring gene Rab geranylgeranyltransferase BET4 Neighboring gene spindle checkpoint protein MAD2 Neighboring gene tRNA-Met Neighboring gene uncharacterized protein

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_001142.9

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Structure of a C-terminal fragment of its Vps53 subunit suggests similarity of Golgi-associated retrograde protein (GARP) complex to a family of tethering complexes. Vasan N, et al. Proc Natl Acad Sci U S A, 2010 Aug 10. PMID 20660722, Free PMC Article
    2. VPS53 mutations cause progressive cerebello-cerebral atrophy type 2 (PCCA2). Feinstein M, et al. J Med Genet, 2014 May. PMID 24577744
    3. Mutation in a homolog of yeast Vps53p accounts for the heat and osmotic hypersensitive phenotypes in Arabidopsis hit1-1 mutant. Lee CF, et al. Planta, 2006 Jul. PMID 16408208
    4. Domains within the GARP subunit Vps54 confer separate functions in complex assembly and early endosome recognition. Quenneville NR, et al. Mol Biol Cell, 2006 Apr. PMID 16452629, Free PMC Article
    5. A systematic approach to identify recycling endocytic cargo depending on the GARP complex. Eising S, et al. Elife, 2019 Jan 29. PMID 30694181, Free PMC Article

    See all (82) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. VPS53 mutations cause progressive cerebello-cerebral atrophy type 2.
      Title: VPS53 mutations cause progressive cerebello-cerebral atrophy type 2 (PCCA2).
    2. the structure of a C-terminal fragment of the Vps53 subunit, important for binding endosome-derived vesicles, at a resolution of 2.9 A; structure of the Vps53 C terminus suggests that GARP belongs to this family of complexes.
      Title: Structure of a C-terminal fragment of its Vps53 subunit suggests similarity of Golgi-associated retrograde protein (GARP) complex to a family of tethering complexes.
    3. A different category of mutants that blocks Atg9 sorting from mitochondria, has been characterised.
      Title: Atg9 sorting from mitochondria is impaired in early secretion and VFT-complex mutants in Saccharomyces cerevisiae.
    4. The growth of yeast vps53Delta null mutant also shows reduced thermotolerance, and expression of HIT1 in this mutant can partially complement the defect, supporting the possibility of a conserved biological function for Vps53p and HIT1.
      Title: Mutation in a homolog of yeast Vps53p accounts for the heat and osmotic hypersensitive phenotypes in Arabidopsis hit1-1 mutant.
    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 molecular_function ND
    No biological Data available
    more info
    		  
    Process Evidence Code Pubs
    involved_in Golgi to vacuole transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in intracellular sphingolipid homeostasis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in retrograde transport, endosome to Golgi IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in retrograde transport, endosome to Golgi IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in retrograde transport, endosome to Golgi IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of GARP complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of GARP complex IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of GARP complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in Golgi apparatus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoplasm HDA PubMed 
    located_in cytosol HDA PubMed 
    located_in endosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in endosome membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    Vps53p
    NP_012505.1
    • Component of the GARP (Golgi-associated retrograde protein) complex; GARP is required for the recycling of proteins from endosomes to the late Golgi, and for mitosis after DNA damage induced checkpoint arrest; required for vacuolar protein sorting; members of the GARP complex are Vps51p-Vps52p-Vps53p-Vps54p; human ortholog is implicated in progressive cerebello-cerebral atrophy type 2 (PCCA2)

    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_001142.9 Reference assembly

      Range
      388385..390853 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001181463.1 → NP_012505.1  TPA: Vps53p [Saccharomyces cerevisiae S288C]

      See identical proteins and their annotated locations for NP_012505.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      D6VWF3, P47061
      UniProtKB/TrEMBL
      A6ZPU6, G2WGY8, N1P388
      Conserved Domains (2) summary
      pfam04100
      Location:5 → 369
      Vps53_N; Vps53-like, N-terminal
      pfam16854
      Location:575 → 779
      VPS53_C; Vacuolar protein sorting-associated protein 53 C-terminus
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P47061.1

    Gene LinkOut

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