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VPS53 Vps53p [ Saccharomyces cerevisiae S288C ]

Gene ID: 853423, updated on 18-Sep-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; cellular 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, Apr 2022]
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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. VPS53 mutations cause progressive cerebello-cerebral atrophy type 2 (PCCA2). Feinstein M, et al. J Med Genet, 2014 May. PMID 24577744
  2. 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
  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. 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
  5. 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

See all (78) 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

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