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VPS52 / YDR484W Overview

Standard Name
VPS52 1 2
Systematic Name
YDR484W
SGD ID
SGD:S000002892
Aliases
SAC2 6
Feature Type
ORF , Verified
Description
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; involved in localization of actin and chitin; members of the GARP complex are Vps51p-Vps52p-Vps53p-Vps54p 1 3 4 5
Name Description
Vacuolar Protein Sorting
Comparative Info
Sequence Details

Sequence

The S. cerevisiae Reference Genome sequence is derived from laboratory strain S288C. Download DNA or protein sequence, view genomic context and coordinates. Click "Sequence Details" to view all sequence information for this locus, including that for other strains.

Summary
VPS52/YDR484W is located on the right arm of chromosome IV near the telomere between KRE2 alpha1,2-mannosyltransferase and VPS72 Htz1p-binding SWR1 complex subunit; coding sequence is 1926 nucleotides long with 19 SNPs, 7 of which cause amino acid polymorphisms

Analyze Sequence

S288C only

BLASTN | BLASTP | Design Primers | Restriction Fragment Map | Restriction Fragment Sizes | Six-Frame Translation

S288C vs. other species

BLASTN vs. fungi | BLASTP at NCBI | BLASTP vs. fungi

S288C vs. other strains

Strain Alignment | Variant Viewer

Protein Details

Protein

Basic sequence-derived (length, molecular weight, isoelectric point) and experimentally-determined (median abundance, median absolute deviation) protein information. Click "Protein Details" for further information about the protein such as half-life, abundance, domains, domains shared with other proteins, protein sequence retrieval for various strains, physico-chemical properties, protein modification sites, and external identifiers for the protein.

Summary
Vps52p is 641 amino acids long, longer-lived, low in abundance; ubiquitinylated on K172, phosphorylated on 3 serines
Length (a.a.)
641
Mol. Weight (Da)
74322.5
Isoelectric Point
5.46
Median Abundance (molecules/cell)
2363 +/- 534
Half-life (hr)
11.2

Alleles

Curated mutant alleles for the specified gene, listed alphabetically. Click on the allele name to open the allele page. Click "SGD search" to view all alleles in search results.

View all VPS52 alleles in SGD search

Gene Ontology Details

Gene Ontology

GO Annotations consist of four mandatory components: a gene product, a term from one of the three Gene Ontology (GO) controlled vocabularies (Molecular Function, Biological Process, and Cellular Component), a reference, and an evidence code. SGD has manually curated and high-throughput GO Annotations, both derived from the literature, as well as computational, or predicted, annotations. Click "Gene Ontology Details" to view all GO information and evidence for this locus as well as biological processes it shares with other genes.

Summary
Rab family GTPase-binding protein subunit of GARP complex; involved in Golgi to vacuole transport, upregulation of autophagy, sphingolipid homeostasis, and endosome-to-Golgi retrograde transport; localizes to cytosol and Golgi apparatus

View computational annotations

Molecular Function

Manually Curated

Biological Process

Manually Curated

Cellular Component

Manually Curated

Complex

Macromolecular complex annotations are imported from the Complex Portal. These annotations have been derived from physical molecular interaction evidence extracted from the literature and cross-referenced in the entry, or by curator inference from information on homologs in closely related species or by inference from scientific background.

Phenotype Details

Phenotype

Phenotype annotations for a gene are curated single mutant phenotypes that require an observable (e.g., "cell shape"), a qualifier (e.g., "abnormal"), a mutant type (e.g., null), strain background, and a reference. In addition, annotations are classified as classical genetics or high-throughput (e.g., large scale survey, systematic mutation set). Whenever possible, allele information and additional details are provided. Click "Phenotype Details" to view all phenotype annotations and evidence for this locus as well as phenotypes it shares with other genes.

Summary
VPS52/YDR484W is a non-essential gene; null mutants are viable but exhibit a wide range of phenotypes including decreased resistance to both acidic and alkaline pH, abnormal actin cytoskeleton morphology, decreased anaerobic growth, abnormal and decreased autophagy, abnormal colony appearance, decreased competitive fitness, decreased desiccation resistance, increased heat sensitivity, decreased resistance to hydrostatic pressure and ionic stress, decreased killer toxin resistance, abnormal meiosis, decreased metal resistance, abnormal mitochondrial morphology, increased oxidative stress resistance, decreased small molecule transport, decreased sporulation efficiency, decreased stress resistance, decreased toxin resistance, impaired nitrogen source utilization, decreased UV resistance, abnormal vacuolar morphology, decreased vegetative growth rate, and decreased viability.

Classical Genetics

null

Large-scale Survey

null
Interaction Details

Interaction

Interaction annotations are curated by BioGRID and include physical or genetic interactions observed between at least two genes. An interaction annotation is composed of the interaction type, name of the interactor, assay type (e.g., Two-Hybrid), annotation type (e.g., manual or high-throughput), and a reference, as well as other experimental details. Click "Interaction Details" to view all interaction annotations and evidence for this locus, including an interaction visualization.

Summary
Vps52p interacts physically with proteins involved in protein targeting; VPS52 interacts genetically with genes involved in Golgi vesicle transport

594 total interactions for 429 unique genes

Physical Interactions

  • Affinity Capture-MS: 28
  • Affinity Capture-RNA: 4
  • Affinity Capture-Western: 18
  • Co-fractionation: 1
  • Co-localization: 1
  • PCA: 1
  • Reconstituted Complex: 1
  • Two-hybrid: 5

Genetic Interactions

  • Dosage Growth Defect: 1
  • Negative Genetic: 369
  • Phenotypic Enhancement: 20
  • Phenotypic Suppression: 42
  • Positive Genetic: 73
  • Synthetic Growth Defect: 10
  • Synthetic Haploinsufficiency: 1
  • Synthetic Lethality: 15
  • Synthetic Rescue: 4
Regulation Details

Regulation

The number of putative Regulators (genes that regulate it) and Targets (genes it regulates) for the given locus, based on experimental evidence. This evidence includes data generated through high-throughput techniques. Click "Regulation Details" to view all regulation annotations, shared GO enrichment among regulation Targets, and a regulator/target diagram for the locus.

Summary
VPS52 promoter is bound by Med6p and Xbp1p during response to heat
Regulators
2
Targets
0
Expression Details

Expression

Expression data are derived from records contained in the Gene Expression Omnibus (GEO), and are first log2 transformed and normalized. Referenced datasets may contain one or more condition(s), and as a result there may be a greater number of conditions than datasets represented in a single clickable histogram bar. The histogram division at 0.0 separates the down-regulated (green) conditions and datasets from those that are up-regulated (red). Click "Expression Details" to view all expression annotations and details for this locus, including a visualization of genes that share a similar expression pattern.

Literature Details

Literature

All manually curated literature for the specified gene, organized into topics according to their relevance to the gene (Primary Literature, Additional Literature, or Review). Click "Literature Details" to view all literature information for this locus, including shared literature between genes.

Primary
40
Additional
36
Reviews
12

Resources

AlphaFold Protein Structure | Entrez Gene | Entrez RefSeq Protein | FungiDB | Search all NCBI | UniParc | UniProtKB