VPS3 / YDR495C Overview
- Standard Name
- VPS3 1 2
- Systematic Name
- YDR495C
- SGD ID
- SGD:S000002903
- Aliases
- PEP6 7 , VPL3 8 , VPT17 1
- Feature Type
- ORF , Verified
- Description
- Component of CORVET membrane tethering complex; cytoplasmic protein required for the sorting and processing of soluble vacuolar proteins, acidification of the vacuolar lumen, and assembly of the vacuolar H+-ATPase 1 3 4 5 6
- Name Description
- Vacuolar Protein Sorting 1 2
- Comparative Info
-
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
- VPS3/YDR495C is located on the right arm of chromosome IV near the telomere between RSM28 mitochondrial ribosomal protein of the small subunit and PUF6 Pumilio-homology domain protein; coding sequence is 3036 nucleotides long with 37 SNPs, 16 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
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
- Vps3p is 1011 amino acids long, of average half-life, very low in abundance; contains disordered region at N-terminus; phosphorylated on 11 residues
- Length (a.a.)
- 1011
- Mol. Weight (Da)
- 116877.0
- Isoelectric Point
- 4.76
- Median Abundance (molecules/cell)
- 1316 +/- 327
- Half-life (hr)
- 10.0
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 VPS3 alleles in SGD search
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
- Subunit of CORVET multimeric protein complex that acts as an endosomal tether; involved in vacuolar protein targeting, vacuolar acidification, and vacuolar inheritance
View computational annotations
Molecular Function
- Manually Curated
- enables molecular function unknown (ND)
Biological Process
- Manually Curated
- involved in protein targeting to vacuole (IMP)
- involved in vacuolar acidification (IMP)
- involved in vacuole inheritance (IMP)
Cellular Component
- Manually Curated
- part of CORVET complex (IDA)
- located in endosome (IDA)
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
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
- VPS3/YDR495C is a non-essential gene; null mutants are viable, slow-growing, and associated with several mutant phenotypes that significantly affect cellular functions and overall fitness. In null mutants, biofilm formation is decreased, chronological lifespan is reduced, and competitive fitness is diminished. The morphology of the endomembrane system is abnormal, suggesting disruptions in intracellular organization and transport processes. Furthermore, these mutants show increased sensitivity to heat and decreased resistance to hyperosmotic stress and metal exposure, highlighting their vulnerability to various environmental challenges. Oxidative stress resistance is also reduced, which may compromise cellular integrity under stress conditions. While replicative lifespan is increased, sporulation is decreased, indicating potential trade-offs in reproductive success. Telomere length is diminished, which could affect cellular aging and stability, and vacuolar morphology is abnormal, potentially disrupting cellular storage and waste management. In cases of reduced function of VPS3, vacuolar morphology and transport are both abnormal, further emphasizing the gene's role in maintaining vacuolar integrity and function. When VPS3 is overexpressed, vacuolar morphology remains abnormal, suggesting that excessive levels of the gene may also lead to disruptions in vacuolar structure.
Classical Genetics
- null
- reduction of function
- overexpression
- null
- biofilm formation: decreased
- chemical compound accumulation: abnormal
- chemical compound accumulation: decreased
- chemical compound accumulation: increased
- chemical compound excretion: increased
- chronological lifespan: decreased
- competitive fitness: decreased
- heat sensitivity: increased
- hyperosmotic stress resistance: decreased
- metal resistance: decreased
- oxidative stress resistance: decreased
- protein/peptide distribution: abnormal
- protein/peptide modification: decreased
- resistance to chemicals: decreased
- resistance to chemicals: increased
- resistance to chemicals: normal
- respiratory growth: decreased rate
- respiratory growth: increased
- sporulation efficiency: decreased
- sporulation: decreased
- stress resistance: decreased
- telomere length: decreased
- toxin resistance: decreased
- toxin resistance: increased
- utilization of carbon source: increased
- utilization of nitrogen source: absent
- vacuolar morphology: abnormal
- vegetative growth: decreased rate
- viable
Large-scale Survey
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
- Vps3p interacts physically with proteins involved in vesicle organization and protein targeting; VPS3 interacts genetically with genes involved in Golgi vesicle transport
235 total interactions for 143 unique genes
Physical Interactions
- Affinity Capture-MS: 35
- Affinity Capture-RNA: 3
- Affinity Capture-Western: 26
- PCA: 1
- Reconstituted Complex: 5
- Two-hybrid: 11
Genetic Interactions
- Dosage Growth Defect: 2
- Dosage Rescue: 2
- Negative Genetic: 62
- Phenotypic Enhancement: 29
- Phenotypic Suppression: 20
- Positive Genetic: 5
- Synthetic Growth Defect: 20
- Synthetic Lethality: 14
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.
- Regulators
- 2
- Targets
- 0
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.
Summary Paragraph
A summary of the locus, written by SGD Biocurators following a thorough review of the literature. Links to gene names and curated GO terms are included within the Summary Paragraphs.
Last Updated: 2025-04-14
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.