VMA2 / YBR127C Overview
- Standard Name
- VMA2 1
- Systematic Name
- YBR127C
- SGD ID
- SGD:S000000331
- Aliases
- VAT2 16 , ATPSV
- Feature Type
- ORF , Verified
- Description
- Subunit B of V1 peripheral membrane domain of vacuolar H+-ATPase; electrogenic proton pump found throughout the endomembrane system; contains nucleotide binding sites; also detected in the cytoplasm; protein abundance increases in response to DNA replication stress; human homolog ATP6V1B1, implicated in autosomal-recessive distal renal tubular acidosis (RTA) with sensorineural deafness, complements yeast null mutant 2 3 4 5 6 7
- Name Description
- Vacuolar Membrane Atpase 1
- 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.
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
- Protein abundance increases in response to DNA replication stress
- Length (a.a.)
- 517
- Mol. Weight (Da)
- 57728.7
- Isoelectric Point
- 4.69
- Median Abundance (molecules/cell)
- 37171 +/- 10094
- Half-life (hr)
- 9.6
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 VMA2 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
- Hydrogen ion transporting ATPase involved in vacuolar acidification, calcium homeostasis, and the assembly of proteasome storage granules; localizes to vacuolar membranes and vacuole-mitochondrion membrane contact sites; subunit of the V1 domain of the vacuolar proton-transporting V-type ATPase
View computational annotations
Molecular Function
- Manually Curated
Biological Process
- Manually Curated
- involved in intracellular calcium ion homeostasis (IMP)
- involved in pexophagy (IMP)
- involved in proteasome storage granule assembly (IMP)
- involved in transmembrane transport (IMP)
- involved in vacuolar acidification (IMP)
Cellular Component
- Manually Curated
- located in cytoplasm (HDA)
- located in cytoplasmic stress granule (HDA)
- located in fungal-type vacuole membrane (IDA, HDA)
- located in membrane raft (IDA)
- part of vacuolar proton-transporting V-type ATPase, V1 domain (IDA)
- located in vacuole-mitochondrion membrane contact site (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
- Non-essential gene; null mutant is sensitive to metal ions such as Zn2+, Cd2+, and Ni2+, and accumulates reduced levels of inorganic polyphosphates; null mutant exhibits shortened chronological and replicative lifespan, is sensitive to oxidative stress, and shows earlier onset of mitochondrial dysfunction during aging; in large-scale studies, the null mutant shows reduced competitive fitness in several different media; homozygous null mutant diploid is sensitive to desiccation and freeze-thaw stress, requires myo-inositol, and fails to respire; null mutant is sensitive to a variety of chemicals
Classical Genetics
- null
- chemical compound accumulation: decreased
- chemical compound accumulation: increased
- lipid particle morphology: abnormal
- metal resistance: decreased
- mitochondrial morphology: abnormal
- oxidative stress resistance: decreased
- protein/peptide modification: decreased
- replicative lifespan: decreased
- resistance to chemicals: decreased
- respiratory growth: decreased
- RNA accumulation: decreased
- vegetative growth: decreased rate
- null
- alkaline pH resistance: decreased
- auxotrophy
- chemical compound accumulation: decreased
- chemical compound accumulation: increased
- chemical compound excretion: increased
- chronological lifespan: decreased
- competitive fitness: decreased
- desiccation resistance: decreased
- endocytosis: decreased
- freeze-thaw resistance: decreased
- innate thermotolerance: decreased
- lipid particle morphology: abnormal
- metal resistance: decreased
- oxidative stress resistance: decreased
- resistance to chemicals: decreased
- resistance to chemicals: increased
- resistance to enzymatic treatment: decreased
- respiratory growth: absent
- respiratory growth: decreased rate
- respiratory growth: increased
- sporulation: absent
- stress resistance: decreased
- toxin resistance: decreased
- utilization of carbon source: decreased rate
- utilization of iron source: decreased
- utilization of nitrogen source: absent
- utilization of nitrogen source: decreased rate
- vacuolar morphology: abnormal
- vegetative growth: decreased
- vegetative growth: decreased rate
- viable
- reduction of function
Large-scale Survey
Disease
Disease Annotations consist of three mandatory components: a gene product, a term from the Disease Ontology (DO) controlled vocabulary and an evidence code. SGD provides manually curated DO Annotations derived from the literature. Click "Disease Details" to view all Disease information and evidence for this locus as well as diseases it shares with other genes.
- Summary
- Yeast VMA2 is homologous to human ATP6V1B1 and ATP6V1B2, and has been used to study renal tubular acidosis and follicular lymphoma
Manually Curated
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.
371 total interactions for 262 unique genes
Physical Interactions
- Affinity Capture-MS: 192
- Affinity Capture-RNA: 10
- Affinity Capture-Western: 22
- Co-crystal Structure: 2
- Co-fractionation: 6
- Co-purification: 3
- Cross-Linking-MS (XL-MS): 2
- FRET: 2
- PCA: 1
- Protein-peptide: 4
- Proximity Label-MS: 4
- Reconstituted Complex: 3
- Two-hybrid: 2
Genetic Interactions
- Dosage Growth Defect: 2
- Dosage Lethality: 4
- Dosage Rescue: 2
- Negative Genetic: 39
- Phenotypic Enhancement: 10
- Phenotypic Suppression: 4
- Positive Genetic: 10
- Synthetic Growth Defect: 21
- Synthetic Lethality: 23
- Synthetic Rescue: 3
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
- 6
- 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: 2000-05-11
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.