VMA2/YBR127C Summary Help

Standard Name VMA2 1
Systematic Name YBR127C
Alias VAT2
Feature Type ORF, Verified
Description Subunit B of V1 peripheral membrane domain of vacuolar H+-ATPase; an 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 (2, 3, 4, 5 and see Summary Paragraph)
Also known as: ATPSV
Name Description Vacuolar Membrane Atpase 1
Chromosomal Location
ChrII:492822 to 491269 | ORF Map | GBrowse
Note: this feature is encoded on the Crick strand.
Gene Ontology Annotations All VMA2 GO evidence and references
  View Computational GO annotations for VMA2
Molecular Function
Manually curated
Biological Process
Manually curated
Cellular Component
Manually curated
Regulators 5 genes
Classical genetics
Large-scale survey
216 total interaction(s) for 142 unique genes/features.
Physical Interactions
  • Affinity Capture-MS: 87
  • Affinity Capture-RNA: 7
  • Affinity Capture-Western: 21
  • Co-crystal Structure: 2
  • Co-fractionation: 6
  • Co-purification: 2
  • FRET: 2
  • Protein-peptide: 4
  • Reconstituted Complex: 1
  • Two-hybrid: 2

Genetic Interactions
  • Dosage Lethality: 4
  • Dosage Rescue: 1
  • Negative Genetic: 37
  • Phenotypic Enhancement: 5
  • Positive Genetic: 10
  • Synthetic Growth Defect: 8
  • Synthetic Lethality: 15
  • Synthetic Rescue: 2

Expression Summary
Length (a.a.) 517
Molecular Weight (Da) 57,749
Isoelectric Point (pI) 4.79
Phosphorylation PhosphoGRID | PhosphoPep Database
sequence information
ChrII:492822 to 491269 | ORF Map | GBrowse
Note: this feature is encoded on the Crick strand.
Last Update Coordinates: 2011-02-03 | Sequence: 1997-01-28
Subfeature details
Most Recent Updates
Coordinates Sequence
CDS 1..1554 492822..491269 2011-02-03 1997-01-28
Retrieve sequences
Analyze Sequence
S288C only
S288C vs. other species
S288C vs. other strains
External Links All Associated Seq | E.C. | Entrez Gene | Entrez RefSeq Protein | MIPS | Search all NCBI (Entrez) | UniProtKB
Primary SGDIDS000000331

VMA2 encodes the B subunit of the yeast V-ATPase V1 domain (3). Vacuolar (H )-ATPases (V-ATPases) are ATP-dependent proton pumps that acidify intracellular vacuolar compartments. Vacuolar acidification is important for many cellular processes, including endocytosis, targeting of newly synthesized lysosomal enzymes, and other molecular targeting processes. The V-ATPase consists of two separable domains. The V1 domain has eight known subunits, is peripherally associated with the vacuolar membrane, and catalyzes ATP hydrolysis. The V0 domain is an integral membrane structure of five subunits, and transports protons across the membrane. The structure, function, and assembly of V-ATPases are reviewed in references 2, 6, 7 and 8.

The B subunit (Vma2p) of the V-ATPase contains nucleotide binding sites, but does not catalyze ATP hydrolysis (2). Some vma2 point mutations reduce the ATPase and proton transport activities of the V-ATPase holoenzyme, suggesting that ATP binding to the noncatalytic sites may regulate V-ATPase activity (9, 10).26 PH,PR,CC, The vma2 null mutation is synthetically lethal with mutations that cause defects in endocytosis (11, 12).

V-ATPases have been identified in numerous eukaryotes (2, 8); the vma2 null phenotype can be fully complemented by expression of the Candida tropicalis V-ATPase B subunit, and partially complemented by the bovine B subunit (13).

Last updated: 2000-05-11 Contact SGD

References cited on this page View Complete Literature Guide for VMA2
1) Tomashek JJ, et al.  (1997) Reconstitution in vitro of the V1 complex from the yeast vacuolar proton-translocating ATPase. Assembly recapitulates mechanism. J Biol Chem 272(26):16618-23
2) Forgac M  (1999) Structure and properties of the vacuolar (H+)-ATPases. J Biol Chem 274(19):12951-4
3) Nelson H, et al.  (1989) A conserved gene encoding the 57-kDa subunit of the yeast vacuolar H+-ATPase. J Biol Chem 264(3):1775-8
4) Kumar A, et al.  (2002) Subcellular localization of the yeast proteome. Genes Dev 16(6):707-19
5) Tkach JM, et al.  (2012) Dissecting DNA damage response pathways by analysing protein localization and abundance changes during DNA replication stress. Nat Cell Biol 14(9):966-76
6) Graham LA and Stevens TH  (1999) Assembly of the yeast vacuolar proton-translocating ATPase. J Bioenerg Biomembr 31(1):39-47
7) Kane PM  (1999) Biosynthesis and regulation of the yeast vacuolar H+-ATPase. J Bioenerg Biomembr 31(1):49-56
8) Stevens TH and Forgac M  (1997) Structure, function and regulation of the vacuolar (H+)-ATPase. Annu Rev Cell Dev Biol 13:779-808
9) Liu Q, et al.  (1996) Site-directed mutagenesis of the yeast V-ATPase B subunit (Vma2p). J Biol Chem 271(4):2018-22
10) Vasilyeva E, et al.  (2000) Cysteine scanning mutagenesis of the noncatalytic nucleotide binding site of the yeast V-ATPase. J Biol Chem 275(1):255-60
11) Munn AL and Riezman H  (1994) Endocytosis is required for the growth of vacuolar H(+)-ATPase-defective yeast: identification of six new END genes. J Cell Biol 127(2):373-86
12) Seron K, et al.  (1998) A yeast t-SNARE involved in endocytosis. Mol Biol Cell 9(10):2873-89
13) Pan YX, et al.  (1993) Saccharomyces cerevisiae expression of exogenous vacuolar ATPase subunits B. Biochim Biophys Acta 1151(2):175-85