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Protein

V-type proton ATPase subunit d

Gene

VMA6

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Vacuolar ATPase is responsible for acidifying a variety of intracellular compartments in eukaryotic cells. The active enzyme consists of a catalytic V1 domain attached to an integral membrane V0 proton pore complex. This subunit is a non-integral membrane component of the membrane pore domain and is required for proper assembly of the V0 sector. Might be involved in the regulated assembly of V1 subunits onto the membrane sector or alternatively may prevent the passage of protons through V0 pores.

GO - Molecular functioni

  • proton-transporting ATPase activity, rotational mechanism Source: SGD

GO - Biological processi

  • ATP hydrolysis coupled proton transport Source: InterPro
  • vacuolar acidification Source: SGD
  • vacuolar transport Source: SGD
Complete GO annotation...

Keywords - Biological processi

Hydrogen ion transport, Ion transport, Transport

Enzyme and pathway databases

BioCyciYEAST:G3O-32502-MONOMER.
ReactomeiR-SCE-77387. Insulin receptor recycling.
R-SCE-917977. Transferrin endocytosis and recycling.

Protein family/group databases

TCDBi3.A.2.2.3. the h(+)- or na(+)-translocating f-type, v-type and a-type atpase (f-atpase) superfamily.

Names & Taxonomyi

Protein namesi
Recommended name:
V-type proton ATPase subunit d
Short name:
V-ATPase subunit d
Alternative name(s):
V-ATPase 39 kDa subunit
V-ATPase subunit M39
Vacuolar proton pump subunit d
Gene namesi
Name:VMA6
Ordered Locus Names:YLR447C
ORF Names:L9324.8
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XII

Organism-specific databases

EuPathDBiFungiDB:YLR447C.
SGDiS000004439. VMA6.

Subcellular locationi

GO - Cellular componenti

  • fungal-type vacuole membrane Source: SGD
  • vacuolar proton-transporting V-type ATPase, V0 domain Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Membrane, Vacuole

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 345345V-type proton ATPase subunit dPRO_0000119360Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei1 – 11N-acetylmethionineCombined sources1 Publication

Keywords - PTMi

Acetylation

Proteomic databases

MaxQBiP32366.
PeptideAtlasiP32366.

Interactioni

Subunit structurei

V-ATPase is a heteromultimeric enzyme composed of a peripheral catalytic V1 complex (components A to H) attached to an integral membrane V0 proton pore complex (components: a, c, c', c'', d and e).1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
VMA1P172552EBI-20201,EBI-20245
VMA22P387844EBI-20201,EBI-20329
VMA7P391115EBI-20201,EBI-20272
VPH1P325635EBI-20201,EBI-20455

Protein-protein interaction databases

BioGridi31705. 66 interactions.
DIPiDIP-1737N.
IntActiP32366. 34 interactions.
MINTiMINT-386520.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3J9Telectron microscopy6.90Q1-345[»]
3J9Uelectron microscopy7.60Q1-345[»]
3J9Velectron microscopy8.30Q1-345[»]
ProteinModelPortaliP32366.
SMRiP32366. Positions 1-345.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the V-ATPase V0D/AC39 subunit family.Curated

Phylogenomic databases

GeneTreeiENSGT00390000002200.
HOGENOMiHOG000199065.
InParanoidiP32366.
KOiK02146.
OMAiFMDFITY.
OrthoDBiEOG7Z95WZ.

Family and domain databases

InterProiIPR002843. ATPase_V0-cplx_csu/dsu.
IPR016727. ATPase_V0-cplx_dsu.
[Graphical view]
PANTHERiPTHR11028. PTHR11028. 1 hit.
PfamiPF01992. vATP-synt_AC39. 1 hit.
[Graphical view]
PIRSFiPIRSF018497. V-ATP_synth_D. 1 hit.
SUPFAMiSSF103486. SSF103486. 1 hit.

Sequencei

Sequence statusi: Complete.

P32366-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEGVYFNIDN GFIEGVVRGY RNGLLSNNQY INLTQCDTLE DLKLQLSSTD
60 70 80 90 100
YGNFLSSVSS ESLTTSLIQE YASSKLYHEF NYIRDQSSGS TRKFMDYITY
110 120 130 140 150
GYMIDNVALM ITGTIHDRDK GEILQRCHPL GWFDTLPTLS VATDLESLYE
160 170 180 190 200
TVLVDTPLAP YFKNCFDTAE ELDDMNIEII RNKLYKAYLE DFYNFVTEEI
210 220 230 240 250
PEPAKECMQT LLGFEADRRS INIALNSLQS SDIDPDLKSD LLPNIGKLYP
260 270 280 290 300
LATFHLAQAQ DFEGVRAALA NVYEYRGFLE TGNLEDHFYQ LEMELCRDAF
310 320 330 340
TQQFAISTVW AWMKSKEQEV RNITWIAECI AQNQRERINN YISVY
Length:345
Mass (Da):39,791
Last modified:October 1, 1996 - v2
Checksum:i53A19450CAF35632
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti32 – 321N → T in AAA35210 (PubMed:8509410).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L11584 Genomic DNA. Translation: AAA35210.1.
U22382 Genomic DNA. Translation: AAB67533.1.
BK006945 Genomic DNA. Translation: DAA09747.1.
PIRiS55969.
RefSeqiNP_013552.3. NM_001182335.3.

Genome annotation databases

EnsemblFungiiYLR447C; YLR447C; YLR447C.
GeneIDi851168.
KEGGisce:YLR447C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L11584 Genomic DNA. Translation: AAA35210.1.
U22382 Genomic DNA. Translation: AAB67533.1.
BK006945 Genomic DNA. Translation: DAA09747.1.
PIRiS55969.
RefSeqiNP_013552.3. NM_001182335.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3J9Telectron microscopy6.90Q1-345[»]
3J9Uelectron microscopy7.60Q1-345[»]
3J9Velectron microscopy8.30Q1-345[»]
ProteinModelPortaliP32366.
SMRiP32366. Positions 1-345.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi31705. 66 interactions.
DIPiDIP-1737N.
IntActiP32366. 34 interactions.
MINTiMINT-386520.

Protein family/group databases

TCDBi3.A.2.2.3. the h(+)- or na(+)-translocating f-type, v-type and a-type atpase (f-atpase) superfamily.

Proteomic databases

MaxQBiP32366.
PeptideAtlasiP32366.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYLR447C; YLR447C; YLR447C.
GeneIDi851168.
KEGGisce:YLR447C.

Organism-specific databases

EuPathDBiFungiDB:YLR447C.
SGDiS000004439. VMA6.

Phylogenomic databases

GeneTreeiENSGT00390000002200.
HOGENOMiHOG000199065.
InParanoidiP32366.
KOiK02146.
OMAiFMDFITY.
OrthoDBiEOG7Z95WZ.

Enzyme and pathway databases

BioCyciYEAST:G3O-32502-MONOMER.
ReactomeiR-SCE-77387. Insulin receptor recycling.
R-SCE-917977. Transferrin endocytosis and recycling.

Miscellaneous databases

NextBioi967972.
PROiP32366.

Family and domain databases

InterProiIPR002843. ATPase_V0-cplx_csu/dsu.
IPR016727. ATPase_V0-cplx_dsu.
[Graphical view]
PANTHERiPTHR11028. PTHR11028. 1 hit.
PfamiPF01992. vATP-synt_AC39. 1 hit.
[Graphical view]
PIRSFiPIRSF018497. V-ATP_synth_D. 1 hit.
SUPFAMiSSF103486. SSF103486. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The Saccharomyces cerevisiae VMA6 gene encodes the 36-kDa subunit of the vacuolar H(+)-ATPase membrane sector."
    Bauerle C., Ho M.N., Lindorfer M.A., Stevens T.H.
    J. Biol. Chem. 268:12749-12757(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 45-61; 188-198; 256-266; 268-276 AND 338-344, SUBUNIT.
  2. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XII."
    Johnston M., Hillier L.W., Riles L., Albermann K., Andre B., Ansorge W., Benes V., Brueckner M., Delius H., Dubois E., Duesterhoeft A., Entian K.-D., Floeth M., Goffeau A., Hebling U., Heumann K., Heuss-Neitzel D., Hilbert H.
    , Hilger F., Kleine K., Koetter P., Louis E.J., Messenguy F., Mewes H.-W., Miosga T., Moestl D., Mueller-Auer S., Nentwich U., Obermaier B., Piravandi E., Pohl T.M., Portetelle D., Purnelle B., Rechmann S., Rieger M., Rinke M., Rose M., Scharfe M., Scherens B., Scholler P., Schwager C., Schwarz S., Underwood A.P., Urrestarazu L.A., Vandenbol M., Verhasselt P., Vierendeels F., Voet M., Volckaert G., Voss H., Wambutt R., Wedler E., Wedler H., Zimmermann F.K., Zollner A., Hani J., Hoheisel J.D.
    Nature 387:87-90(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  3. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  4. Bienvenut W.V., Peters C.
    Submitted (JUN-2005) to UniProtKB
    Cited for: PROTEIN SEQUENCE OF 1-18; 76-84; 164-181; 187-276; 298-314 AND 322-335, CLEAVAGE OF INITIATOR METHIONINE, ACETYLATION AT MET-1, IDENTIFICATION BY MASS SPECTROMETRY.
  5. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  6. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  7. Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiVA0D_YEAST
AccessioniPrimary (citable) accession number: P32366
Secondary accession number(s): D6VZ81
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1993
Last sequence update: October 1, 1996
Last modified: May 11, 2016
This is version 156 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 1630 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome XII
    Yeast (Saccharomyces cerevisiae) chromosome XII: entries and gene names

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.