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Protein

V-type proton ATPase subunit B

Gene

VMA2

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

Non-catalytic subunit of the peripheral V1 complex of vacuolar ATPase. V-ATPase is responsible for acidifying a variety of intracellular compartments in eukaryotic cells. It is an electrogenic proton pump that generates a proton motive force of 180 mv, inside positive and acidic, in the vacuolar membrane vesicles.1 Publication

GO - Molecular functioni

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

GO - Biological processi

  • ATP hydrolysis coupled proton transport Source: InterPro
  • ATP metabolic process Source: InterPro
  • cellular calcium ion homeostasis Source: SGD
  • proteasome storage granule assembly Source: SGD
  • transmembrane transport Source: SGD
  • vacuolar acidification Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Hydrogen ion transport, Ion transport, Transport

Enzyme and pathway databases

BioCyciYEAST:G3O-29082-MONOMER.
ReactomeiR-SCE-1222556. ROS, RNS production in response to bacteria.
R-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 B
Short name:
V-ATPase subunit B
Alternative name(s):
V-ATPase 57 kDa subunit
Vacuolar proton pump subunit B
Gene namesi
Name:VMA2
Synonyms:VAT2
Ordered Locus Names:YBR127C
ORF Names:YBR1002
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome II

Organism-specific databases

EuPathDBiFungiDB:YBR127C.
SGDiS000000331. VMA2.

Subcellular locationi

GO - Cellular componenti

  • cytoplasmic stress granule Source: SGD
  • fungal-type vacuole membrane Source: SGD
  • vacuolar proton-transporting V-type ATPase, V1 domain Source: SGD
  • vacuole-mitochondrion membrane contact site Source: SGD
Complete GO annotation...

Pathology & Biotechi

Chemistry databases

ChEMBLiCHEMBL6106.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001446481 – 517V-type proton ATPase subunit BAdd BLAST517

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei4PhosphoserineCombined sources1
Cross-linki14Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
Modified residuei137PhosphoserineCombined sources1
Modified residuei503PhosphoserineCombined sources1
Modified residuei504PhosphoserineCombined sources1
Cross-linki508Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
Modified residuei511Phosphoserine; by ATM or ATRCombined sources1
Modified residuei515PhosphoserineCombined sources1

Keywords - PTMi

Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

MaxQBiP16140.
PRIDEiP16140.

PTM databases

iPTMnetiP16140.

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). Interacts with RAV1 and RAV2 components of the RAVE complex, which are essential for the stability and assembly of V-ATPase.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
RAV1P471044EBI-20254,EBI-25471

Protein-protein interaction databases

BioGridi32828. 158 interactors.
DIPiDIP-2292N.
IntActiP16140. 520 interactors.
MINTiMINT-563511.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3J9Telectron microscopy6.90B/D/F1-517[»]
3J9Uelectron microscopy7.60B/D/F1-517[»]
3J9Velectron microscopy8.30B/D/F1-517[»]
5BW9X-ray7.00D/E/F/d/e/f1-517[»]
5D80X-ray6.20D/E/F/d/e/f1-517[»]
ProteinModelPortaliP16140.
SMRiP16140.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the ATPase alpha/beta chains family.Curated

Phylogenomic databases

GeneTreeiENSGT00550000074724.
HOGENOMiHOG000165320.
InParanoidiP16140.
KOiK02147.
OMAiQDIMERS.
OrthoDBiEOG092C24CZ.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
HAMAPiMF_00310. ATP_synth_B_arch. 1 hit.
InterProiIPR020003. ATPase_a/bsu_AS.
IPR004100. ATPase_F1/V1/A1_a/bsu_N.
IPR000194. ATPase_F1/V1/A1_a/bsu_nucl-bd.
IPR005723. ATPase_V1-cplx_bsu.
IPR027417. P-loop_NTPase.
IPR022879. V-ATPase_su_B/beta.
[Graphical view]
PfamiPF00006. ATP-synt_ab. 1 hit.
PF02874. ATP-synt_ab_N. 1 hit.
[Graphical view]
PIRSFiPIRSF039114. V-ATPsynth_beta/V-ATPase_B. 1 hit.
SUPFAMiSSF52540. SSF52540. 1 hit.
TIGRFAMsiTIGR01040. V-ATPase_V1_B. 1 hit.
PROSITEiPS00152. ATPASE_ALPHA_BETA. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P16140-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MVLSDKELFA INKKAVEQGF NVKPRLNYNT VSGVNGPLVI LEKVKFPRYN
60 70 80 90 100
EIVNLTLPDG TVRQGQVLEI RGDRAIVQVF EGTSGIDVKK TTVEFTGESL
110 120 130 140 150
RIPVSEDMLG RIFDGSGRPI DNGPKVFAED YLDINGSPIN PYARIYPEEM
160 170 180 190 200
ISTGVSAIDT MNSIARGQKI PIFSASGLPH NEIAAQICRQ AGLVRPTKDV
210 220 230 240 250
HDGHEENFSI VFAAMGVNLE TARFFKQDFE ENGSLERTSL FLNLANDPTI
260 270 280 290 300
ERIITPRLAL TTAEYLAYQT ERHVLTILTD MSSYADALRE VSAAREEVPG
310 320 330 340 350
RRGYPGYMYT DLSTIYERAG RVEGRNGSIT QIPILTMPND DITHPIPDLT
360 370 380 390 400
GYITEGQIFV DRQLHNKGIY PPINVLPSLS RLMKSAIGEG MTRKDHGDVS
410 420 430 440 450
NQLYAKYAIG KDAAAMKAVV GEEALSIEDK LSLEFLEKFE KTFITQGAYE
460 470 480 490 500
DRTVFESLDQ AWSLLRIYPK EMLNRISPKI LDEFYDRARD DADEDEEDPD
510
TRSSGKKKDA SQEESLI
Length:517
Mass (Da):57,749
Last modified:October 1, 1994 - v2
Checksum:i02A7DEC571EFF7C2
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti14K → V AA sequence (PubMed:2141385).Curated1
Sequence conflicti79V → L in AAA66890 (PubMed:2521486).Curated1
Sequence conflicti227Q → R in AAA30389 (PubMed:1371275).Curated1
Sequence conflicti500 – 517DTRSS…EESLI → TQEAPVRRRTPAKKNL in AAA66890 (PubMed:2521486).CuratedAdd BLAST18

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J04450 Genomic DNA. Translation: AAA66890.1.
X75891 Genomic DNA. Translation: CAA53486.1.
Z35996 Genomic DNA. Translation: CAA85084.1.
AY693158 Genomic DNA. Translation: AAT93177.1.
M83130 mRNA. Translation: AAA30389.1.
BK006936 Genomic DNA. Translation: DAA07244.1.
PIRiB42254.
S45996.
RefSeqiNP_009685.3. NM_001178475.3.

Genome annotation databases

EnsemblFungiiYBR127C; YBR127C; YBR127C.
GeneIDi852424.
KEGGisce:YBR127C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J04450 Genomic DNA. Translation: AAA66890.1.
X75891 Genomic DNA. Translation: CAA53486.1.
Z35996 Genomic DNA. Translation: CAA85084.1.
AY693158 Genomic DNA. Translation: AAT93177.1.
M83130 mRNA. Translation: AAA30389.1.
BK006936 Genomic DNA. Translation: DAA07244.1.
PIRiB42254.
S45996.
RefSeqiNP_009685.3. NM_001178475.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3J9Telectron microscopy6.90B/D/F1-517[»]
3J9Uelectron microscopy7.60B/D/F1-517[»]
3J9Velectron microscopy8.30B/D/F1-517[»]
5BW9X-ray7.00D/E/F/d/e/f1-517[»]
5D80X-ray6.20D/E/F/d/e/f1-517[»]
ProteinModelPortaliP16140.
SMRiP16140.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi32828. 158 interactors.
DIPiDIP-2292N.
IntActiP16140. 520 interactors.
MINTiMINT-563511.

Chemistry databases

ChEMBLiCHEMBL6106.

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.

PTM databases

iPTMnetiP16140.

Proteomic databases

MaxQBiP16140.
PRIDEiP16140.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYBR127C; YBR127C; YBR127C.
GeneIDi852424.
KEGGisce:YBR127C.

Organism-specific databases

EuPathDBiFungiDB:YBR127C.
SGDiS000000331. VMA2.

Phylogenomic databases

GeneTreeiENSGT00550000074724.
HOGENOMiHOG000165320.
InParanoidiP16140.
KOiK02147.
OMAiQDIMERS.
OrthoDBiEOG092C24CZ.

Enzyme and pathway databases

BioCyciYEAST:G3O-29082-MONOMER.
ReactomeiR-SCE-1222556. ROS, RNS production in response to bacteria.
R-SCE-77387. Insulin receptor recycling.
R-SCE-917977. Transferrin endocytosis and recycling.

Miscellaneous databases

PROiP16140.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
HAMAPiMF_00310. ATP_synth_B_arch. 1 hit.
InterProiIPR020003. ATPase_a/bsu_AS.
IPR004100. ATPase_F1/V1/A1_a/bsu_N.
IPR000194. ATPase_F1/V1/A1_a/bsu_nucl-bd.
IPR005723. ATPase_V1-cplx_bsu.
IPR027417. P-loop_NTPase.
IPR022879. V-ATPase_su_B/beta.
[Graphical view]
PfamiPF00006. ATP-synt_ab. 1 hit.
PF02874. ATP-synt_ab_N. 1 hit.
[Graphical view]
PIRSFiPIRSF039114. V-ATPsynth_beta/V-ATPase_B. 1 hit.
SUPFAMiSSF52540. SSF52540. 1 hit.
TIGRFAMsiTIGR01040. V-ATPase_V1_B. 1 hit.
PROSITEiPS00152. ATPASE_ALPHA_BETA. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiVATB_YEAST
AccessioniPrimary (citable) accession number: P16140
Secondary accession number(s): D6VQC4, P32123
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 1, 1990
Last sequence update: October 1, 1994
Last modified: November 30, 2016
This is version 179 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 131000 molecules/cell in log phase SD medium.1 Publication

Caution

PubMed:1371275 sequence was incorrectly thought to originate from bovine.Curated

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 II
    Yeast (Saccharomyces cerevisiae) chromosome II: 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.