VATD_YEAST
ID VATD_YEAST Reviewed; 256 AA.
AC P32610; D3DLJ9;
DT 01-OCT-1993, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1993, sequence version 1.
DT 03-AUG-2022, entry version 191.
DE RecName: Full=V-type proton ATPase subunit D {ECO:0000303|PubMed:7831318};
DE Short=V-ATPase subunit D;
DE AltName: Full=Vacuolar proton pump subunit D;
GN Name=VMA8 {ECO:0000303|PubMed:7797485};
GN OrderedLocusNames=YEL051W {ECO:0000312|SGD:S000000777};
GN ORFNames=SYGP-ORF11;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 6-12; 170-179 AND
RP 182-187, FUNCTION, AND SUBCELLULAR LOCATION.
RX PubMed=7797485; DOI=10.1074/jbc.270.25.15037;
RA Graham L.A., Hill K.J., Stevens T.H.;
RT "VMA8 encodes a 32-kDa V1 subunit of the Saccharomyces cerevisiae vacuolar
RT H(+)-ATPase required for function and assembly of the enzyme complex.";
RL J. Biol. Chem. 270:15037-15044(1995).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169868;
RA Dietrich F.S., Mulligan J.T., Hennessy K.M., Yelton M.A., Allen E.,
RA Araujo R., Aviles E., Berno A., Brennan T., Carpenter J., Chen E.,
RA Cherry J.M., Chung E., Duncan M., Guzman E., Hartzell G., Hunicke-Smith S.,
RA Hyman R.W., Kayser A., Komp C., Lashkari D., Lew H., Lin D., Mosedale D.,
RA Nakahara K., Namath A., Norgren R., Oefner P., Oh C., Petel F.X.,
RA Roberts D., Sehl P., Schramm S., Shogren T., Smith V., Taylor P., Wei Y.,
RA Botstein D., Davis R.W.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome V.";
RL Nature 387:78-81(1997).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [4]
RP FUNCTION.
RX PubMed=7831318; DOI=10.1073/pnas.92.2.497;
RA Nelson H., Mandiyan S., Nelson N.;
RT "A bovine cDNA and a yeast gene (VMA8) encoding the subunit D of the
RT vacuolar H(+)-ATPase.";
RL Proc. Natl. Acad. Sci. U.S.A. 92:497-501(1995).
RN [5]
RP INTERACTION WITH RAV1 AND RAV2.
RX PubMed=11283612; DOI=10.1038/35070067;
RA Seol J.H., Shevchenko A., Shevchenko A., Deshaies R.J.;
RT "Skp1 forms multiple protein complexes, including RAVE, a regulator of V-
RT ATPase assembly.";
RL Nat. Cell Biol. 3:384-391(2001).
RN [6]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [7] {ECO:0007744|PDB:3J9T, ECO:0007744|PDB:3J9U, ECO:0007744|PDB:3J9V}
RP STRUCTURE BY ELECTRON MICROSCOPY (6.90 ANGSTROMS), AND IDENTIFICATION IN
RP THE V-ATPASE COMPLEX.
RX PubMed=25971514; DOI=10.1038/nature14365;
RA Zhao J., Benlekbir S., Rubinstein J.L.;
RT "Electron cryomicroscopy observation of rotational states in a eukaryotic
RT V-ATPase.";
RL Nature 521:241-245(2015).
RN [8] {ECO:0007744|PDB:5BW9, ECO:0007744|PDB:5D80}
RP X-RAY CRYSTALLOGRAPHY (6.20 ANGSTROMS), AND IDENTIFICATION IN THE V-ATPASE
RP COMPLEX.
RX PubMed=27295975; DOI=10.15252/embj.201593447;
RA Oot R.A., Kane P.M., Berry E.A., Wilkens S.;
RT "Crystal structure of yeast V1-ATPase in the autoinhibited state.";
RL EMBO J. 35:1694-1706(2016).
CC -!- FUNCTION: Subunit of the V1 complex of vacuolar(H+)-ATPase (V-ATPase),
CC a multisubunit enzyme composed of a peripheral complex (V1) that
CC hydrolyzes ATP and a membrane integral complex (V0) that translocates
CC protons (PubMed:7797485, PubMed:7831318). V-ATPase is responsible for
CC acidifying and maintaining the pH of intracellular compartments
CC (PubMed:7797485, PubMed:7831318). {ECO:0000269|PubMed:7797485,
CC ECO:0000269|PubMed:7831318}.
CC -!- SUBUNIT: V-ATPase is a heteromultimeric enzyme composed of a peripheral
CC catalytic V1 complex (components A to H) attached to an integral
CC membrane V0 proton pore complex (components: a, c, c', c'', d, e, f and
CC VOA1) (PubMed:25971514, PubMed:27295975). Interacts with RAV1 and RAV2
CC components of the RAVE complex, which are essential for the stability
CC and assembly of V-ATPase (PubMed:11283612).
CC {ECO:0000269|PubMed:11283612, ECO:0000269|PubMed:25971514,
CC ECO:0000269|PubMed:27295975}.
CC -!- INTERACTION:
CC P32610; P47104: RAV1; NbExp=2; IntAct=EBI-20264, EBI-25471;
CC P32610; P32366: VMA6; NbExp=4; IntAct=EBI-20264, EBI-20201;
CC P32610; P39111: VMA7; NbExp=3; IntAct=EBI-20264, EBI-20272;
CC -!- SUBCELLULAR LOCATION: Vacuole membrane {ECO:0000269|PubMed:7797485};
CC Peripheral membrane protein {ECO:0000305}; Cytoplasmic side
CC {ECO:0000305}.
CC -!- MISCELLANEOUS: Present with 8500 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the V-ATPase D subunit family. {ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; U18779; AAB64991.1; -; Genomic_DNA.
DR EMBL; BK006939; DAA07603.1; -; Genomic_DNA.
DR PIR; S30826; S30826.
DR RefSeq; NP_010863.1; NM_001178866.1.
DR PDB; 3J9T; EM; 6.90 A; M=1-256.
DR PDB; 3J9U; EM; 7.60 A; M=1-256.
DR PDB; 3J9V; EM; 8.30 A; M=1-256.
DR PDB; 4RND; X-ray; 3.18 A; A/C=1-256.
DR PDB; 5BW9; X-ray; 7.00 A; G/g=1-256.
DR PDB; 5D80; X-ray; 6.20 A; G/g=1-256.
DR PDB; 5VOX; EM; 6.80 A; M=1-256.
DR PDB; 5VOY; EM; 7.90 A; M=1-256.
DR PDB; 5VOZ; EM; 7.60 A; M=1-256.
DR PDB; 6O7V; EM; 6.60 A; M=1-256.
DR PDB; 6O7W; EM; 7.00 A; M=1-256.
DR PDB; 6O7X; EM; 8.70 A; M=1-256.
DR PDB; 7FDA; EM; 4.20 A; M=1-256.
DR PDB; 7FDB; EM; 4.80 A; M=1-256.
DR PDB; 7FDC; EM; 6.60 A; M=1-256.
DR PDB; 7FDE; EM; 3.80 A; M=1-256.
DR PDBsum; 3J9T; -.
DR PDBsum; 3J9U; -.
DR PDBsum; 3J9V; -.
DR PDBsum; 4RND; -.
DR PDBsum; 5BW9; -.
DR PDBsum; 5D80; -.
DR PDBsum; 5VOX; -.
DR PDBsum; 5VOY; -.
DR PDBsum; 5VOZ; -.
DR PDBsum; 6O7V; -.
DR PDBsum; 6O7W; -.
DR PDBsum; 6O7X; -.
DR PDBsum; 7FDA; -.
DR PDBsum; 7FDB; -.
DR PDBsum; 7FDC; -.
DR PDBsum; 7FDE; -.
DR AlphaFoldDB; P32610; -.
DR SMR; P32610; -.
DR BioGRID; 36678; 429.
DR ComplexPortal; CPX-1192; Vacuolar proton translocating ATPase complex, Golgi variant.
DR ComplexPortal; CPX-1193; Vacuolar proton translocating ATPase complex, vacuole variant.
DR DIP; DIP-2959N; -.
DR IntAct; P32610; 48.
DR MINT; P32610; -.
DR STRING; 4932.YEL051W; -.
DR TCDB; 3.A.2.2.3; the h(+)- or na(+)-translocating f-type, v-type and a-type atpase (f-atpase) superfamily.
DR iPTMnet; P32610; -.
DR MaxQB; P32610; -.
DR PaxDb; P32610; -.
DR PRIDE; P32610; -.
DR EnsemblFungi; YEL051W_mRNA; YEL051W; YEL051W.
DR GeneID; 856659; -.
DR KEGG; sce:YEL051W; -.
DR SGD; S000000777; VMA8.
DR VEuPathDB; FungiDB:YEL051W; -.
DR eggNOG; KOG1647; Eukaryota.
DR GeneTree; ENSGT00390000010770; -.
DR HOGENOM; CLU_069688_0_1_1; -.
DR InParanoid; P32610; -.
DR OMA; SKNIMGV; -.
DR BioCyc; YEAST:G3O-30169-MON; -.
DR Reactome; R-SCE-1222556; ROS and RNS production in phagocytes.
DR Reactome; R-SCE-6798695; Neutrophil degranulation.
DR Reactome; R-SCE-77387; Insulin receptor recycling.
DR Reactome; R-SCE-917977; Transferrin endocytosis and recycling.
DR Reactome; R-SCE-9639288; Amino acids regulate mTORC1.
DR PRO; PR:P32610; -.
DR Proteomes; UP000002311; Chromosome V.
DR RNAct; P32610; protein.
DR GO; GO:0010008; C:endosome membrane; IC:ComplexPortal.
DR GO; GO:0000329; C:fungal-type vacuole membrane; HDA:SGD.
DR GO; GO:0000139; C:Golgi membrane; IC:ComplexPortal.
DR GO; GO:0016020; C:membrane; IDA:ComplexPortal.
DR GO; GO:0033176; C:proton-transporting V-type ATPase complex; IPI:ComplexPortal.
DR GO; GO:0005774; C:vacuolar membrane; IBA:GO_Central.
DR GO; GO:0016471; C:vacuolar proton-transporting V-type ATPase complex; IDA:SGD.
DR GO; GO:0000221; C:vacuolar proton-transporting V-type ATPase, V1 domain; IDA:UniProtKB.
DR GO; GO:0046961; F:proton-transporting ATPase activity, rotational mechanism; IC:UniProtKB.
DR GO; GO:0048388; P:endosomal lumen acidification; IC:ComplexPortal.
DR GO; GO:0061795; P:Golgi lumen acidification; IC:ComplexPortal.
DR GO; GO:1902600; P:proton transmembrane transport; IDA:ComplexPortal.
DR GO; GO:0007035; P:vacuolar acidification; IMP:SGD.
DR InterPro; IPR002699; V_ATPase_D.
DR PANTHER; PTHR11671; PTHR11671; 1.
DR Pfam; PF01813; ATP-synt_D; 1.
DR TIGRFAMs; TIGR00309; V_ATPase_subD; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Hydrogen ion transport;
KW Ion transport; Membrane; Reference proteome; Transport; Vacuole.
FT CHAIN 1..256
FT /note="V-type proton ATPase subunit D"
FT /id="PRO_0000144244"
FT REGION 211..256
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 211..234
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT HELIX 29..75
FT /evidence="ECO:0007829|PDB:4RND"
FT HELIX 79..85
FT /evidence="ECO:0007829|PDB:4RND"
FT STRAND 91..101
FT /evidence="ECO:0007829|PDB:4RND"
FT STRAND 104..113
FT /evidence="ECO:0007829|PDB:4RND"
FT STRAND 115..117
FT /evidence="ECO:0007829|PDB:4RND"
FT HELIX 128..175
FT /evidence="ECO:0007829|PDB:4RND"
FT HELIX 177..202
FT /evidence="ECO:0007829|PDB:4RND"
SQ SEQUENCE 256 AA; 29194 MW; FDE93E1FAF0AEC5B CRC64;
MSGNREQVFP TRMTLGLMKT KLKGANQGYS LLKRKSEALT KRFRDITKRI DDAKQKMGRV
MQTAAFSLAE VSYATGENIG YQVQESVSTA RFKVRARQEN VSGVYLSQFE SYIDPEINDF
RLTGLGRGGQ QVQRAKEIYS RAVETLVELA SLQTAFIILD EVIKVTNRRV NAIEHVIIPR
TENTIAYINS ELDELDREEF YRLKKVQEKK QNETAKLDAE MKLKRDRAEQ DASEVAADEE
PQGETLVADQ EDDVIF
