VA0D_YEAST
ID VA0D_YEAST Reviewed; 345 AA.
AC P32366; D6VZ81;
DT 01-OCT-1993, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1996, sequence version 2.
DT 03-AUG-2022, entry version 205.
DE RecName: Full=V-type proton ATPase subunit d;
DE Short=V-ATPase subunit d;
DE AltName: Full=V-ATPase 39 kDa subunit;
DE AltName: Full=V-ATPase subunit M39;
DE AltName: Full=Vacuolar proton pump subunit d;
GN Name=VMA6 {ECO:0000303|PubMed:8509410}; OrderedLocusNames=YLR447C;
GN ORFNames=L9324.8;
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 45-61; 188-198;
RP 256-266; 268-276 AND 338-344, FUNCTION, AND SUBUNIT.
RX PubMed=8509410; DOI=10.1016/s0021-9258(18)31452-2;
RA Bauerle C., Ho M.N., Lindorfer M.A., Stevens T.H.;
RT "The Saccharomyces cerevisiae VMA6 gene encodes the 36-kDa subunit of the
RT vacuolar H(+)-ATPase membrane sector.";
RL J. Biol. Chem. 268:12749-12757(1993).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169871;
RA Johnston M., Hillier L.W., Riles L., Albermann K., Andre B., Ansorge W.,
RA Benes V., Brueckner M., Delius H., Dubois E., Duesterhoeft A.,
RA Entian K.-D., Floeth M., Goffeau A., Hebling U., Heumann K.,
RA Heuss-Neitzel D., Hilbert H., Hilger F., Kleine K., Koetter P., Louis E.J.,
RA Messenguy F., Mewes H.-W., Miosga T., Moestl D., Mueller-Auer S.,
RA Nentwich U., Obermaier B., Piravandi E., Pohl T.M., Portetelle D.,
RA Purnelle B., Rechmann S., Rieger M., Rinke M., Rose M., Scharfe M.,
RA Scherens B., Scholler P., Schwager C., Schwarz S., Underwood A.P.,
RA Urrestarazu L.A., Vandenbol M., Verhasselt P., Vierendeels F., Voet M.,
RA Volckaert G., Voss H., Wambutt R., Wedler E., Wedler H., Zimmermann F.K.,
RA Zollner A., Hani J., Hoheisel J.D.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XII.";
RL Nature 387:87-90(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 PROTEIN SEQUENCE OF 1-18; 76-84; 164-181; 187-276; 298-314 AND 322-335,
RP CLEAVAGE OF INITIATOR METHIONINE, ACETYLATION AT MET-1, AND IDENTIFICATION
RP BY MASS SPECTROMETRY.
RA Bienvenut W.V., Peters C.;
RL Submitted (JUN-2005) to UniProtKB.
RN [5]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX PubMed=14562095; DOI=10.1038/nature02026;
RA Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA Weissman J.S., O'Shea E.K.;
RT "Global analysis of protein localization in budding yeast.";
RL Nature 425:686-691(2003).
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]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22814378; DOI=10.1073/pnas.1210303109;
RA Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A.,
RA Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E.,
RA Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.;
RT "N-terminal acetylome analyses and functional insights of the N-terminal
RT acetyltransferase NatB.";
RL Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
RN [8] {ECO:0007744|PDB:5TJ5}
RP STRUCTURE BY ELECTRON MICROSCOPY (3.90 ANGSTROMS) OF 4-341, AND
RP IDENTIFICATION IN THE V-ATPASE COMPLEX.
RX PubMed=27776355; DOI=10.1038/nature19828;
RA Mazhab-Jafari M.T., Rohou A., Schmidt C., Bueler S.A., Benlekbir S.,
RA Robinson C.V., Rubinstein J.L.;
RT "Atomic model for the membrane-embedded VO motor of a eukaryotic V-
RT ATPase.";
RL Nature 539:118-122(2016).
RN [9] {ECO:0007744|PDB:6C6L}
RP STRUCTURE BY ELECTRON MICROSCOPY (3.50 ANGSTROMS), AND IDENTIFICATION IN
RP THE V-ATPASE COMPLEX.
RX PubMed=29526695; DOI=10.1016/j.molcel.2018.02.006;
RA Roh S.H., Stam N.J., Hryc C.F., Couoh-Cardel S., Pintilie G., Chiu W.,
RA Wilkens S.;
RT "The 3.5-A CryoEM Structure of Nanodisc-Reconstituted Yeast Vacuolar ATPase
RT Vo Proton Channel.";
RL Mol. Cell 69:993-1004.e3(2018).
CC -!- FUNCTION: Subunit of the V0 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:8509410). V-ATPase is responsible for acidifying and
CC maintaining the pH of intracellular compartments (PubMed:8509410). This
CC subunit is a non-integral membrane component of the membrane pore
CC domain and is required for proper assembly of the V0 sector
CC (PubMed:8509410). Might be involved in the regulated assembly of V1
CC subunits onto the membrane sector or alternatively may prevent the
CC passage of protons through V0 pores (PubMed:8509410).
CC {ECO:0000269|PubMed:8509410, ECO:0000303|PubMed:8509410}.
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). {ECO:0000269|PubMed:27776355, ECO:0000269|PubMed:29526695,
CC ECO:0000269|PubMed:8509410}.
CC -!- INTERACTION:
CC P32366; P37296: STV1; NbExp=2; IntAct=EBI-20201, EBI-18479;
CC P32366; P17255: VMA1; NbExp=6; IntAct=EBI-20201, EBI-20245;
CC P32366; P41807: VMA13; NbExp=4; IntAct=EBI-20201, EBI-20281;
CC P32366; P31412: VMA5; NbExp=4; IntAct=EBI-20201, EBI-20260;
CC P32366; P39111: VMA7; NbExp=7; IntAct=EBI-20201, EBI-20272;
CC P32366; P32610: VMA8; NbExp=4; IntAct=EBI-20201, EBI-20264;
CC P32366; P32563: VPH1; NbExp=12; IntAct=EBI-20201, EBI-20455;
CC -!- SUBCELLULAR LOCATION: Vacuole membrane {ECO:0000269|PubMed:14562095};
CC Peripheral membrane protein {ECO:0000269|PubMed:14562095}.
CC -!- MISCELLANEOUS: Present with 1630 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the V-ATPase V0D/AC39 subunit family.
CC {ECO:0000305}.
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DR EMBL; L11584; AAA35210.1; -; Genomic_DNA.
DR EMBL; U22382; AAB67533.1; -; Genomic_DNA.
DR EMBL; BK006945; DAA09747.1; -; Genomic_DNA.
DR PIR; S55969; S55969.
DR RefSeq; NP_013552.3; NM_001182335.3.
DR PDB; 3J9T; EM; 6.90 A; Q=1-345.
DR PDB; 3J9U; EM; 7.60 A; Q=1-345.
DR PDB; 3J9V; EM; 8.30 A; Q=1-345.
DR PDB; 5TJ5; EM; 3.90 A; P=4-155, P=176-201, P=284-341.
DR PDB; 5VOX; EM; 6.80 A; Q=1-345.
DR PDB; 5VOY; EM; 7.90 A; Q=1-345.
DR PDB; 5VOZ; EM; 7.60 A; Q=1-345.
DR PDB; 6C6L; EM; 3.50 A; B=1-345.
DR PDB; 6M0R; EM; 2.70 A; B=1-345.
DR PDB; 6M0S; EM; 3.60 A; B=1-345.
DR PDB; 6O7T; EM; 3.20 A; d=1-345.
DR PDB; 6O7U; EM; 3.10 A; d=1-345.
DR PDB; 6O7V; EM; 6.60 A; d=1-345.
DR PDB; 6O7W; EM; 7.00 A; d=1-345.
DR PDB; 6O7X; EM; 8.70 A; d=1-345.
DR PDB; 6PE4; EM; 3.10 A; D=1-345.
DR PDB; 6PE5; EM; 3.20 A; D=1-345.
DR PDB; 7FDA; EM; 4.20 A; S=1-345.
DR PDB; 7FDB; EM; 4.80 A; S=1-345.
DR PDB; 7FDC; EM; 6.60 A; S=1-345.
DR PDB; 7TAO; EM; 3.20 A; B=1-345.
DR PDB; 7TAP; EM; 2.80 A; B=1-345.
DR PDB; 7TMR; EM; 3.50 A; d=1-345.
DR PDB; 7TMS; EM; 3.80 A; d=1-345.
DR PDBsum; 3J9T; -.
DR PDBsum; 3J9U; -.
DR PDBsum; 3J9V; -.
DR PDBsum; 5TJ5; -.
DR PDBsum; 5VOX; -.
DR PDBsum; 5VOY; -.
DR PDBsum; 5VOZ; -.
DR PDBsum; 6C6L; -.
DR PDBsum; 6M0R; -.
DR PDBsum; 6M0S; -.
DR PDBsum; 6O7T; -.
DR PDBsum; 6O7U; -.
DR PDBsum; 6O7V; -.
DR PDBsum; 6O7W; -.
DR PDBsum; 6O7X; -.
DR PDBsum; 6PE4; -.
DR PDBsum; 6PE5; -.
DR PDBsum; 7FDA; -.
DR PDBsum; 7FDB; -.
DR PDBsum; 7FDC; -.
DR PDBsum; 7TAO; -.
DR PDBsum; 7TAP; -.
DR PDBsum; 7TMR; -.
DR PDBsum; 7TMS; -.
DR AlphaFoldDB; P32366; -.
DR SMR; P32366; -.
DR BioGRID; 31705; 77.
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-1737N; -.
DR IntAct; P32366; 36.
DR MINT; P32366; -.
DR STRING; 4932.YLR447C; -.
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; P32366; -.
DR MaxQB; P32366; -.
DR PaxDb; P32366; -.
DR PRIDE; P32366; -.
DR EnsemblFungi; YLR447C_mRNA; YLR447C; YLR447C.
DR GeneID; 851168; -.
DR KEGG; sce:YLR447C; -.
DR SGD; S000004439; VMA6.
DR VEuPathDB; FungiDB:YLR447C; -.
DR eggNOG; KOG2957; Eukaryota.
DR GeneTree; ENSGT00390000002200; -.
DR HOGENOM; CLU_051277_0_0_1; -.
DR InParanoid; P32366; -.
DR OMA; MLSRAED; -.
DR BioCyc; YEAST:G3O-32502-MON; -.
DR Reactome; R-SCE-1222556; ROS and RNS production in phagocytes.
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:P32366; -.
DR Proteomes; UP000002311; Chromosome XII.
DR RNAct; P32366; protein.
DR GO; GO:0010008; C:endosome membrane; IC:ComplexPortal.
DR GO; GO:0000329; C:fungal-type vacuole membrane; IDA: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:0016471; C:vacuolar proton-transporting V-type ATPase complex; IPI:ComplexPortal.
DR GO; GO:0000220; C:vacuolar proton-transporting V-type ATPase, V0 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; IBA:GO_Central.
DR GO; GO:0007034; P:vacuolar transport; IDA:SGD.
DR Gene3D; 1.10.132.50; -; 1.
DR Gene3D; 1.20.1690.10; -; 2.
DR InterPro; IPR036079; ATPase_su_c/d_sf.
DR InterPro; IPR002843; ATPase_V0-cplx_csu/dsu.
DR InterPro; IPR016727; ATPase_V0-cplx_dsu.
DR InterPro; IPR044911; V-type_ATPase_su_c/d_dom_3.
DR InterPro; IPR035067; V-type_ATPase_suC/d.
DR PANTHER; PTHR11028; PTHR11028; 1.
DR Pfam; PF01992; vATP-synt_AC39; 1.
DR PIRSF; PIRSF018497; V-ATP_synth_D; 1.
DR SUPFAM; SSF103486; SSF103486; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Direct protein sequencing;
KW Hydrogen ion transport; Ion transport; Membrane; Reference proteome;
KW Transport; Vacuole.
FT CHAIN 1..345
FT /note="V-type proton ATPase subunit d"
FT /id="PRO_0000119360"
FT MOD_RES 1
FT /note="N-acetylmethionine"
FT /evidence="ECO:0000269|Ref.4, ECO:0007744|PubMed:22814378"
FT CONFLICT 32
FT /note="N -> T (in Ref. 1; AAA35210)"
FT /evidence="ECO:0000305"
FT HELIX 2..5
FT /evidence="ECO:0007829|PDB:6M0R"
FT HELIX 7..22
FT /evidence="ECO:0007829|PDB:6M0R"
FT HELIX 27..34
FT /evidence="ECO:0007829|PDB:6M0R"
FT HELIX 39..46
FT /evidence="ECO:0007829|PDB:6M0R"
FT TURN 47..51
FT /evidence="ECO:0007829|PDB:6O7U"
FT TURN 54..57
FT /evidence="ECO:0007829|PDB:6M0R"
FT STRAND 60..62
FT /evidence="ECO:0007829|PDB:6PE4"
FT HELIX 65..86
FT /evidence="ECO:0007829|PDB:6M0R"
FT HELIX 90..97
FT /evidence="ECO:0007829|PDB:6M0R"
FT HELIX 100..115
FT /evidence="ECO:0007829|PDB:6M0R"
FT HELIX 120..124
FT /evidence="ECO:0007829|PDB:6M0R"
FT STRAND 125..127
FT /evidence="ECO:0007829|PDB:6PE4"
FT HELIX 129..131
FT /evidence="ECO:0007829|PDB:6M0R"
FT HELIX 137..140
FT /evidence="ECO:0007829|PDB:6M0R"
FT HELIX 145..151
FT /evidence="ECO:0007829|PDB:6M0R"
FT TURN 152..155
FT /evidence="ECO:0007829|PDB:6M0R"
FT HELIX 159..165
FT /evidence="ECO:0007829|PDB:6M0R"
FT TURN 169..171
FT /evidence="ECO:0007829|PDB:6C6L"
FT HELIX 174..198
FT /evidence="ECO:0007829|PDB:6M0R"
FT HELIX 204..229
FT /evidence="ECO:0007829|PDB:6M0R"
FT HELIX 235..238
FT /evidence="ECO:0007829|PDB:6M0R"
FT TURN 239..241
FT /evidence="ECO:0007829|PDB:6M0R"
FT STRAND 244..248
FT /evidence="ECO:0007829|PDB:6M0R"
FT HELIX 251..257
FT /evidence="ECO:0007829|PDB:6M0R"
FT HELIX 262..269
FT /evidence="ECO:0007829|PDB:6M0R"
FT TURN 273..277
FT /evidence="ECO:0007829|PDB:6O7T"
FT TURN 278..280
FT /evidence="ECO:0007829|PDB:6M0R"
FT HELIX 284..299
FT /evidence="ECO:0007829|PDB:6M0R"
FT STRAND 300..304
FT /evidence="ECO:0007829|PDB:6O7U"
FT HELIX 308..331
FT /evidence="ECO:0007829|PDB:6M0R"
FT HELIX 335..337
FT /evidence="ECO:0007829|PDB:6PE5"
FT HELIX 338..340
FT /evidence="ECO:0007829|PDB:6M0R"
SQ SEQUENCE 345 AA; 39791 MW; 53A19450CAF35632 CRC64;
MEGVYFNIDN GFIEGVVRGY RNGLLSNNQY INLTQCDTLE DLKLQLSSTD YGNFLSSVSS
ESLTTSLIQE YASSKLYHEF NYIRDQSSGS TRKFMDYITY GYMIDNVALM ITGTIHDRDK
GEILQRCHPL GWFDTLPTLS VATDLESLYE TVLVDTPLAP YFKNCFDTAE ELDDMNIEII
RNKLYKAYLE DFYNFVTEEI PEPAKECMQT LLGFEADRRS INIALNSLQS SDIDPDLKSD
LLPNIGKLYP LATFHLAQAQ DFEGVRAALA NVYEYRGFLE TGNLEDHFYQ LEMELCRDAF
TQQFAISTVW AWMKSKEQEV RNITWIAECI AQNQRERINN YISVY
