VATH_YEAST
ID VATH_YEAST Reviewed; 478 AA.
AC P41807; D6W446;
DT 01-NOV-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1995, sequence version 1.
DT 03-AUG-2022, entry version 201.
DE RecName: Full=V-type proton ATPase subunit H;
DE Short=V-ATPase subunit H;
DE AltName: Full=V-ATPase 54 kDa subunit;
DE AltName: Full=Vacuolar proton pump subunit H;
GN Name=VMA13 {ECO:0000303|PubMed:8349704}; Synonyms=CLS11;
GN OrderedLocusNames=YPR036W; ORFNames=YP3085.02;
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], FUNCTION, IDENTIFICATION IN THE V-ATPASE
RP COMPLEX, AND SUBCELLULAR LOCATION.
RC STRAIN=ATCC 26786 / X2180-1A;
RX PubMed=8349704; DOI=10.1016/s0021-9258(17)46842-6;
RA Ho M.N., Hirata R., Umemoto N., Ohya Y., Takatsuki A., Stevens T.H.,
RA Anraku Y.;
RT "VMA13 encodes a 54-kDa vacuolar H(+)-ATPase subunit required for activity
RT but not assembly of the enzyme complex in Saccharomyces cerevisiae.";
RL J. Biol. Chem. 268:18286-18292(1993).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169875;
RA Bussey H., Storms R.K., Ahmed A., Albermann K., Allen E., Ansorge W.,
RA Araujo R., Aparicio A., Barrell B.G., Badcock K., Benes V., Botstein D.,
RA Bowman S., Brueckner M., Carpenter J., Cherry J.M., Chung E.,
RA Churcher C.M., Coster F., Davis K., Davis R.W., Dietrich F.S., Delius H.,
RA DiPaolo T., Dubois E., Duesterhoeft A., Duncan M., Floeth M., Fortin N.,
RA Friesen J.D., Fritz C., Goffeau A., Hall J., Hebling U., Heumann K.,
RA Hilbert H., Hillier L.W., Hunicke-Smith S., Hyman R.W., Johnston M.,
RA Kalman S., Kleine K., Komp C., Kurdi O., Lashkari D., Lew H., Lin A.,
RA Lin D., Louis E.J., Marathe R., Messenguy F., Mewes H.-W., Mirtipati S.,
RA Moestl D., Mueller-Auer S., Namath A., Nentwich U., Oefner P., Pearson D.,
RA Petel F.X., Pohl T.M., Purnelle B., Rajandream M.A., Rechmann S.,
RA Rieger M., Riles L., Roberts D., Schaefer M., Scharfe M., Scherens B.,
RA Schramm S., Schroeder M., Sdicu A.-M., Tettelin H., Urrestarazu L.A.,
RA Ushinsky S., Vierendeels F., Vissers S., Voss H., Walsh S.V., Wambutt R.,
RA Wang Y., Wedler E., Wedler H., Winnett E., Zhong W.-W., Zollner A.,
RA Vo D.H., Hani J.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI.";
RL Nature 387:103-105(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 INTERACTION WITH YND1.
RX PubMed=10954728; DOI=10.1074/jbc.m006932200;
RA Zhong X., Malhotra R., Guidotti G.;
RT "Regulation of yeast ectoapyrase ynd1p activity by activator subunit Vma13p
RT of vacuolar H+-ATPase.";
RL J. Biol. Chem. 275:35592-35599(2000).
RN [5]
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 [6]
RP IDENTIFICATION IN THE V-ATPASE COMPLEX, MASS SPECTROMETRY, AND CLEAVAGE OF
RP INITIATOR METHIONINE.
RX PubMed=18055462; DOI=10.1074/jbc.m707924200;
RA Kitagawa N., Mazon H., Heck A.J.R., Wilkens S.;
RT "Stoichiometry of the peripheral stalk subunits E and G of yeast V1-ATPase
RT determined by mass spectrometry.";
RL J. Biol. Chem. 283:3329-3337(2008).
RN [7]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200;
RA Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT "A multidimensional chromatography technology for in-depth phosphoproteome
RT analysis.";
RL Mol. Cell. Proteomics 7:1389-1396(2008).
RN [8]
RP IDENTIFICATION BY MASS 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 [9]
RP X-RAY CRYSTALLOGRAPHY (2.95 ANGSTROMS).
RX PubMed=11416198; DOI=10.1073/pnas.131192798;
RA Sagermann M., Stevens T.H., Matthews B.W.;
RT "Crystal structure of the regulatory subunit H of the V-type ATPase of
RT Saccharomyces cerevisiae.";
RL Proc. Natl. Acad. Sci. U.S.A. 98:7134-7139(2001).
RN [10] {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 [11] {ECO:0007744|PDB:5BW9, ECO:0007744|PDB:5D80}
RP X-RAY CRYSTALLOGRAPHY (6.20 ANGSTROMS), FUNCTION, IDENTIFICATION IN THE
RP V-ATPASE COMPLEX, DISRUPTION PHENOTYPE, AND MUTAGENESIS OF 405-LYS--ILE-418
RP AND ASP-410.
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:8349704, PubMed:27295975). V-ATPase is responsible for
CC acidifying and maintaining the pH of intracellular compartments
CC (PubMed:8349704, PubMed:27295975). This subunit is essential for
CC activity, but not assembly, of the enzyme complex (PubMed:8349704,
CC PubMed:27295975). This subunit is also required for silencing the
CC ATPase activity of V-ATPase when V1 is detached from V0
CC (PubMed:27295975). {ECO:0000269|PubMed:27295975,
CC ECO:0000269|PubMed:8349704}.
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:8349704, PubMed:25971514, PubMed:18055462,
CC PubMed:27295975). Interacts with YND1 (PubMed:10954728).
CC {ECO:0000269|PubMed:10954728, ECO:0000269|PubMed:18055462,
CC ECO:0000269|PubMed:25971514, ECO:0000269|PubMed:27295975,
CC ECO:0000269|PubMed:8349704}.
CC -!- INTERACTION:
CC P41807; P32366: VMA6; NbExp=4; IntAct=EBI-20281, EBI-20201;
CC P41807; P39111: VMA7; NbExp=3; IntAct=EBI-20281, EBI-20272;
CC P41807; P32563: VPH1; NbExp=3; IntAct=EBI-20281, EBI-20455;
CC -!- SUBCELLULAR LOCATION: Vacuole membrane {ECO:0000269|PubMed:8349704};
CC Peripheral membrane protein {ECO:0000305}; Cytoplasmic side
CC {ECO:0000305}.
CC -!- MASS SPECTROMETRY: Mass=54298.1; Mass_error=22.1; Method=Electrospray;
CC Evidence={ECO:0000269|PubMed:18055462};
CC -!- DISRUPTION PHENOTYPE: Increases the ATPase activity of membrane-
CC detached V-ATPase V1 (PubMed:27295975). Abolishes growth at pH 7.5 and
CC in the presence of calcium chloride, abrogates growth at pH 5.0
CC (PubMed:27295975). {ECO:0000269|PubMed:27295975}.
CC -!- MISCELLANEOUS: Present with 22500 molecules/cell in log phase SD
CC medium. {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the V-ATPase H subunit family. {ECO:0000305}.
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DR EMBL; D13916; BAA03011.1; -; Genomic_DNA.
DR EMBL; Z68111; CAA92142.1; -; Genomic_DNA.
DR EMBL; Z71255; CAA94986.1; -; Genomic_DNA.
DR EMBL; BK006949; DAA11462.1; -; Genomic_DNA.
DR PIR; A47429; A47429.
DR RefSeq; NP_015361.1; NM_001184133.1.
DR PDB; 1HO8; X-ray; 2.95 A; A=1-478.
DR PDB; 3J9T; EM; 6.90 A; P=1-478.
DR PDB; 3J9U; EM; 7.60 A; P=1-478.
DR PDB; 3J9V; EM; 8.30 A; P=1-478.
DR PDB; 5BW9; X-ray; 7.00 A; H/h=1-478.
DR PDB; 5D80; X-ray; 6.20 A; H/h=1-478.
DR PDB; 5VOX; EM; 6.80 A; P=1-478.
DR PDB; 5VOY; EM; 7.90 A; P=1-478.
DR PDB; 5VOZ; EM; 7.60 A; P=1-478.
DR PDB; 6O7V; EM; 6.60 A; P=1-478.
DR PDB; 6O7W; EM; 7.00 A; P=1-478.
DR PDB; 6O7X; EM; 8.70 A; P=1-478.
DR PDB; 7FDA; EM; 4.20 A; P=1-359.
DR PDB; 7FDB; EM; 4.80 A; P=1-359.
DR PDB; 7FDC; EM; 6.60 A; P=1-359.
DR PDB; 7TMM; EM; 3.50 A; P=1-478.
DR PDB; 7TMO; EM; 3.30 A; P=1-478.
DR PDB; 7TMP; EM; 3.30 A; P=1-478.
DR PDB; 7TMQ; EM; 3.30 A; P=1-478.
DR PDB; 7TMR; EM; 3.50 A; P=1-478.
DR PDB; 7TMS; EM; 3.80 A; P=1-478.
DR PDBsum; 1HO8; -.
DR PDBsum; 3J9T; -.
DR PDBsum; 3J9U; -.
DR PDBsum; 3J9V; -.
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; 7TMM; -.
DR PDBsum; 7TMO; -.
DR PDBsum; 7TMP; -.
DR PDBsum; 7TMQ; -.
DR PDBsum; 7TMR; -.
DR PDBsum; 7TMS; -.
DR AlphaFoldDB; P41807; -.
DR SMR; P41807; -.
DR BioGRID; 36214; 433.
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-6640N; -.
DR IntAct; P41807; 23.
DR MINT; P41807; -.
DR STRING; 4932.YPR036W; -.
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; P41807; -.
DR MaxQB; P41807; -.
DR PaxDb; P41807; -.
DR PRIDE; P41807; -.
DR EnsemblFungi; YPR036W_mRNA; YPR036W; YPR036W.
DR GeneID; 856148; -.
DR KEGG; sce:YPR036W; -.
DR SGD; S000006240; VMA13.
DR VEuPathDB; FungiDB:YPR036W; -.
DR eggNOG; KOG2759; Eukaryota.
DR GeneTree; ENSGT00390000003289; -.
DR HOGENOM; CLU_025709_4_0_1; -.
DR InParanoid; P41807; -.
DR OMA; CWSPPHI; -.
DR BioCyc; YEAST:G3O-34194-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 EvolutionaryTrace; P41807; -.
DR PRO; PR:P41807; -.
DR Proteomes; UP000002311; Chromosome XVI.
DR RNAct; P41807; 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:0000221; C:vacuolar proton-transporting V-type ATPase, V1 domain; IDA:UniProtKB.
DR GO; GO:0046961; F:proton-transporting ATPase activity, rotational mechanism; TAS:SGD.
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 Gene3D; 1.25.10.10; -; 1.
DR Gene3D; 1.25.40.150; -; 1.
DR InterPro; IPR011989; ARM-like.
DR InterPro; IPR016024; ARM-type_fold.
DR InterPro; IPR004908; ATPase_V1-cplx_hsu.
DR InterPro; IPR011987; ATPase_V1-cplx_hsu_C.
DR InterPro; IPR038497; ATPase_V1-cplx_hsu_C_sf.
DR PANTHER; PTHR10698; PTHR10698; 1.
DR Pfam; PF11698; V-ATPase_H_C; 1.
DR Pfam; PF03224; V-ATPase_H_N; 1.
DR PIRSF; PIRSF032184; ATPase_V1_H; 1.
DR SUPFAM; SSF48371; SSF48371; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Hydrogen ion transport; Ion transport; Membrane;
KW Reference proteome; Transport; Vacuole.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:18055462"
FT CHAIN 2..478
FT /note="V-type proton ATPase subunit H"
FT /id="PRO_0000124202"
FT MUTAGEN 405..418
FT /note="KVRNGDVNAKQEKI->GDVN: Increases the ATPase activity
FT of membrane-detached V-ATPase V1, appears to have no effect
FT on cell population growth."
FT /evidence="ECO:0000269|PubMed:27295975"
FT MUTAGEN 410
FT /note="D->A: Appears to have no effect on the ATPase
FT activity of membrane-detached V-ATPase V1 or on cell
FT population growth."
FT /evidence="ECO:0000269|PubMed:27295975"
FT HELIX 11..22
FT /evidence="ECO:0007829|PDB:1HO8"
FT HELIX 27..32
FT /evidence="ECO:0007829|PDB:1HO8"
FT HELIX 38..52
FT /evidence="ECO:0007829|PDB:1HO8"
FT HELIX 77..85
FT /evidence="ECO:0007829|PDB:1HO8"
FT HELIX 90..105
FT /evidence="ECO:0007829|PDB:1HO8"
FT STRAND 107..110
FT /evidence="ECO:0007829|PDB:1HO8"
FT HELIX 111..119
FT /evidence="ECO:0007829|PDB:1HO8"
FT HELIX 123..130
FT /evidence="ECO:0007829|PDB:1HO8"
FT HELIX 136..150
FT /evidence="ECO:0007829|PDB:1HO8"
FT TURN 153..155
FT /evidence="ECO:0007829|PDB:1HO8"
FT HELIX 158..166
FT /evidence="ECO:0007829|PDB:1HO8"
FT HELIX 168..175
FT /evidence="ECO:0007829|PDB:1HO8"
FT HELIX 180..194
FT /evidence="ECO:0007829|PDB:1HO8"
FT HELIX 197..204
FT /evidence="ECO:0007829|PDB:1HO8"
FT HELIX 207..222
FT /evidence="ECO:0007829|PDB:1HO8"
FT HELIX 239..253
FT /evidence="ECO:0007829|PDB:1HO8"
FT HELIX 257..264
FT /evidence="ECO:0007829|PDB:1HO8"
FT HELIX 268..280
FT /evidence="ECO:0007829|PDB:1HO8"
FT HELIX 284..296
FT /evidence="ECO:0007829|PDB:1HO8"
FT STRAND 299..302
FT /evidence="ECO:0007829|PDB:1HO8"
FT HELIX 305..316
FT /evidence="ECO:0007829|PDB:1HO8"
FT HELIX 318..326
FT /evidence="ECO:0007829|PDB:1HO8"
FT HELIX 333..351
FT /evidence="ECO:0007829|PDB:1HO8"
FT HELIX 355..365
FT /evidence="ECO:0007829|PDB:1HO8"
FT HELIX 372..375
FT /evidence="ECO:0007829|PDB:1HO8"
FT HELIX 377..383
FT /evidence="ECO:0007829|PDB:1HO8"
FT HELIX 385..387
FT /evidence="ECO:0007829|PDB:1HO8"
FT HELIX 390..392
FT /evidence="ECO:0007829|PDB:1HO8"
FT HELIX 393..407
FT /evidence="ECO:0007829|PDB:1HO8"
FT HELIX 414..433
FT /evidence="ECO:0007829|PDB:1HO8"
FT HELIX 435..437
FT /evidence="ECO:0007829|PDB:1HO8"
FT HELIX 438..444
FT /evidence="ECO:0007829|PDB:1HO8"
FT HELIX 446..453
FT /evidence="ECO:0007829|PDB:1HO8"
FT HELIX 459..475
FT /evidence="ECO:0007829|PDB:1HO8"
SQ SEQUENCE 478 AA; 54416 MW; 54131FF9C2C87594 CRC64;
MGATKILMDS THFNEIRSII RSRSVAWDAL ARSEELSEID ASTAKALESI LVKKNIGDGL
SSSNNAHSGF KVNGKTLIPL IHLLSTSDNE DCKKSVQNLI AELLSSDKYG DDTVKFFQED
PKQLEQLFDV SLKGDFQTVL ISGFNVVSLL VQNGLHNVKL VEKLLKNNNL INILQNIEQM
DTCYVCIRLL QELAVIPEYR DVIWLHEKKF MPTLFKILQR ATDSQLATRI VATNSNHLGI
QLQYHSLLLI WLLTFNPVFA NELVQKYLSD FLDLLKLVKI TIKEKVSRLC ISIILQCCST
RVKQHKKVIK QLLLLGNALP TVQSLSERKY SDEELRQDIS NLKEILENEY QELTSFDEYV
AELDSKLLCW SPPHVDNGFW SDNIDEFKKD NYKIFRQLIE LLQAKVRNGD VNAKQEKIII
QVALNDITHV VELLPESIDV LDKTGGKADI MELLNHSDSR VKYEALKATQ AIIGYTFK
