ATPD_YEAST
ID ATPD_YEAST Reviewed; 160 AA.
AC Q12165; D6VRY4;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 188.
DE RecName: Full=ATP synthase subunit delta, mitochondrial;
DE AltName: Full=F-ATPase delta subunit;
DE Flags: Precursor;
GN Name=ATP16; OrderedLocusNames=YDL004W; ORFNames=D2935, YD8119.03;
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], AND PROTEIN SEQUENCE OF 23-72; 112-121
RP AND 141-160.
RC STRAIN=D273-10B/A;
RX PubMed=8026496; DOI=10.1111/j.1432-1033.1994.tb18932.x;
RA Giraud M.-F., Velours J.;
RT "ATP synthase of yeast mitochondria. Isolation of the F1 delta subunit,
RT sequence and disruption of the structural gene.";
RL Eur. J. Biochem. 222:851-859(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169867;
RA Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G.,
RA Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C.,
RA Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F.,
RA Delaveau T., del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M.,
RA Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T.,
RA Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C.,
RA Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S.,
RA Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L.,
RA Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H.,
RA Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M.,
RA Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M.,
RA Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A.,
RA Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G.,
RA Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E.,
RA Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S.,
RA Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D.,
RA Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V.,
RA Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E.,
RA Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M.,
RA Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D.,
RA Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X.,
RA Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A.,
RA Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R.,
RA Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T.,
RA Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L.,
RA Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E.,
RA Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L.,
RA Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M.,
RA Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K.,
RA Mewes H.-W., Zollner A., Zaccaria P.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV.";
RL Nature 387:75-78(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 NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=17322287; DOI=10.1101/gr.6037607;
RA Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F.,
RA Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J.,
RA Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J.,
RA Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D.,
RA LaBaer J.;
RT "Approaching a complete repository of sequence-verified protein-encoding
RT clones for Saccharomyces cerevisiae.";
RL Genome Res. 17:536-543(2007).
RN [5]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ATCC 76625 / YPH499;
RX PubMed=17761666; DOI=10.1074/mcp.m700098-mcp200;
RA Reinders J., Wagner K., Zahedi R.P., Stojanovski D., Eyrich B.,
RA van der Laan M., Rehling P., Sickmann A., Pfanner N., Meisinger C.;
RT "Profiling phosphoproteins of yeast mitochondria reveals a role of
RT phosphorylation in assembly of the ATP synthase.";
RL Mol. Cell. Proteomics 6:1896-1906(2007).
RN [6]
RP 3D-STRUCTURE MODELING, FUNCTION, IDENTIFICATION IN THE F-TYPE ATPASE
RP COMPLEX, AND SUBCELLULAR LOCATION.
RX PubMed=10576729; DOI=10.1126/science.286.5445.1700;
RA Stock D., Leslie A.G., Walker J.E.;
RT "Molecular architecture of the rotary motor in ATP synthase.";
RL Science 286:1700-1705(1999).
CC -!- FUNCTION: Mitochondrial membrane ATP synthase (F(1)F(0) ATP synthase or
CC Complex V) produces ATP from ADP in the presence of a proton gradient
CC across the membrane which is generated by electron transport complexes
CC of the respiratory chain. F-type ATPases consist of two structural
CC domains, F(1) - containing the extramembraneous catalytic core, and
CC F(0) - containing the membrane proton channel, linked together by a
CC central stalk and a peripheral stalk. During catalysis, ATP turnover in
CC the catalytic domain of F(1) is coupled via a rotary mechanism of the
CC central stalk subunits to proton translocation. Part of the complex
CC F(1) domain and of the central stalk which is part of the complex
CC rotary element. Rotation of the central stalk against the surrounding
CC alpha(3)beta(3) subunits leads to hydrolysis of ATP in three separate
CC catalytic sites on the beta subunits. {ECO:0000269|PubMed:10576729}.
CC -!- SUBUNIT: F-type ATPases have 2 components, CF(1) - the catalytic core
CC - and CF(0) - the membrane proton channel. CF(1) has five subunits:
CC alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main
CC subunits: a, b and c. {ECO:0000269|PubMed:10576729}.
CC -!- SUBCELLULAR LOCATION: Mitochondrion. Mitochondrion inner membrane
CC {ECO:0000269|PubMed:10576729}.
CC -!- SIMILARITY: Belongs to the ATPase epsilon chain family. {ECO:0000305}.
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DR EMBL; Z21857; CAA79912.1; -; Genomic_DNA.
DR EMBL; Z48008; CAA88057.1; -; Genomic_DNA.
DR EMBL; Z48432; CAA88355.1; -; Genomic_DNA.
DR EMBL; Z74052; CAA98560.1; -; Genomic_DNA.
DR EMBL; AY558155; AAS56481.1; -; Genomic_DNA.
DR EMBL; BK006938; DAA11844.1; -; Genomic_DNA.
DR PIR; S45632; S45632.
DR RefSeq; NP_010280.1; NM_001180063.1.
DR PDB; 2HLD; X-ray; 2.80 A; H/Q/Z=23-160.
DR PDB; 2WPD; X-ray; 3.43 A; H=23-160.
DR PDB; 2XOK; X-ray; 3.01 A; H=1-160.
DR PDB; 3FKS; X-ray; 3.59 A; H/Q/Z=23-160.
DR PDB; 3OE7; X-ray; 3.19 A; H/Q/Z=24-160.
DR PDB; 3OEE; X-ray; 2.74 A; H/Q/Z=23-160.
DR PDB; 3OEH; X-ray; 3.00 A; H/Q/Z=23-160.
DR PDB; 3OFN; X-ray; 3.20 A; H/Q=23-160.
DR PDB; 3ZIA; X-ray; 2.50 A; H/R=23-160.
DR PDB; 3ZRY; X-ray; 6.50 A; H=23-160.
DR PDB; 4B2Q; EM; 37.00 A; H/h=29-160.
DR PDB; 6B8H; EM; 3.60 A; H/l=23-160.
DR PDB; 6CP3; EM; 3.80 A; H=23-160.
DR PDB; 6CP6; EM; 3.60 A; H=23-160.
DR PDBsum; 2HLD; -.
DR PDBsum; 2WPD; -.
DR PDBsum; 2XOK; -.
DR PDBsum; 3FKS; -.
DR PDBsum; 3OE7; -.
DR PDBsum; 3OEE; -.
DR PDBsum; 3OEH; -.
DR PDBsum; 3OFN; -.
DR PDBsum; 3ZIA; -.
DR PDBsum; 3ZRY; -.
DR PDBsum; 4B2Q; -.
DR PDBsum; 6B8H; -.
DR PDBsum; 6CP3; -.
DR PDBsum; 6CP6; -.
DR AlphaFoldDB; Q12165; -.
DR SMR; Q12165; -.
DR BioGRID; 32050; 18.
DR ComplexPortal; CPX-3281; Mitochondrial proton-transporting ATP synthase complex.
DR DIP; DIP-3032N; -.
DR IntAct; Q12165; 6.
DR MINT; Q12165; -.
DR STRING; 4932.YDL004W; -.
DR TCDB; 3.A.2.1.3; the h(+)- or na(+)-translocating f-type, v-type and a-type atpase (f-atpase) superfamily.
DR iPTMnet; Q12165; -.
DR MaxQB; Q12165; -.
DR PaxDb; Q12165; -.
DR PRIDE; Q12165; -.
DR EnsemblFungi; YDL004W_mRNA; YDL004W; YDL004W.
DR GeneID; 851560; -.
DR KEGG; sce:YDL004W; -.
DR SGD; S000002162; ATP16.
DR VEuPathDB; FungiDB:YDL004W; -.
DR eggNOG; KOG1758; Eukaryota.
DR GeneTree; ENSGT00390000017576; -.
DR HOGENOM; CLU_084338_0_0_1; -.
DR InParanoid; Q12165; -.
DR OMA; TLPHQTI; -.
DR BioCyc; YEAST:G3O-29435-MON; -.
DR Reactome; R-SCE-163210; Formation of ATP by chemiosmotic coupling.
DR Reactome; R-SCE-8949613; Cristae formation.
DR EvolutionaryTrace; Q12165; -.
DR PRO; PR:Q12165; -.
DR Proteomes; UP000002311; Chromosome IV.
DR RNAct; Q12165; protein.
DR GO; GO:0005743; C:mitochondrial inner membrane; IDA:ComplexPortal.
DR GO; GO:0005753; C:mitochondrial proton-transporting ATP synthase complex; IC:ComplexPortal.
DR GO; GO:0000275; C:mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1); IBA:GO_Central.
DR GO; GO:0005756; C:mitochondrial proton-transporting ATP synthase, central stalk; IDA:SGD.
DR GO; GO:0005739; C:mitochondrion; HDA:SGD.
DR GO; GO:0046933; F:proton-transporting ATP synthase activity, rotational mechanism; IEA:InterPro.
DR GO; GO:0015986; P:proton motive force-driven ATP synthesis; IDA:SGD.
DR CDD; cd12152; F1-ATPase_delta; 1.
DR Gene3D; 2.60.15.10; -; 1.
DR HAMAP; MF_00530; ATP_synth_epsil_bac; 1.
DR InterPro; IPR001469; ATP_synth_F1_dsu/esu.
DR InterPro; IPR020546; ATP_synth_F1_dsu/esu_N.
DR InterPro; IPR036771; ATPsynth_dsu/esu_N.
DR PANTHER; PTHR13822; PTHR13822; 1.
DR Pfam; PF02823; ATP-synt_DE_N; 1.
DR SUPFAM; SSF51344; SSF51344; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP synthesis; CF(1); Direct protein sequencing;
KW Hydrogen ion transport; Ion transport; Membrane; Mitochondrion;
KW Mitochondrion inner membrane; Reference proteome; Transit peptide;
KW Transport.
FT TRANSIT 1..22
FT /note="Mitochondrion"
FT /evidence="ECO:0000269|PubMed:8026496"
FT CHAIN 23..160
FT /note="ATP synthase subunit delta, mitochondrial"
FT /id="PRO_0000002671"
FT STRAND 34..37
FT /evidence="ECO:0007829|PDB:3ZIA"
FT STRAND 44..46
FT /evidence="ECO:0007829|PDB:3OFN"
FT STRAND 51..54
FT /evidence="ECO:0007829|PDB:3ZIA"
FT STRAND 56..59
FT /evidence="ECO:0007829|PDB:3ZIA"
FT STRAND 61..63
FT /evidence="ECO:0007829|PDB:3ZIA"
FT STRAND 70..74
FT /evidence="ECO:0007829|PDB:3ZIA"
FT STRAND 78..83
FT /evidence="ECO:0007829|PDB:3ZIA"
FT STRAND 86..92
FT /evidence="ECO:0007829|PDB:3ZIA"
FT STRAND 95..100
FT /evidence="ECO:0007829|PDB:3ZIA"
FT TURN 101..103
FT /evidence="ECO:0007829|PDB:3ZIA"
FT STRAND 104..110
FT /evidence="ECO:0007829|PDB:3ZIA"
FT STRAND 112..114
FT /evidence="ECO:0007829|PDB:3OFN"
FT HELIX 115..117
FT /evidence="ECO:0007829|PDB:3ZIA"
FT HELIX 120..133
FT /evidence="ECO:0007829|PDB:3ZIA"
FT STRAND 136..139
FT /evidence="ECO:0007829|PDB:3ZIA"
FT HELIX 140..156
FT /evidence="ECO:0007829|PDB:3ZIA"
SQ SEQUENCE 160 AA; 17020 MW; AE8D0BA364107977 CRC64;
MLRSIIGKSA SRSLNFVAKR SYAEAAAASS GLKLQFALPH ETLYSGSEVT QVNLPAKSGR
IGVLANHVPT VEQLLPGVVE VMEGSNSKKF FISGGFATVQ PDSQLCVTAI EAFPLESFSQ
ENIKNLLAEA KKNVSSSDAR EAAEAAIQVE VLENLQSVLK
