PDP1_YEAST
ID PDP1_YEAST Reviewed; 572 AA.
AC Q12511; D6W2F1;
DT 25-OCT-2004, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 171.
DE RecName: Full=[Pyruvate dehydrogenase [acetyl-transferring]]-phosphatase 1, mitochondrial;
DE Short=PDP 1;
DE EC=3.1.3.43 {ECO:0000305|PubMed:18180296};
DE AltName: Full=Phosphatase two C protein 5;
DE AltName: Full=Protein phosphatase 2C homolog 5;
DE Short=PP2C-5;
DE AltName: Full=Protein phosphatase of PDH protein 1;
DE AltName: Full=Pyruvate dehydrogenase complex phosphatase 1;
DE Short=PDC phosphatase 1;
DE Flags: Precursor;
GN Name=PTC5; Synonyms=PPP1; OrderedLocusNames=YOR090C; ORFNames=YOR3157C;
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].
RX PubMed=9200815;
RX DOI=10.1002/(sici)1097-0061(19970615)13:7<655::aid-yea120>3.0.co;2-i;
RA Voss H., Benes V., Andrade M.A., Valencia A., Rechmann S., Teodoru C.,
RA Schwager C., Paces V., Sander C., Ansorge W.;
RT "DNA sequencing and analysis of 130 kb from yeast chromosome XV.";
RL Yeast 13:655-672(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169874;
RA Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W., Arino J.,
RA Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R., Boyer J., Camasses A.,
RA Casamayor A., Casas C., Cheret G., Cziepluch C., Daignan-Fornier B.,
RA Dang V.-D., de Haan M., Delius H., Durand P., Fairhead C., Feldmann H.,
RA Gaillon L., Galisson F., Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E.,
RA Grivell L.A., Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U.,
RA Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B.,
RA Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A.,
RA Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J., Maarse A.C.,
RA Madania A., Mannhaupt G., Marck C., Martin R.P., Mewes H.-W., Michaux G.,
RA Paces V., Parle-McDermott A.G., Pearson B.M., Perrin A., Pettersson B.,
RA Poch O., Pohl T.M., Poirey R., Portetelle D., Pujol A., Purnelle B.,
RA Ramezani Rad M., Rechmann S., Schwager C., Schweizer M., Sor F., Sterky F.,
RA Tarassov I.A., Teodoru C., Tettelin H., Thierry A., Tobiasch E.,
RA Tzermia M., Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I.,
RA Vlcek C., Voet M., Volckaert G., Voss H., Wambutt R., Wedler H.,
RA Wiemann S., Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XV.";
RL Nature 387:98-102(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 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 [5]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RC STRAIN=ATCC 76625 / YPH499;
RX PubMed=14576278; DOI=10.1073/pnas.2135385100;
RA Sickmann A., Reinders J., Wagner Y., Joppich C., Zahedi R.P., Meyer H.E.,
RA Schoenfisch B., Perschil I., Chacinska A., Guiard B., Rehling P.,
RA Pfanner N., Meisinger C.;
RT "The proteome of Saccharomyces cerevisiae mitochondria.";
RL Proc. Natl. Acad. Sci. U.S.A. 100:13207-13212(2003).
RN [6]
RP FUNCTION, AND SUBCELLULAR LOCATION.
RX PubMed=16643908; DOI=10.1016/j.febslet.2006.04.002;
RA Krause-Buchholz U., Gey U., Wunschmann J., Becker S., Rodel G.;
RT "YIL042c and YOR090c encode the kinase and phosphatase of the Saccharomyces
RT cerevisiae pyruvate dehydrogenase complex.";
RL FEBS Lett. 580:2553-2560(2006).
RN [7]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=18180296; DOI=10.1074/jbc.m708779200;
RA Gey U., Czupalla C., Hoflack B., Rodel G., Krause-Buchholz U.;
RT "Yeast pyruvate dehydrogenase complex is regulated by a concerted activity
RT of two kinases and two phosphatases.";
RL J. Biol. Chem. 283:9759-9767(2008).
RN [8]
RP IDENTIFICATION BY MASS SPECTROMETRY, AND SUBCELLULAR LOCATION [LARGE SCALE
RP ANALYSIS].
RX PubMed=22984289; DOI=10.1074/mcp.m112.021105;
RA Voegtle F.N., Burkhart J.M., Rao S., Gerbeth C., Hinrichs J.,
RA Martinou J.C., Chacinska A., Sickmann A., Zahedi R.P., Meisinger C.;
RT "Intermembrane space proteome of yeast mitochondria.";
RL Mol. Cell. Proteomics 11:1840-1852(2012).
CC -!- FUNCTION: Catalyzes the dephosphorylation and concomitant reactivation
CC of the E1 alpha subunit (PDA1) of the pyruvate dehydrogenase complex.
CC {ECO:0000269|PubMed:16643908, ECO:0000269|PubMed:18180296}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + O-phospho-L-seryl-[pyruvate dehydrogenase E1 alpha
CC subunit] = L-seryl-[pyruvate dehydrogenase E1 alpha subunit] +
CC phosphate; Xref=Rhea:RHEA:12669, Rhea:RHEA-COMP:13689, Rhea:RHEA-
CC COMP:13690, ChEBI:CHEBI:15377, ChEBI:CHEBI:29999, ChEBI:CHEBI:43474,
CC ChEBI:CHEBI:83421; EC=3.1.3.43;
CC Evidence={ECO:0000305|PubMed:18180296};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:12670;
CC Evidence={ECO:0000305|PubMed:18180296};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000250};
CC Note=Binds 2 magnesium or manganese ions per subunit. {ECO:0000250};
CC -!- SUBCELLULAR LOCATION: Mitochondrion intermembrane space
CC {ECO:0000269|PubMed:14576278, ECO:0000269|PubMed:16643908,
CC ECO:0000269|PubMed:22984289}.
CC -!- PTM: Processed by mitochondrial inner membrane protease (IMP) complex
CC and released to the intermembrane space.
CC -!- MISCELLANEOUS: Present with 7550 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the PP2C family. {ECO:0000305}.
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DR EMBL; X94335; CAA64011.1; -; Genomic_DNA.
DR EMBL; Z74998; CAA99287.1; -; Genomic_DNA.
DR EMBL; BK006948; DAA10867.1; -; Genomic_DNA.
DR PIR; S61650; S61650.
DR RefSeq; NP_014733.1; NM_001183509.1.
DR AlphaFoldDB; Q12511; -.
DR SMR; Q12511; -.
DR BioGRID; 34488; 121.
DR DIP; DIP-6439N; -.
DR IntAct; Q12511; 9.
DR MINT; Q12511; -.
DR STRING; 4932.YOR090C; -.
DR iPTMnet; Q12511; -.
DR MaxQB; Q12511; -.
DR PaxDb; Q12511; -.
DR PRIDE; Q12511; -.
DR EnsemblFungi; YOR090C_mRNA; YOR090C; YOR090C.
DR GeneID; 854257; -.
DR KEGG; sce:YOR090C; -.
DR SGD; S000005616; PTC5.
DR VEuPathDB; FungiDB:YOR090C; -.
DR eggNOG; KOG0700; Eukaryota.
DR GeneTree; ENSGT00940000172263; -.
DR HOGENOM; CLU_021928_3_2_1; -.
DR InParanoid; Q12511; -.
DR OMA; DHNAWNP; -.
DR BioCyc; YEAST:G3O-33624-MON; -.
DR PRO; PR:Q12511; -.
DR Proteomes; UP000002311; Chromosome XV.
DR RNAct; Q12511; protein.
DR GO; GO:0005758; C:mitochondrial intermembrane space; IDA:SGD.
DR GO; GO:0005739; C:mitochondrion; IDA:SGD.
DR GO; GO:0004741; F:[pyruvate dehydrogenase (lipoamide)] phosphatase activity; IMP:SGD.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004722; F:protein serine/threonine phosphatase activity; IDA:SGD.
DR GO; GO:0070262; P:peptidyl-serine dephosphorylation; IMP:SGD.
DR GO; GO:1904184; P:positive regulation of pyruvate dehydrogenase activity; IMP:SGD.
DR GO; GO:0006470; P:protein dephosphorylation; IBA:GO_Central.
DR CDD; cd00143; PP2Cc; 1.
DR Gene3D; 3.60.40.10; -; 1.
DR InterPro; IPR015655; PP2C.
DR InterPro; IPR000222; PP2C_BS.
DR InterPro; IPR036457; PPM-type_dom_sf.
DR InterPro; IPR001932; PPM-type_phosphatase_dom.
DR PANTHER; PTHR13832; PTHR13832; 1.
DR Pfam; PF00481; PP2C; 1.
DR SMART; SM00332; PP2Cc; 1.
DR SUPFAM; SSF81606; SSF81606; 1.
DR PROSITE; PS01032; PPM_1; 1.
DR PROSITE; PS51746; PPM_2; 1.
PE 1: Evidence at protein level;
KW Hydrolase; Magnesium; Manganese; Metal-binding; Mitochondrion;
KW Protein phosphatase; Reference proteome; Transit peptide.
FT TRANSIT 1..?
FT /note="Mitochondrion"
FT /evidence="ECO:0000255"
FT CHAIN ?..572
FT /note="[Pyruvate dehydrogenase [acetyl-transferring]]-
FT phosphatase 1, mitochondrial"
FT /id="PRO_0000057778"
FT DOMAIN 153..543
FT /note="PPM-type phosphatase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01082"
FT REGION 95..122
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 470..492
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 477..492
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 197
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 197
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 198
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 424
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 480
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
SQ SEQUENCE 572 AA; 63669 MW; 07A5AF33FA72CC2A CRC64;
MSPLTRTVAI KKTVKVLSKC QSGREYTQKF LQRAYSTSHA NSTYYSRTKL FISSHSKALN
IALLSGSLLL TYSYYSPKKI LSLDTINGIK DYSTNTSGNI NMPSPNPKGT ETQKSQRSQN
DQSVLILNDS KIEAKLHDRE ESHFVNRGTG IFRYDVAQLP SNHPIEDDHV EQIITIPIES
EDGKSIEKDL YFFGIFDGHG GPFTSEKLSK DLVRYVAYQL GQVYDQNKTV FHSDPNQLID
SAISKGFLKL DNDLVIESFR KLFQDPNNTN IANTLPAISG SCALLSLYNS TNSILKVAVT
GDSRALICGL DNEGNWTVKS LSTDQTGDNL DEVRRIRKEH PGEPNVIRNG RILGSLQPSR
AFGDYRYKIK EVDGKPLSDL PEVAKLYFRR EPRDFKTPPY VTAEPVITSA KIGENTKFMV
MGSDGLFELL TNEEIASLVI RWMDKNMNLA PVKAEPGKLP KVIDVSEDKE AQRPAFRYKD
NNSSSPSGSN PEYLIEDKNV ATHLIRNALS AGGRKEYVSA LVSIPSPMSR RYRDDLTVTV
AFFGDSGTPS IVSNATSIVM NPEATTKPKP RL
