PCD1_YEAST
ID PCD1_YEAST Reviewed; 340 AA.
AC Q12524; D6VYE6;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 160.
DE RecName: Full=Peroxisomal coenzyme A diphosphatase 1, peroxisomal;
DE EC=3.6.1.55;
DE Flags: Precursor;
GN Name=PCD1; OrderedLocusNames=YLR151C; ORFNames=L9634.8;
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 [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 [2]
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 [3]
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 [4]
RP PROTEIN SEQUENCE OF 8-15, ENZYME ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES,
RP AND SUBCELLULAR LOCATION.
RX PubMed=10922370; DOI=10.1074/jbc.m005015200;
RA Cartwright J.L., Gasmi L., Spiller D.G., McLennan A.G.;
RT "The Saccharomyces cerevisiae PCD1 gene encodes a peroxisomal nudix
RT hydrolase active toward coenzyme A and its derivatives.";
RL J. Biol. Chem. 275:32925-32930(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 POSSIBLE ENZYME ACTIVITY, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=15475388; DOI=10.1093/nar/gkh868;
RA Nunoshiba T., Ishida R., Sasaki M., Iwai S., Nakabeppu Y., Yamamoto K.;
RT "A novel Nudix hydrolase for oxidized purine nucleoside triphosphates
RT encoded by ORFYLR151c (PCD1 gene) in Saccharomyces cerevisiae.";
RL Nucleic Acids Res. 32:5339-5348(2004).
CC -!- FUNCTION: Coenzyme A diphosphatase which mediates the cleavage of CoA
CC into 3',5'-ADP and 4'-phosphopantetheine. Has a strong preference for
CC oxidized CoA disulfide (CoASSCoA) as substrate. May be required to
CC remove potentially toxic oxidized CoA disulfide to maintain the
CC capacity for beta-oxidation of fatty acids. Can degrade 8-oxo-dGTP in
CC vitro; however, such activity may not be relevant in vivo.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=8-oxo-dGTP + H2O = 8-oxo-dGMP + diphosphate + H(+);
CC Xref=Rhea:RHEA:31575, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:33019, ChEBI:CHEBI:63224, ChEBI:CHEBI:77896; EC=3.6.1.55;
CC Evidence={ECO:0000269|PubMed:10922370};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000250};
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=280 uM for CoA {ECO:0000269|PubMed:10922370,
CC ECO:0000269|PubMed:15475388};
CC KM=24 uM for CoASSCoA {ECO:0000269|PubMed:10922370,
CC ECO:0000269|PubMed:15475388};
CC KM=23.8 uM for 8-oxo-dGTP {ECO:0000269|PubMed:10922370,
CC ECO:0000269|PubMed:15475388};
CC pH dependence:
CC Optimum pH is 7.0. {ECO:0000269|PubMed:10922370,
CC ECO:0000269|PubMed:15475388};
CC -!- SUBCELLULAR LOCATION: Peroxisome {ECO:0000269|PubMed:10922370}.
CC -!- PTM: The size of the cleaved transit peptide can be of 7 or 8 residues.
CC -!- MISCELLANEOUS: Present with 238 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the Nudix hydrolase family. PCD1 subfamily.
CC {ECO:0000305}.
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DR EMBL; Z73323; CAA97723.1; -; Genomic_DNA.
DR EMBL; U53879; AAB82385.1; -; Genomic_DNA.
DR EMBL; AY557953; AAS56279.1; -; Genomic_DNA.
DR EMBL; BK006945; DAA09462.1; -; Genomic_DNA.
DR PIR; S65000; S65000.
DR RefSeq; NP_013252.1; NM_001182038.1.
DR AlphaFoldDB; Q12524; -.
DR BioGRID; 31420; 37.
DR DIP; DIP-4808N; -.
DR STRING; 4932.YLR151C; -.
DR MaxQB; Q12524; -.
DR PaxDb; Q12524; -.
DR PRIDE; Q12524; -.
DR EnsemblFungi; YLR151C_mRNA; YLR151C; YLR151C.
DR GeneID; 850844; -.
DR KEGG; sce:YLR151C; -.
DR SGD; S000004141; PCD1.
DR VEuPathDB; FungiDB:YLR151C; -.
DR eggNOG; KOG3069; Eukaryota.
DR GeneTree; ENSGT01000000220104; -.
DR HOGENOM; CLU_040940_1_0_1; -.
DR InParanoid; Q12524; -.
DR OMA; FGDEDMI; -.
DR BioCyc; YEAST:YLR151C-MON; -.
DR Reactome; R-SCE-9033241; Peroxisomal protein import.
DR SABIO-RK; Q12524; -.
DR PRO; PR:Q12524; -.
DR Proteomes; UP000002311; Chromosome XII.
DR RNAct; Q12524; protein.
DR GO; GO:0005829; C:cytosol; HDA:SGD.
DR GO; GO:0005777; C:peroxisome; IDA:SGD.
DR GO; GO:0035539; F:8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity; IEA:UniProtKB-EC.
DR GO; GO:0008413; F:8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity; IDA:SGD.
DR GO; GO:0003986; F:acetyl-CoA hydrolase activity; IBA:GO_Central.
DR GO; GO:0010945; F:CoA pyrophosphatase activity; IDA:SGD.
DR GO; GO:0000287; F:magnesium ion binding; IEA:InterPro.
DR GO; GO:0030145; F:manganese ion binding; IEA:InterPro.
DR GO; GO:0015938; P:coenzyme A catabolic process; IBA:GO_Central.
DR GO; GO:0006281; P:DNA repair; IMP:SGD.
DR GO; GO:0009132; P:nucleoside diphosphate metabolic process; IEA:InterPro.
DR CDD; cd03426; CoAse; 1.
DR InterPro; IPR045121; CoAse.
DR InterPro; IPR015797; NUDIX_hydrolase-like_dom_sf.
DR InterPro; IPR000086; NUDIX_hydrolase_dom.
DR InterPro; IPR000059; NUDIX_hydrolase_NudL_CS.
DR PANTHER; PTHR12992; PTHR12992; 1.
DR Pfam; PF00293; NUDIX; 1.
DR SUPFAM; SSF55811; SSF55811; 1.
DR PROSITE; PS51462; NUDIX; 1.
DR PROSITE; PS01293; NUDIX_COA; 1.
PE 1: Evidence at protein level;
KW Direct protein sequencing; Hydrolase; Magnesium; Manganese; Metal-binding;
KW Peroxisome; Reference proteome; Transit peptide.
FT TRANSIT 1..7
FT /note="Peroxisome"
FT /evidence="ECO:0000269|PubMed:10922370"
FT CHAIN 8..340
FT /note="Peroxisomal coenzyme A diphosphatase 1, peroxisomal"
FT /id="PRO_0000036186"
FT DOMAIN 37..199
FT /note="Nudix hydrolase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00794"
FT MOTIF 77..99
FT /note="Nudix box"
FT BINDING 93
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 97
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
SQ SEQUENCE 340 AA; 39755 MW; A8900907266564BE CRC64;
MILSQRRMLS SKQLIENLIR YKFHKTPYTR SSIWPFKRNS AVIILLFIGM KGELRVLLTK
RSRTLRSFSG DVSFPGGKAD YFQETFESVA RREAEEEIGL PHDPEVLHKE FGMKLDNLVM
DMPCYLSRTF LSVKPMVCFL YKDKLEKHED KYKVPLDIRK FFGKLNPGET SSLFSVPLND
LVIHLLPEAD EDVKSYQAEY FERKEYKLNW GGIKWLIMHY HFHVANNNEM PWLQTIEDLS
SSDEDGVDGG IFRFRDLWGL TCKILFDVSC IANGLMDEKL KGELGHEDLI VGLHDYGNQM
QPNGRSEWEI GMINGDRNLK YSDVIPEYYM KHLLECRSLW
