PGM3_YEAST
ID PGM3_YEAST Reviewed; 622 AA.
AC Q03262; D6W0A5;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 1.
DT 03-AUG-2022, entry version 176.
DE RecName: Full=Phosphoribomutase {ECO:0000303|PubMed:23103740};
DE Short=PRM;
DE EC=5.4.2.7 {ECO:0000269|PubMed:23103740};
DE AltName: Full=Phosphoglucomutase 3 {ECO:0000303|PubMed:18042468};
DE Short=PGM 3;
GN Name=PRM15 {ECO:0000303|PubMed:23670538};
GN Synonyms=PGM3 {ECO:0000303|PubMed:18042468};
GN OrderedLocusNames=YMR278W {ECO:0000312|SGD:S000004891}; ORFNames=YM8021.04;
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=9169872;
RA Bowman S., Churcher C.M., Badcock K., Brown D., Chillingworth T.,
RA Connor R., Dedman K., Devlin K., Gentles S., Hamlin N., Hunt S., Jagels K.,
RA Lye G., Moule S., Odell C., Pearson D., Rajandream M.A., Rice P.,
RA Skelton J., Walsh S.V., Whitehead S., Barrell B.G.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XIII.";
RL Nature 387:90-93(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 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 [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 PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-158, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=YAL6B;
RX PubMed=15665377; DOI=10.1074/mcp.m400219-mcp200;
RA Gruhler A., Olsen J.V., Mohammed S., Mortensen P., Faergeman N.J., Mann M.,
RA Jensen O.N.;
RT "Quantitative phosphoproteomics applied to the yeast pheromone signaling
RT pathway.";
RL Mol. Cell. Proteomics 4:310-327(2005).
RN [6]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ADR376;
RX PubMed=17330950; DOI=10.1021/pr060559j;
RA Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J.,
RA Elias J.E., Gygi S.P.;
RT "Large-scale phosphorylation analysis of alpha-factor-arrested
RT Saccharomyces cerevisiae.";
RL J. Proteome Res. 6:1190-1197(2007).
RN [7]
RP FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, AND MUTAGENESIS OF SER-158 AND
RP PRO-326.
RX PubMed=18042468; DOI=10.1016/j.bbrc.2007.11.065;
RA Tiwari A., Bhat J.P.;
RT "Molecular characterization reveals that YMR278w encoded protein is
RT environmental stress response homologue of Saccharomyces cerevisiae PGM2.";
RL Biochem. Biophys. Res. Commun. 366:340-345(2008).
RN [8]
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 [9]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19779198; DOI=10.1126/science.1172867;
RA Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
RT "Global analysis of Cdk1 substrate phosphorylation sites provides insights
RT into evolution.";
RL Science 325:1682-1686(2009).
RN [10]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND DISRUPTION
RP PHENOTYPE.
RX PubMed=23103740; DOI=10.1016/j.febslet.2012.09.042;
RA Walther T., Baylac A., Alkim C., Vax A., Cordier H., Francois J.M.;
RT "The PGM3 gene encodes the major phosphoribomutase in the yeast
RT Saccharomyces cerevisiae.";
RL FEBS Lett. 586:4114-4118(2012).
RN [11]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=23670538; DOI=10.1038/msb.2013.21;
RA Xu Y.F., Letisse F., Absalan F., Lu W., Kuznetsova E., Brown G.,
RA Caudy A.A., Yakunin A.F., Broach J.R., Rabinowitz J.D.;
RT "Nucleotide degradation and ribose salvage in yeast.";
RL Mol. Syst. Biol. 9:665-665(2013).
CC -!- FUNCTION: Major phosphoribomutase that converts ribose 1-phosphate to
CC ribose 5-phosphate. Involved in ribose salvage via the pentose
CC phosphate pathway. {ECO:0000269|PubMed:18042468}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=alpha-D-ribose 1-phosphate = D-ribose 5-phosphate;
CC Xref=Rhea:RHEA:18793, ChEBI:CHEBI:57720, ChEBI:CHEBI:78346;
CC EC=5.4.2.7; Evidence={ECO:0000269|PubMed:23103740};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000250|UniProtKB:P00949};
CC Note=Binds 1 Mg(2+) ion per subunit. {ECO:0000250|UniProtKB:P00949};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=2.0 mM for D-glucose 1-phosphate {ECO:0000269|PubMed:18042468};
CC KM=112 uM for D-glucose 1-phosphate {ECO:0000269|PubMed:23103740};
CC KM=750 uM for D-ribose 1-phosphate {ECO:0000269|PubMed:23103740};
CC Vmax=0.11 umol/min/mg enzyme for D-glucose 1-phosphate
CC {ECO:0000269|PubMed:23103740};
CC Vmax=0.29 umol/min/mg enzyme for D-ribose 1-phosphate
CC {ECO:0000269|PubMed:23103740};
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}. Nucleus
CC {ECO:0000269|PubMed:14562095}.
CC -!- DISRUPTION PHENOTYPE: Hyperaccumulates ribose 1-phosphate and upstream
CC purines upon glucose-induced purine nucleoside recycling.
CC {ECO:0000269|PubMed:23103740, ECO:0000269|PubMed:23670538}.
CC -!- MISCELLANEOUS: Present with 4960 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the phosphohexose mutase family. {ECO:0000305}.
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DR EMBL; Z49704; CAA89776.1; -; Genomic_DNA.
DR EMBL; BK006946; DAA10179.1; -; Genomic_DNA.
DR PIR; S54585; S54585.
DR RefSeq; NP_014005.1; NM_001182785.1.
DR AlphaFoldDB; Q03262; -.
DR SMR; Q03262; -.
DR BioGRID; 35457; 50.
DR DIP; DIP-5066N; -.
DR STRING; 4932.YMR278W; -.
DR iPTMnet; Q03262; -.
DR MaxQB; Q03262; -.
DR PaxDb; Q03262; -.
DR PRIDE; Q03262; -.
DR EnsemblFungi; YMR278W_mRNA; YMR278W; YMR278W.
DR GeneID; 855321; -.
DR KEGG; sce:YMR278W; -.
DR SGD; S000004891; PRM15.
DR VEuPathDB; FungiDB:YMR278W; -.
DR eggNOG; KOG1220; Eukaryota.
DR GeneTree; ENSGT00940000168144; -.
DR HOGENOM; CLU_016950_0_1_1; -.
DR InParanoid; Q03262; -.
DR OMA; PQDNGYK; -.
DR BioCyc; YEAST:G3O-32949-MON; -.
DR Reactome; R-SCE-3322077; Glycogen synthesis.
DR Reactome; R-SCE-6798695; Neutrophil degranulation.
DR Reactome; R-SCE-70171; Glycolysis.
DR Reactome; R-SCE-70221; Glycogen breakdown (glycogenolysis).
DR Reactome; R-SCE-70370; Galactose catabolism.
DR Reactome; R-SCE-71336; Pentose phosphate pathway.
DR SABIO-RK; Q03262; -.
DR PRO; PR:Q03262; -.
DR Proteomes; UP000002311; Chromosome XIII.
DR RNAct; Q03262; protein.
DR GO; GO:0005737; C:cytoplasm; HDA:SGD.
DR GO; GO:0005634; C:nucleus; HDA:SGD.
DR GO; GO:0000287; F:magnesium ion binding; IEA:InterPro.
DR GO; GO:0008973; F:phosphopentomutase activity; IDA:SGD.
DR GO; GO:0006006; P:glucose metabolic process; IEA:UniProtKB-KW.
DR GO; GO:0046115; P:guanosine catabolic process; IMP:SGD.
DR GO; GO:0006148; P:inosine catabolic process; IMP:SGD.
DR GO; GO:0006166; P:purine ribonucleoside salvage; IMP:SGD.
DR InterPro; IPR005844; A-D-PHexomutase_a/b/a-I.
DR InterPro; IPR016055; A-D-PHexomutase_a/b/a-I/II/III.
DR InterPro; IPR005845; A-D-PHexomutase_a/b/a-II.
DR InterPro; IPR005846; A-D-PHexomutase_a/b/a-III.
DR InterPro; IPR005843; A-D-PHexomutase_C.
DR InterPro; IPR036900; A-D-PHexomutase_C_sf.
DR InterPro; IPR016066; A-D-PHexomutase_CS.
DR Pfam; PF02878; PGM_PMM_I; 1.
DR Pfam; PF02879; PGM_PMM_II; 1.
DR Pfam; PF02880; PGM_PMM_III; 1.
DR Pfam; PF00408; PGM_PMM_IV; 1.
DR SUPFAM; SSF53738; SSF53738; 3.
DR SUPFAM; SSF55957; SSF55957; 1.
DR PROSITE; PS00710; PGM_PMM; 1.
PE 1: Evidence at protein level;
KW Carbohydrate metabolism; Cytoplasm; Glucose metabolism; Isomerase;
KW Magnesium; Metal-binding; Nucleus; Phosphoprotein; Reference proteome.
FT CHAIN 1..622
FT /note="Phosphoribomutase"
FT /id="PRO_0000148022"
FT ACT_SITE 158
FT /note="Phosphoserine intermediate"
FT /evidence="ECO:0000250|UniProtKB:P00949"
FT BINDING 57
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00949"
FT BINDING 61
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00949"
FT BINDING 158..159
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00949"
FT BINDING 158
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /note="via phosphate group"
FT /evidence="ECO:0000250|UniProtKB:P00949"
FT BINDING 168
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00949"
FT BINDING 325
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:P00949"
FT BINDING 327
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:P00949"
FT BINDING 329..330
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00949"
FT BINDING 329
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:P00949"
FT BINDING 404
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00949"
FT BINDING 428..430
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00949"
FT BINDING 442
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00949"
FT MOD_RES 158
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:15665377"
FT MUTAGEN 158
FT /note="S->T: Loss of function."
FT /evidence="ECO:0000269|PubMed:18042468"
FT MUTAGEN 326
FT /note="P->G: No effect."
FT /evidence="ECO:0000269|PubMed:18042468"
SQ SEQUENCE 622 AA; 71069 MW; E402A69551B36CD3 CRC64;
MLQGILETVP SDLKDPISLW FKQDRNPKTI EEVTALCKKS DWNELHKRFD SRIQFGTAGL
RSQMQAGFSR MNTLVVIQAS QGLATYVRQQ FPDNLVAVVG HDHRFHSKEF ARATAAAFLL
KGFKVHYLNP DHEFVHTPLV PFAVDKLKAS VGVMITASHN PKMDNGYKVY YSNGCQIIPP
HDHAISDSID ANLEPWANVW DFDDVLNKAL KQGKLMYSRE EMLKLYLEEV SKNLVEINPL
KLEVKAKPWF VYTPMHGVGF DIFSTIVKKT LCLVEGKDYL CVPEQQNPDP SFPTVGFPNP
EEKGALDIGI NLAEKHDIDL LVANDPDADR FSVAVKDMQS GEWRQLTGNE IGFLFAFYEY
QKYKSMDKEF QHVHPLAMLN STVSSQMIKK MAEIEGFHYE DTLTGFKWIG NRAILLEKKG
YYVPFGFEEA IGYMFPAMEH DKDGISASIV FLQAYCKWKI DHNLDPLNVL ENGFKKYGVF
KEYNGYYVVP NPTVTKDIFD YIRNVYTPEG ASYPSSIGEE IEVLYYRDLT TGYQSDTINH
KPTLPVDPTS QMITVSARPS NGSENEHIRF TIRGSGTEPK LKVYIEACAN EEQRASFLAK
LTWNVLRREW FRPDEMNIVT KF
