GPD2_YEAST
ID GPD2_YEAST Reviewed; 440 AA.
AC P41911; D6W208; P50905;
DT 01-NOV-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1996, sequence version 2.
DT 03-AUG-2022, entry version 197.
DE RecName: Full=Glycerol-3-phosphate dehydrogenase [NAD(+)] 2, mitochondrial {ECO:0000303|PubMed:7476212};
DE EC=1.1.1.8 {ECO:0000269|PubMed:9171333};
DE Flags: Precursor;
GN Name=GPD2 {ECO:0000303|PubMed:7476212}; Synonyms=GPD3;
GN OrderedLocusNames=YOL059W; ORFNames=O1222;
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 FUNCTION.
RX PubMed=7476212; DOI=10.1111/j.1365-2958.1995.mmi_17010095.x;
RA Eriksson P., Andre L., Ansell R., Blomberg A., Adler L.;
RT "Cloning and characterization of GPD2, a second gene encoding sn-glycerol
RT 3-phosphate dehydrogenase (NAD+) in Saccharomyces cerevisiae, and its
RT comparison with GPD1.";
RL Mol. Microbiol. 17:95-107(1995).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 90843 / S288c / FY73;
RX PubMed=8789261;
RX DOI=10.1002/(sici)1097-0061(199601)12:1<67::aid-yea884>3.0.co;2-f;
RA Mannhaupt G., Vetter I., Schwarzlose C., Mitzel S., Feldmann H.;
RT "Analysis of a 26 kb region on the left arm of yeast chromosome XV.";
RL Yeast 12:67-76(1996).
RN [3]
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 [4]
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 [5]
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 [6]
RP FUNCTION.
RX PubMed=8979347; DOI=10.1128/aem.63.1.128-132.1997;
RA Bjoerkqvist S., Ansell R., Adler L., Liden G.;
RT "Physiological response to anaerobicity of glycerol-3-phosphate
RT dehydrogenase mutants of Saccharomyces cerevisiae.";
RL Appl. Environ. Microbiol. 63:128-132(1997).
RN [7]
RP INDUCTION, DISRUPTION PHENOTYPE, FUNCTION, CATALYTIC ACTIVITY, AND
RP BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=9171333; DOI=10.1093/emboj/16.9.2179;
RA Ansell R., Granath K., Hohmann S., Thevelein J.M., Adler L.;
RT "The two isoenzymes for yeast NAD+-dependent glycerol 3-phosphate
RT dehydrogenase encoded by GPD1 and GPD2 have distinct roles in
RT osmoadaptation and redox regulation.";
RL EMBO J. 16:2179-2187(1997).
RN [8]
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 [9]
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 [10]
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 [11]
RP SUBCELLULAR LOCATION, AND INDUCTION.
RX PubMed=15210723; DOI=10.1074/jbc.m403310200;
RA Valadi A., Granath K., Gustafsson L., Adler L.;
RT "Distinct intracellular localization of Gpd1p and Gpd2p, the two yeast
RT isoforms of NAD+-dependent glycerol-3-phosphate dehydrogenase, explains
RT their different contributions to redox-driven glycerol production.";
RL J. Biol. Chem. 279:39677-39685(2004).
RN [12]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-72 AND SER-75, AND
RP IDENTIFICATION BY 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 [13]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-72 AND SER-75, AND
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 [14]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-70; SER-72 AND SER-75, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=17287358; DOI=10.1073/pnas.0607084104;
RA Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L.,
RA Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F.;
RT "Analysis of phosphorylation sites on proteins from Saccharomyces
RT cerevisiae by electron transfer dissociation (ETD) mass spectrometry.";
RL Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007).
RN [15]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-72 AND SER-75, AND
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 [16]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-72 AND SER-75, AND
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).
CC -!- FUNCTION: Catalyzes the production of glycerol under anaerobic growth
CC conditions. Glycerol production serves as a redox sink by consuming the
CC excess cytosolic NADH during anaerobic metabolism.
CC {ECO:0000269|PubMed:7476212, ECO:0000269|PubMed:8979347,
CC ECO:0000269|PubMed:9171333}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=NAD(+) + sn-glycerol 3-phosphate = dihydroxyacetone phosphate
CC + H(+) + NADH; Xref=Rhea:RHEA:11092, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:57540, ChEBI:CHEBI:57597, ChEBI:CHEBI:57642,
CC ChEBI:CHEBI:57945; EC=1.1.1.8; Evidence={ECO:0000269|PubMed:9171333};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.018 mM for NADH {ECO:0000269|PubMed:9171333};
CC KM=0.86 mM for dihydroxyacetone phosphate
CC {ECO:0000269|PubMed:9171333};
CC -!- SUBCELLULAR LOCATION: Cytoplasm. Mitochondrion.
CC -!- INDUCTION: By anaerobic growth conditions and other conditions leading
CC to accumulation of cytosolic NADH. {ECO:0000269|PubMed:15210723,
CC ECO:0000269|PubMed:9171333}.
CC -!- DISRUPTION PHENOTYPE: Leads to poor growth under anaerobic conditions
CC (PubMed:9171333). Does not produce detectable glycerol, is highly
CC osmosensitive and fails to grow under anoxic conditions, when GPD1 is
CC also deleted (PubMed:9171333). {ECO:0000269|PubMed:9171333}.
CC -!- MISCELLANEOUS: Present with 8966 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the NAD-dependent glycerol-3-phosphate
CC dehydrogenase family. {ECO:0000305}.
CC -!- CAUTION: It is uncertain whether Met-1 or Met-49 is the initiator.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAA84532.1; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; Z35169; CAA84532.1; ALT_FRAME; Genomic_DNA.
DR EMBL; X91067; CAA62526.1; -; Genomic_DNA.
DR EMBL; Z74801; CAA99068.1; -; Genomic_DNA.
DR EMBL; AY558560; AAS56886.1; -; Genomic_DNA.
DR EMBL; BK006948; DAA10724.1; -; Genomic_DNA.
DR PIR; S61719; S61719.
DR RefSeq; NP_014582.1; NM_001183314.1.
DR AlphaFoldDB; P41911; -.
DR SMR; P41911; -.
DR BioGRID; 34342; 130.
DR DIP; DIP-1348N; -.
DR IntAct; P41911; 7.
DR MINT; P41911; -.
DR STRING; 4932.YOL059W; -.
DR MoonProt; P41911; -.
DR iPTMnet; P41911; -.
DR MaxQB; P41911; -.
DR PaxDb; P41911; -.
DR PRIDE; P41911; -.
DR EnsemblFungi; YOL059W_mRNA; YOL059W; YOL059W.
DR GeneID; 854095; -.
DR KEGG; sce:YOL059W; -.
DR SGD; S000005420; GPD2.
DR VEuPathDB; FungiDB:YOL059W; -.
DR eggNOG; KOG2711; Eukaryota.
DR GeneTree; ENSGT00390000003114; -.
DR HOGENOM; CLU_033449_2_4_1; -.
DR InParanoid; P41911; -.
DR OMA; NRMFGNM; -.
DR BioCyc; YEAST:YOL059W-MON; -.
DR Reactome; R-SCE-1483166; Synthesis of PA.
DR PRO; PR:P41911; -.
DR Proteomes; UP000002311; Chromosome XV.
DR RNAct; P41911; protein.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0009331; C:glycerol-3-phosphate dehydrogenase complex; IEA:InterPro.
DR GO; GO:0005739; C:mitochondrion; IDA:SGD.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0004367; F:glycerol-3-phosphate dehydrogenase [NAD+] activity; IMP:SGD.
DR GO; GO:0051287; F:NAD binding; IEA:InterPro.
DR GO; GO:0042803; F:protein homodimerization activity; IEA:InterPro.
DR GO; GO:0006071; P:glycerol metabolic process; IMP:SGD.
DR GO; GO:0046168; P:glycerol-3-phosphate catabolic process; IEA:InterPro.
DR GO; GO:0006072; P:glycerol-3-phosphate metabolic process; IBA:GO_Central.
DR GO; GO:0006116; P:NADH oxidation; IMP:SGD.
DR Gene3D; 1.10.1040.10; -; 1.
DR InterPro; IPR008927; 6-PGluconate_DH-like_C_sf.
DR InterPro; IPR013328; 6PGD_dom2.
DR InterPro; IPR006168; G3P_DH_NAD-dep.
DR InterPro; IPR006109; G3P_DH_NAD-dep_C.
DR InterPro; IPR017751; G3P_DH_NAD-dep_euk.
DR InterPro; IPR011128; G3P_DH_NAD-dep_N.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR Pfam; PF07479; NAD_Gly3P_dh_C; 1.
DR Pfam; PF01210; NAD_Gly3P_dh_N; 1.
DR PRINTS; PR00077; GPDHDRGNASE.
DR SUPFAM; SSF48179; SSF48179; 1.
DR SUPFAM; SSF51735; SSF51735; 1.
DR TIGRFAMs; TIGR03376; glycerol3P_DH; 1.
DR PROSITE; PS00957; NAD_G3PDH; 1.
PE 1: Evidence at protein level;
KW Cytoplasm; Mitochondrion; NAD; Oxidoreductase; Phosphoprotein;
KW Reference proteome; Transit peptide.
FT TRANSIT 1..16
FT /note="Mitochondrion"
FT /evidence="ECO:0000255"
FT CHAIN 17..440
FT /note="Glycerol-3-phosphate dehydrogenase [NAD(+)] 2,
FT mitochondrial"
FT /id="PRO_0000043410"
FT ACT_SITE 294
FT /note="Proton acceptor"
FT /evidence="ECO:0000250|UniProtKB:P21695"
FT BINDING 90..95
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P21695"
FT BINDING 122
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P21695"
FT BINDING 178
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P21695"
FT BINDING 201
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P21695"
FT BINDING 234
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P21695"
FT BINDING 359..360
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P21695"
FT BINDING 359
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P21695"
FT BINDING 388
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P21695"
FT MOD_RES 70
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17287358"
FT MOD_RES 72
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:15665377,
FT ECO:0007744|PubMed:17287358, ECO:0007744|PubMed:17330950,
FT ECO:0007744|PubMed:18407956, ECO:0007744|PubMed:19779198"
FT MOD_RES 75
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:15665377,
FT ECO:0007744|PubMed:17287358, ECO:0007744|PubMed:17330950,
FT ECO:0007744|PubMed:18407956, ECO:0007744|PubMed:19779198"
SQ SEQUENCE 440 AA; 49422 MW; FA6C07034D3EC720 CRC64;
MLAVRRLTRY TFLKRTHPVL YTRRAYKILP SRSTFLRRSL LQTQLHSKMT AHTNIKQHKH
CHEDHPIRRS DSAVSIVHLK RAPFKVTVIG SGNWGTTIAK VIAENTELHS HIFEPEVRMW
VFDEKIGDEN LTDIINTRHQ NVKYLPNIDL PHNLVADPDL LHSIKGADIL VFNIPHQFLP
NIVKQLQGHV APHVRAISCL KGFELGSKGV QLLSSYVTDE LGIQCGALSG ANLAPEVAKE
HWSETTVAYQ LPKDYQGDGK DVDHKILKLL FHRPYFHVNV IDDVAGISIA GALKNVVALA
CGFVEGMGWG NNASAAIQRL GLGEIIKFGR MFFPESKVET YYQESAGVAD LITTCSGGRN
VKVATYMAKT GKSALEAEKE LLNGQSAQGI ITCREVHEWL QTCELTQEFP LFEAVYQIVY
NNVRMEDLPE MIEELDIDDE
