SERA_YEAST
ID SERA_YEAST Reviewed; 469 AA.
AC P40054; D3DLY8;
DT 01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1995, sequence version 1.
DT 03-AUG-2022, entry version 200.
DE RecName: Full=D-3-phosphoglycerate dehydrogenase 1;
DE Short=3-PGDH 1;
DE EC=1.1.1.95;
DE AltName: Full=2-oxoglutarate reductase {ECO:0000305};
DE EC=1.1.1.399 {ECO:0000269|PubMed:26774271};
GN Name=SER3; OrderedLocusNames=YER081W;
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=9169868;
RA Dietrich F.S., Mulligan J.T., Hennessy K.M., Yelton M.A., Allen E.,
RA Araujo R., Aviles E., Berno A., Brennan T., Carpenter J., Chen E.,
RA Cherry J.M., Chung E., Duncan M., Guzman E., Hartzell G., Hunicke-Smith S.,
RA Hyman R.W., Kayser A., Komp C., Lashkari D., Lew H., Lin D., Mosedale D.,
RA Nakahara K., Namath A., Norgren R., Oefner P., Oh C., Petel F.X.,
RA Roberts D., Sehl P., Schramm S., Shogren T., Smith V., Taylor P., Wei Y.,
RA Botstein D., Davis R.W.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome V.";
RL Nature 387:78-81(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 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 [4]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-22, AND IDENTIFICATION BY
RP 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 [5]
RP FUNCTION, CATALYTIC ACTIVITY, AND BIOPHYSICOCHEMICAL PROPERTIES.
RC STRAIN=ATCC 201388 / BY4741;
RX PubMed=26774271; DOI=10.1074/jbc.m115.704494;
RA Becker-Kettern J., Paczia N., Conrotte J.F., Kay D.P., Guignard C.,
RA Jung P.P., Linster C.L.;
RT "Saccharomyces cerevisiae forms D-2-hydroxyglutarate and couples its
RT degradation to D-lactate formation via a cytosolic transhydrogenase.";
RL J. Biol. Chem. 291:6036-6058(2016).
CC -!- FUNCTION: Catalyzes the reversible oxidation of 3-phospho-D-glycerate
CC to 3-phosphonooxypyruvate, the first step of the phosphorylated L-
CC serine biosynthesis pathway. Also catalyzes the reversible oxidation of
CC 2-hydroxyglutarate to 2-oxoglutarate. {ECO:0000269|PubMed:26774271}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(2R)-3-phosphoglycerate + NAD(+) = 3-phosphooxypyruvate + H(+)
CC + NADH; Xref=Rhea:RHEA:12641, ChEBI:CHEBI:15378, ChEBI:CHEBI:18110,
CC ChEBI:CHEBI:57540, ChEBI:CHEBI:57945, ChEBI:CHEBI:58272; EC=1.1.1.95;
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(R)-2-hydroxyglutarate + NAD(+) = 2-oxoglutarate + H(+) +
CC NADH; Xref=Rhea:RHEA:49612, ChEBI:CHEBI:15378, ChEBI:CHEBI:15801,
CC ChEBI:CHEBI:16810, ChEBI:CHEBI:57540, ChEBI:CHEBI:57945;
CC EC=1.1.1.399; Evidence={ECO:0000269|PubMed:26774271};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=49 uM for 2-oxoglutarate {ECO:0000269|PubMed:26774271};
CC Note=kcat is 0.2 sec(-1) for 2-oxoglutarate reduction.
CC {ECO:0000269|PubMed:26774271};
CC -!- PATHWAY: Amino-acid biosynthesis; L-serine biosynthesis; L-serine from
CC 3-phospho-D-glycerate: step 1/3.
CC -!- INTERACTION:
CC P40054; P40510: SER33; NbExp=5; IntAct=EBI-16961, EBI-16821;
CC -!- MISCELLANEOUS: Present with 7670 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the D-isomer specific 2-hydroxyacid
CC dehydrogenase family. {ECO:0000305}.
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DR EMBL; U18839; AAB64636.1; -; Genomic_DNA.
DR EMBL; BK006939; DAA07742.1; -; Genomic_DNA.
DR PIR; S50584; S50584.
DR RefSeq; NP_011004.3; NM_001178972.3.
DR AlphaFoldDB; P40054; -.
DR SMR; P40054; -.
DR BioGRID; 36826; 82.
DR DIP; DIP-5336N; -.
DR IntAct; P40054; 7.
DR MINT; P40054; -.
DR STRING; 4932.YER081W; -.
DR MoonDB; P40054; Predicted.
DR iPTMnet; P40054; -.
DR MaxQB; P40054; -.
DR PaxDb; P40054; -.
DR PRIDE; P40054; -.
DR EnsemblFungi; YER081W_mRNA; YER081W; YER081W.
DR GeneID; 856814; -.
DR KEGG; sce:YER081W; -.
DR SGD; S000000883; SER3.
DR VEuPathDB; FungiDB:YER081W; -.
DR eggNOG; KOG0068; Eukaryota.
DR GeneTree; ENSGT00940000176610; -.
DR HOGENOM; CLU_019796_9_2_1; -.
DR InParanoid; P40054; -.
DR OMA; YGNIGTQ; -.
DR BioCyc; YEAST:YER081W-MON; -.
DR UniPathway; UPA00135; UER00196.
DR PRO; PR:P40054; -.
DR Proteomes; UP000002311; Chromosome V.
DR RNAct; P40054; protein.
DR GO; GO:0005737; C:cytoplasm; HDA:SGD.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0061759; F:alpha-ketoglutarate reductase activity; IDA:SGD.
DR GO; GO:0030267; F:glyoxylate reductase (NADP+) activity; IBA:GO_Central.
DR GO; GO:0016618; F:hydroxypyruvate reductase activity; IBA:GO_Central.
DR GO; GO:0051287; F:NAD binding; IEA:InterPro.
DR GO; GO:0004617; F:phosphoglycerate dehydrogenase activity; IMP:SGD.
DR GO; GO:0006564; P:L-serine biosynthetic process; IEA:UniProtKB-KW.
DR GO; GO:0009070; P:serine family amino acid biosynthetic process; IMP:SGD.
DR InterPro; IPR045865; ACT-like_dom_sf.
DR InterPro; IPR002912; ACT_dom.
DR InterPro; IPR006139; D-isomer_2_OHA_DH_cat_dom.
DR InterPro; IPR029753; D-isomer_DH_CS.
DR InterPro; IPR029752; D-isomer_DH_CS1.
DR InterPro; IPR006140; D-isomer_DH_NAD-bd.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR Pfam; PF00389; 2-Hacid_dh; 1.
DR Pfam; PF02826; 2-Hacid_dh_C; 1.
DR SUPFAM; SSF51735; SSF51735; 1.
DR SUPFAM; SSF55021; SSF55021; 1.
DR PROSITE; PS51671; ACT; 1.
DR PROSITE; PS00065; D_2_HYDROXYACID_DH_1; 1.
DR PROSITE; PS00670; D_2_HYDROXYACID_DH_2; 1.
DR PROSITE; PS00671; D_2_HYDROXYACID_DH_3; 1.
PE 1: Evidence at protein level;
KW Amino-acid biosynthesis; NAD; Oxidoreductase; Phosphoprotein;
KW Reference proteome; Serine biosynthesis.
FT CHAIN 1..469
FT /note="D-3-phosphoglycerate dehydrogenase 1"
FT /id="PRO_0000076018"
FT DOMAIN 399..469
FT /note="ACT"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01007"
FT ACT_SITE 287
FT /evidence="ECO:0000250"
FT ACT_SITE 316
FT /evidence="ECO:0000250"
FT ACT_SITE 347
FT /note="Proton donor"
FT /evidence="ECO:0000250"
FT BINDING 208..209
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P0A9T0"
FT BINDING 228
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P0A9T0"
FT BINDING 285..287
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P0A9T0"
FT BINDING 311
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P0A9T0"
FT BINDING 347..350
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P0A9T0"
FT MOD_RES 22
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18407956"
FT MOD_RES 29
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P40510"
FT MOD_RES 33
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P40510"
SQ SEQUENCE 469 AA; 51193 MW; E1E69070BF41A87C CRC64;
MTSIDINNLQ NTFQQAMNMS GSPGAVCTSP TQSFMNTVPQ RLNAVKHPKI LKPFSTGDMK
ILLLENVNQT AITIFEEQGY QVEFYKSSLP EEELIEKIKD VHAIGIRSKT RLTSNVLQHA
KNLVCIGCFC IGTNQVDLDY ATSRGIAVFN SPFSNSRSVA ELVIAEIISL ARQLGDRSIE
LHTGTWNKVA ARCWEVRGKT LGIIGYGHIG SQLSVLAEAM GLHVLYYDIV TIMALGTARQ
VSTLDELLNK SDFVTLHVPA TPETEKMLSA PQFAAMKDGA YVINASRGTV VDIPSLIQAV
KANKIAGAAL DVYPHEPAKN GEGSFNDELN SWTSELVSLP NIILTPHIGG STEEAQSSIG
IEVATALSKY INEGNSVGSV NFPEVALKSL SYDQENTVRV LYIHQNVPGV LKTVNDILSN
HNIEKQFSDS NGEIAYLMAD ISSVDQSDIK DIYEQLNQTS AKISIRLLY
