SERA_ECOLI
ID SERA_ECOLI Reviewed; 410 AA.
AC P0A9T0; P08328; Q2M9S9; Q47633;
DT 01-AUG-1988, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 2.
DT 03-AUG-2022, entry version 142.
DE RecName: Full=D-3-phosphoglycerate dehydrogenase;
DE Short=PGDH;
DE EC=1.1.1.95 {ECO:0000269|PubMed:8550422};
DE AltName: Full=2-oxoglutarate reductase {ECO:0000305};
DE EC=1.1.1.399 {ECO:0000269|PubMed:8550422};
GN Name=serA; OrderedLocusNames=b2913, JW2880;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=3017965; DOI=10.1016/s0021-9258(18)67220-5;
RA Tobey K.L., Grant G.A.;
RT "The nucleotide sequence of the serA gene of Escherichia coli and the amino
RT acid sequence of the encoded protein, D-3-phosphoglycerate dehydrogenase.";
RL J. Biol. Chem. 261:12179-12183(1986).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-99.
RC STRAIN=K12;
RA Roy I., Leadlay P.F.;
RL Submitted (JUN-1992) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-29.
RC STRAIN=K12;
RX PubMed=1917830; DOI=10.1128/jb.173.19.5944-5953.1991;
RA Rex J.H., Aronson B.D., Somerville R.L.;
RT "The tdh and serA operons of Escherichia coli: mutational analysis of the
RT regulatory elements of leucine-responsive genes.";
RL J. Bacteriol. 173:5944-5953(1991).
RN [6]
RP PROTEIN SEQUENCE OF 2-13.
RC STRAIN=K12 / EMG2;
RX PubMed=9298646; DOI=10.1002/elps.1150180807;
RA Link A.J., Robison K., Church G.M.;
RT "Comparing the predicted and observed properties of proteins encoded in the
RT genome of Escherichia coli K-12.";
RL Electrophoresis 18:1259-1313(1997).
RN [7]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND ACTIVITY
RP REGULATION.
RC STRAIN=K12 / JM105 / ATCC 47016;
RX PubMed=8550422; DOI=10.1128/jb.178.1.232-239.1996;
RA Zhao G., Winkler M.E.;
RT "A novel alpha-ketoglutarate reductase activity of the serA-encoded 3-
RT phosphoglycerate dehydrogenase of Escherichia coli K-12 and its possible
RT implications for human 2-hydroxyglutaric aciduria.";
RL J. Bacteriol. 178:232-239(1996).
RN [8]
RP IDENTIFICATION BY 2D-GEL.
RX PubMed=9298644; DOI=10.1002/elps.1150180805;
RA VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.;
RT "Escherichia coli proteome analysis using the gene-protein database.";
RL Electrophoresis 18:1243-1251(1997).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (2.75 ANGSTROMS) IN COMPLEX WITH NAD.
RX PubMed=7719856; DOI=10.1038/nsb0195-69;
RA Schuller D.J., Grant G.A., Banaszak L.J.;
RT "The allosteric ligand site in the Vmax-type cooperative enzyme
RT phosphoglycerate dehydrogenase.";
RL Nat. Struct. Biol. 2:69-76(1995).
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:8550422}.
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 Evidence={ECO:0000269|PubMed:8550422};
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:8550422};
CC -!- ACTIVITY REGULATION: Displays feedback inhibition by L-serine.
CC Inhibited by glycine. {ECO:0000269|PubMed:8550422}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=1.2 mM for 3-phospho-D-glycerate {ECO:0000269|PubMed:8550422};
CC KM=3.2 uM for 3-phosphonooxypyruvate {ECO:0000269|PubMed:8550422};
CC KM=88 uM for 2-oxoglutarate {ECO:0000269|PubMed:8550422};
CC KM=0.37 mM for (R)-2-hydroxyglutarate {ECO:0000269|PubMed:8550422};
CC KM=2.9 mM for (S)-2-hydroxyglutarate {ECO:0000269|PubMed:8550422};
CC Vmax=183 nmol/min/mg enzyme for 3-phospho-D-glycerate oxidation
CC {ECO:0000269|PubMed:8550422};
CC Vmax=9.27 umol/min/mg enzyme for 3-phosphonooxypyruvate reduction
CC {ECO:0000269|PubMed:8550422};
CC Vmax=11.1 umol/min/mg enzyme for 2-oxoglutarate reduction
CC {ECO:0000269|PubMed:8550422};
CC Vmax=237 nmol/min/mg enzyme for (R)-2-hydroxyglutarate oxidation
CC {ECO:0000269|PubMed:8550422};
CC Vmax=83.3 nmol/min/mg enzyme for (S)-2-hydroxyglutarate oxidation
CC {ECO:0000269|PubMed:8550422};
CC Note=kcat is 0.55 sec(-1) for 3-phospho-D-glycerate oxidation. kcat
CC is 27.8 sec(-1) for 3-phosphonooxypyruvate reduction. kcat is 33.3
CC sec(-1) for 2-oxoglutarate reduction. kcat is 0.71 sec(-1) for (R)-2-
CC hydroxyglutarate oxidation. kcat is 0.25 sec(-1) for (S)-2-
CC hydroxyglutarate oxidation. {ECO:0000269|PubMed:8550422};
CC pH dependence:
CC Optimum pH is 8.5 for the reductase activities and 9.0 for the
CC dehydrogenase activities. {ECO:0000269|PubMed:8550422};
CC -!- PATHWAY: Amino-acid biosynthesis; L-serine biosynthesis; L-serine from
CC 3-phospho-D-glycerate: step 1/3.
CC -!- SUBUNIT: Homotetramer.
CC -!- SIMILARITY: Belongs to the D-isomer specific 2-hydroxyacid
CC dehydrogenase family. {ECO:0000305}.
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DR EMBL; L29397; AAA24625.1; -; Genomic_DNA.
DR EMBL; U28377; AAA69080.1; -; Genomic_DNA.
DR EMBL; U00096; AAC75950.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE76977.1; -; Genomic_DNA.
DR EMBL; X66836; CAA47308.1; -; Genomic_DNA.
DR EMBL; M64630; AAA73016.1; -; Genomic_DNA.
DR PIR; A25200; DEECPG.
DR RefSeq; NP_417388.1; NC_000913.3.
DR RefSeq; WP_001151604.1; NZ_STEB01000001.1.
DR PDB; 1PSD; X-ray; 2.75 A; A/B=2-410.
DR PDB; 1SC6; X-ray; 2.09 A; A/B/C/D=7-410.
DR PDB; 1YBA; X-ray; 2.24 A; A/B/C/D=1-410.
DR PDB; 2P9C; X-ray; 2.46 A; A/B=1-410.
DR PDB; 2P9E; X-ray; 2.60 A; A/B/C/D=1-410.
DR PDB; 2P9G; X-ray; 2.80 A; A/B=1-410.
DR PDB; 2PA3; X-ray; 2.74 A; A=1-410.
DR PDBsum; 1PSD; -.
DR PDBsum; 1SC6; -.
DR PDBsum; 1YBA; -.
DR PDBsum; 2P9C; -.
DR PDBsum; 2P9E; -.
DR PDBsum; 2P9G; -.
DR PDBsum; 2PA3; -.
DR AlphaFoldDB; P0A9T0; -.
DR SMR; P0A9T0; -.
DR BioGRID; 4261173; 27.
DR DIP; DIP-10851N; -.
DR IntAct; P0A9T0; 3.
DR STRING; 511145.b2913; -.
DR jPOST; P0A9T0; -.
DR PaxDb; P0A9T0; -.
DR PRIDE; P0A9T0; -.
DR EnsemblBacteria; AAC75950; AAC75950; b2913.
DR EnsemblBacteria; BAE76977; BAE76977; BAE76977.
DR GeneID; 66673210; -.
DR GeneID; 945258; -.
DR KEGG; ecj:JW2880; -.
DR KEGG; eco:b2913; -.
DR PATRIC; fig|1411691.4.peg.3820; -.
DR EchoBASE; EB0937; -.
DR eggNOG; COG0111; Bacteria.
DR HOGENOM; CLU_019796_9_2_6; -.
DR InParanoid; P0A9T0; -.
DR OMA; YGNIGTQ; -.
DR PhylomeDB; P0A9T0; -.
DR BioCyc; EcoCyc:PGLYCDEHYDROG-MON; -.
DR BioCyc; MetaCyc:PGLYCDEHYDROG-MON; -.
DR BRENDA; 1.1.1.95; 2026.
DR SABIO-RK; P0A9T0; -.
DR UniPathway; UPA00135; UER00196.
DR EvolutionaryTrace; P0A9T0; -.
DR PRO; PR:P0A9T0; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0047545; F:2-hydroxyglutarate dehydrogenase activity; IDA:EcoCyc.
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:0042802; F:identical protein binding; IDA:EcoCyc.
DR GO; GO:0070403; F:NAD+ binding; IDA:EcoCyc.
DR GO; GO:0070404; F:NADH binding; IDA:EcoCyc.
DR GO; GO:0004617; F:phosphoglycerate dehydrogenase activity; IDA:EcoCyc.
DR GO; GO:0070905; F:serine binding; IDA:EcoCyc.
DR GO; GO:0006564; P:L-serine biosynthetic process; IMP:EcoCyc.
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 Pfam; PF01842; ACT; 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 3D-structure; Amino-acid biosynthesis; Direct protein sequencing; NAD;
KW Oxidoreductase; Reference proteome; Serine biosynthesis.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:9298646"
FT CHAIN 2..410
FT /note="D-3-phosphoglycerate dehydrogenase"
FT /id="PRO_0000075999"
FT DOMAIN 339..410
FT /note="ACT"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01007"
FT ACT_SITE 240
FT ACT_SITE 269
FT ACT_SITE 292
FT /note="Proton donor"
FT BINDING 161..162
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:7719856"
FT BINDING 181
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:7719856"
FT BINDING 238..240
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:7719856"
FT BINDING 264
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:7719856"
FT BINDING 292..295
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:7719856"
FT TURN 6..8
FT /evidence="ECO:0007829|PDB:1YBA"
FT STRAND 9..11
FT /evidence="ECO:0007829|PDB:1YBA"
FT STRAND 13..15
FT /evidence="ECO:0007829|PDB:1SC6"
FT HELIX 21..29
FT /evidence="ECO:0007829|PDB:1SC6"
FT STRAND 35..37
FT /evidence="ECO:0007829|PDB:1SC6"
FT HELIX 44..50
FT /evidence="ECO:0007829|PDB:1SC6"
FT STRAND 55..59
FT /evidence="ECO:0007829|PDB:1SC6"
FT STRAND 61..63
FT /evidence="ECO:0007829|PDB:2P9C"
FT HELIX 67..72
FT /evidence="ECO:0007829|PDB:1SC6"
FT STRAND 78..81
FT /evidence="ECO:0007829|PDB:1SC6"
FT HELIX 91..96
FT /evidence="ECO:0007829|PDB:1SC6"
FT TURN 105..108
FT /evidence="ECO:0007829|PDB:1SC6"
FT HELIX 109..125
FT /evidence="ECO:0007829|PDB:1SC6"
FT HELIX 127..136
FT /evidence="ECO:0007829|PDB:1SC6"
FT HELIX 143..145
FT /evidence="ECO:0007829|PDB:2PA3"
FT STRAND 153..157
FT /evidence="ECO:0007829|PDB:1SC6"
FT HELIX 161..172
FT /evidence="ECO:0007829|PDB:1SC6"
FT STRAND 176..180
FT /evidence="ECO:0007829|PDB:1SC6"
FT HELIX 197..203
FT /evidence="ECO:0007829|PDB:1SC6"
FT STRAND 205..209
FT /evidence="ECO:0007829|PDB:1SC6"
FT TURN 215..219
FT /evidence="ECO:0007829|PDB:1SC6"
FT HELIX 223..228
FT /evidence="ECO:0007829|PDB:1SC6"
FT STRAND 233..237
FT /evidence="ECO:0007829|PDB:1SC6"
FT STRAND 241..244
FT /evidence="ECO:0007829|PDB:1SC6"
FT HELIX 246..254
FT /evidence="ECO:0007829|PDB:1SC6"
FT STRAND 257..264
FT /evidence="ECO:0007829|PDB:1SC6"
FT TURN 276..278
FT /evidence="ECO:0007829|PDB:1SC6"
FT HELIX 279..281
FT /evidence="ECO:0007829|PDB:1SC6"
FT STRAND 287..290
FT /evidence="ECO:0007829|PDB:1SC6"
FT HELIX 298..318
FT /evidence="ECO:0007829|PDB:1SC6"
FT STRAND 324..327
FT /evidence="ECO:0007829|PDB:1SC6"
FT STRAND 336..346
FT /evidence="ECO:0007829|PDB:1SC6"
FT HELIX 350..360
FT /evidence="ECO:0007829|PDB:1SC6"
FT STRAND 364..372
FT /evidence="ECO:0007829|PDB:1SC6"
FT STRAND 374..384
FT /evidence="ECO:0007829|PDB:1SC6"
FT HELIX 387..398
FT /evidence="ECO:0007829|PDB:1SC6"
FT STRAND 403..410
FT /evidence="ECO:0007829|PDB:1SC6"
SQ SEQUENCE 410 AA; 44176 MW; 61EF5EFC304DF6F0 CRC64;
MAKVSLEKDK IKFLLVEGVH QKALESLRAA GYTNIEFHKG ALDDEQLKES IRDAHFIGLR
SRTHLTEDVI NAAEKLVAIG CFCIGTNQVD LDAAAKRGIP VFNAPFSNTR SVAELVIGEL
LLLLRGVPEA NAKAHRGVWN KLAAGSFEAR GKKLGIIGYG HIGTQLGILA ESLGMYVYFY
DIENKLPLGN ATQVQHLSDL LNMSDVVSLH VPENPSTKNM MGAKEISLMK PGSLLINASR
GTVVDIPALC DALASKHLAG AAIDVFPTEP ATNSDPFTSP LCEFDNVLLT PHIGGSTQEA
QENIGLEVAG KLIKYSDNGS TLSAVNFPEV SLPLHGGRRL MHIHENRPGV LTALNKIFAE
QGVNIAAQYL QTSAQMGYVV IDIEADEDVA EKALQAMKAI PGTIRARLLY
