EzCatDB: T00247
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DB codeT00247
CATH domainDomain 13.40.50.5600 : Rossmann fold
Domain 23.40.50.720 : Rossmann foldCatalytic domain
Domain 33.30.70.260 : Alpha-Beta Plaits
E.C.1.1.1.95
CSA1psd

CATH domainRelated DB codes (homologues)
3.30.70.260 : Alpha-Beta PlaitsD00496
3.40.50.720 : Rossmann foldS00543,S00551,S00552,S00553,S00602,S00604,S00605,S00608,S00610,S00625,S00319,S00328,S00329,S00330,S00331,S00332,D00456,D00457,D00458,S00324,S00320,S00325,S00326,S00327,D00459,S00335,S00336,S00334,T00219,S00339,D00513,D00001,D00002,D00003,D00005,D00007,D00008,D00010,D00012,D00017,D00018,D00023,D00027,D00028,D00031,D00032,D00033,D00034,D00035,D00037,D00048,D00071,D00476,D00481,D00482,D00490,D00492,D00494,D00545,D00601,D00603,D00604,D00605,D00615,D00845,D00857,D00858,M00161,M00171,M00210,T00002,T00010,T00011,T00015,T00227,T00408,T00414,D00827,D00262,D00274,D00275,M00035,T00109

Enzyme Name
UniProtKBKEGG

P0A9T0
Protein nameD-3-phosphoglycerate dehydrogenasephosphoglycerate dehydrogenase
D-3-phosphoglycerate:NAD+ oxidoreductase
alpha-phosphoglycerate dehydrogenase
3-phosphoglycerate dehydrogenase
3-phosphoglyceric acid dehydrogenase
D-3-phosphoglycerate dehydrogenase
glycerate 3-phosphate dehydrogenase
glycerate-1,3-phosphate dehydrogenase
phosphoglycerate oxidoreductase
phosphoglyceric acid dehydrogenase
SerA
3-phosphoglycerate:NAD+ 2-oxidoreductase
SerA 3PG dehydrogenase
3PHP reductase
alphaKG reductase
D- and L-HGA
SynonymsPGDH
EC 1.1.1.95
RefSeqNP_417388.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_491113.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PfamPF00389 (2-Hacid_dh)
PF02826 (2-Hacid_dh_C)
PF01842 (ACT)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00260Glycine, serine and threonine metabolism

UniProtKB:Accession NumberP0A9T0
Entry nameSERA_ECOLI
Activity3-phospho-D-glycerate + NAD(+) = 3- phosphonooxypyruvate + NADH.,2-hydroxyglutarate + NAD(+) = 2-oxoglutarate + NADH.
SubunitHomotetramer.
Subcellular location
Cofactor

Compound table: links to PDB-related databases & PoSSuM

SubstratesProducts
KEGG-idC00597C00003C03232C00004C00080
Compound3-PhosphoglycerateNAD+3-PhosphohydroxypyruvateNADHH+
Typecarbohydrate,carboxyl group,phosphate group/phosphate ionamide group,amine group,nucleotidecarbohydrate,carboxyl group,phosphate group/phosphate ionamide group,amine group,nucleotideothers
ChEBI17050
15846
30933
16908
15378
PubChem724
5893
105
439153
1038
             
1psdA01UnboundUnboundUnboundUnbound 
1psdB01UnboundUnboundUnboundUnbound 
1sc6A01UnboundUnboundUnboundUnbound 
1sc6B01UnboundUnboundUnboundUnbound 
1sc6C01UnboundUnboundUnboundUnbound 
1sc6D01UnboundUnboundUnboundUnbound 
1psdA02UnboundBound:NADUnboundUnbound 
1psdB02UnboundBound:NADUnboundUnbound 
1sc6A02UnboundBound:NADUnboundUnbound 
1sc6B02UnboundBound:NADUnboundUnbound 
1sc6C02UnboundBound:NADUnboundUnbound 
1sc6D02UnboundBound:NADUnboundUnbound 
1psdA03UnboundUnboundUnboundUnbound 
1psdB03UnboundUnboundUnboundUnbound 
1sc6A03UnboundUnboundUnboundUnbound 
1sc6B03UnboundUnboundUnboundUnbound 
1sc6C03UnboundUnboundUnboundUnbound 
1sc6D03UnboundUnboundUnboundUnbound 

Active-site residues
resource
Swiss-prot;P0A9T0
pdbCatalytic residuescomment
          
1psdA01 
 
1psdB01 
 
1sc6A01 
 
1sc6B01 
 
1sc6C01 
 
1sc6D01 
 
1psdA02ARG 240;GLU 269;HIS 292
 
1psdB02ARG 240;GLU 269;HIS 292
 
1sc6A02ARG 240;       ;HIS 292
invisible 266-274, mutant W139G
1sc6B02ARG 240;       ;HIS 292
invisible 266-274, mutant W139G
1sc6C02ARG 240;       ;       
invisible 266-274/292-298 mutant W139G
1sc6D02ARG 240;       ;       
invisible 266-274/292-295 mutant W139G
1psdA03 
 
1psdB03 
 
1sc6A03 
 
1sc6B03 
 
1sc6C03 
 
1sc6D03 
 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[7]p.73
[25]p.3456-3458

references
[1]
PubMed ID7049261
JournalBiosci Rep
Year1981
Volume1
Pages733-41
AuthorsvGrant GA, Zapp ML
TitleD-3-phosphoglycerate dehydrogenase from Escherichia coli: isolation by affinity chromatography and sequence comparison to other dehydrogenases.
[2]
PubMed ID3800969
JournalBiochem J
Year1986
Volume238
Pages919-22
AuthorsLund K, Merrill DK, Guynn RW
TitlePurification and subunit structure of phosphoglycerate dehydrogenase from rabbit liver.
[3]
PubMed ID3017965
JournalJ Biol Chem
Year1986
Volume261
Pages12179-83
AuthorsTobey KL, Grant GA
TitleThe nucleotide sequence of the serA gene of Escherichia coli and the amino acid sequence of the encoded protein, D-3-phosphoglycerate dehydrogenase.
[4]
PubMed ID2692566
JournalBiochem Biophys Res Commun
Year1989
Volume165
Pages1371-4
AuthorsGrant GA
TitleA new family of 2-hydroxyacid dehydrogenases.
[5]
PubMed ID2681152
JournalJ Bacteriol
Year1989
Volume171
Pages6084-92
AuthorsSchoenlein PV, Roa BB, Winkler ME
TitleDivergent transcription of pdxB and homology between the pdxB and serA gene products in Escherichia coli K-12.
[6]
PubMed ID1567457
JournalBiochem Biophys Res Commun
Year1992
Volume184
Pages60-6
AuthorsKochhar S, Hunziker PE, Leong-Morgenthaler P, Hottinger H
TitleEvolutionary relationship of NAD(+)-dependent D-lactate dehydrogenase: comparison of primary structure of 2-hydroxy acid dehydrogenases.
[7]
CommentsX-RAY CRYSTALLOGRAPHY (2.75 ANGSTROMS).
PubMed ID7719856
JournalNat Struct Biol
Year1995
Volume2
Pages69-76
AuthorsSchuller DJ, Grant GA, Banaszak LJ
TitleThe allosteric ligand site in the Vmax-type cooperative enzyme phosphoglycerate dehydrogenase.
Related PDB1psd
Related UniProtKBP0A9T0
[8]
PubMed ID8662776
JournalJ Biol Chem
Year1996
Volume271
Pages13013-7
AuthorsAl-Rabiee R, Lee EJ, Grant GA
TitleThe mechanism of velocity modulated allosteric regulation in D-3-phosphoglycerate dehydrogenase. Cross-linking adjacent regulatory domains with engineered disulfides mimics effector binding.
[9]
PubMed ID8798520
JournalJ Biol Chem
Year1996
Volume271
Pages23235-8
AuthorsAl-Rabiee R, Zhang Y, Grant GA
TitleThe mechanism of velocity modulated allosteric regulation in D-3-phosphoglycerate dehydrogenase. Site-directed mutagenesis of effector binding site residues.
[10]
PubMed ID8771194
JournalProtein Sci
Year1996
Volume5
Pages34-41
AuthorsGrant GA, Schuller DJ, Banaszak LJ
TitleA model for the regulation of D-3-phosphoglycerate dehydrogenase, a Vmax-type allosteric enzyme.
[11]
PubMed ID9163325
JournalBiochem J
Year1997
Volume323
Pages365-70
AuthorsAchouri Y, Rider MH, Schaftingen EV, Robbi M
TitleCloning, sequencing and expression of rat liver 3-phosphoglycerate dehydrogenase.
[12]
PubMed ID9712860
JournalJ Biol Chem
Year1998
Volume273
Pages22389-94
AuthorsGrant GA, Xu XL
TitleProbing the regulatory domain interface of D-3-phosphoglycerate dehydrogenase with engineered tryptophan residues.
[13]
PubMed ID10600116
JournalBiochemistry
Year1999
Volume38
Pages16548-52
AuthorsGrant GA, Xu XL, Hu Z, Purvis AR
TitlePhosphate ion partially relieves the cooperativity of effector binding in D-3-phosphoglycerate dehydrogenase without altering the cooperativity of inhibition.
[14]
PubMed ID10026144
JournalJ Biol Chem
Year1999
Volume274
Pages5357-61
AuthorsGrant GA, Kim SJ, Xu XL, Hu Z
TitleThe contribution of adjacent subunits to the active sites of D-3-phosphoglycerate dehydrogenase.
[15]
PubMed ID10595555
JournalProtein Sci
Year1999
Volume8
Pages2501-5
AuthorsGrant GA, Xu XL, Hu Z
TitleThe relationship between effector binding and inhibition of activity in D-3-phosphoglycerate dehydrogenase.
[16]
PubMed ID10683264
JournalArch Biochem Biophys
Year2000
Volume375
Pages171-4
AuthorsGrant GA, Xu XL, Hu Z
TitleRemoval of the tryptophan 139 side chain in Escherichia coli D-3-phosphoglycerate dehydrogenase produces a dimeric enzyme without cooperative effects.
[17]
PubMed ID10852732
JournalBiochemistry
Year2000
Volume39
Pages7316-9
AuthorsGrant GA, Xu XL, Hu Z
TitleRole of an interdomain Gly-Gly sequence at the regulatory-substrate domain interface in the regulation of Escherichia coli. D-3-phosphoglycerate dehydrogenase.
[18]
PubMed ID11155166
JournalOral Microbiol Immunol
Year2000
Volume15
Pages58-62
AuthorsKawabata S, Terao Y, Hamada S
TitleMolecular cloning, sequence and characterization of a novel streptococcal phosphoglycerate dehydrogenase gene.
[19]
PubMed ID11050089
JournalJ Biol Chem
Year2001
Volume276
Pages1078-83
AuthorsGrant GA, Hu Z, Xu XL
TitleSpecific interactions at the regulatory domain-substrate binding domain interface influence the cooperativity of inhibition and effector binding in Escherichia coli D-3-phosphoglycerate dehydrogenase.
[20]
PubMed ID11278587
JournalJ Biol Chem
Year2001
Volume276
Pages17844-50
AuthorsGrant GA, Hu Z, Xu XL
TitleAmino acid residue mutations uncouple cooperative effects in Escherichia coli D-3-phosphoglycerate dehydrogenase.
[21]
PubMed ID12466884
JournalAppl Microbiol Biotechnol
Year2002
Volume60
Pages437-41
AuthorsPeters-Wendisch P, Netzer R, Eggeling L, Sahm H
Title3-Phosphoglycerate dehydrogenase from Corynebacterium glutamicum: the C-terminal domain is not essential for activity but is required for inhibition by L-serine.
[22]
PubMed ID12199695
JournalEur J Biochem
Year2002
Volume269
Pages4176-84
AuthorsBell JK, Pease PJ, Bell JE, Grant GA, Banaszak LJ
TitleDe-regulation of D-3-phosphoglycerate dehydrogenase by domain removal. Eur J Biochem. 2002 Sep;269(17):4176-84.
[23]
PubMed ID12183470
JournalJ Biol Chem
Year2002
Volume277
Pages39548-53
AuthorsGrant GA, Hu Z, Xu XL
TitleCofactor binding to Escherichia coli D-3-phosphoglycerate dehydrogenase induces multiple conformations which alter effector binding.
[24]
PubMed ID12644455
JournalJ Biol Chem
Year2003
Volume278
Pages18170-6
AuthorsGrant GA, Hu Z, Xu XL
TitleHybrid tetramers reveal elements of cooperativity in Escherichia coli D-3-phosphoglycerate dehydrogenase.
[25]
PubMed ID15035616
JournalBiochemistry
Year2004
Volume43
Pages3450-8
AuthorsBell JK, Grant GA, Banaszak LJ
TitleMulticonformational states in phosphoglycerate dehydrogenase.
Related PDB1sc6
[26]
PubMed ID14718528
JournalJ Biol Chem
Year2004
Volume279
Pages13452-60
AuthorsGrant GA, Xu XL, Hu Z
TitleQuantitative relationships of site to site interaction in Escherichia coli D-3-phosphoglycerate dehydrogenase revealed by asymmetric hybrid tetramers.


createdupdated
2004-03-162009-02-26
Copyright: Nozomi Nagano, JST & CBRC-AIST
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Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
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Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
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