DB code: T00247

CATH domain 3.40.50.5600 : Rossmann fold
3.40.50.720 : Rossmann fold Catalytic domain
3.30.70.260 : Alpha-Beta Plaits
E.C. 1.1.1.95
CSA 1psd
M-CSA 1psd
MACiE

CATH domain Related DB codes (homologues)
3.30.70.260 : Alpha-Beta Plaits D00496
3.40.50.720 : Rossmann fold S00543 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

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P0A9T0 D-3-phosphoglycerate dehydrogenase
PGDH
EC 1.1.1.95
NP_417388.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_491113.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PF00389 (2-Hacid_dh)
PF02826 (2-Hacid_dh_C)
PF01842 (ACT)
[Graphical View]

KEGG enzyme name
phosphoglycerate 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

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P0A9T0 SERA_ECOLI 2-hydroxyglutarate + NAD(+) = 2-oxoglutarate + NADH. 3-phospho-D-glycerate + NAD(+) = 3- phosphonooxypyruvate + NADH. Homotetramer.

KEGG Pathways
Map code Pathways E.C.
MAP00260 Glycine, serine and threonine metabolism

Compound table
Substrates Products Intermediates
KEGG-id C00597 C00003 C03232 C00004 C00080
E.C.
Compound 3-Phosphoglycerate NAD+ 3-Phosphohydroxypyruvate NADH H+
Type carbohydrate,carboxyl group,phosphate group/phosphate ion amide group,amine group,nucleotide carbohydrate,carboxyl group,phosphate group/phosphate ion amide group,amine group,nucleotide others
ChEBI 17050
15846
30933
16908
15378
PubChem 724
5893
105
439153
1038
1psdA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1psdB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1sc6A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1sc6B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1sc6C01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1sc6D01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1psdA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:NAD Unbound Unbound
1psdB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:NAD Unbound Unbound
1sc6A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:NAD Unbound Unbound
1sc6B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:NAD Unbound Unbound
1sc6C02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:NAD Unbound Unbound
1sc6D02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:NAD Unbound Unbound
1psdA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1psdB03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1sc6A03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1sc6B03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1sc6C03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1sc6D03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
Swiss-prot;P0A9T0

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1psdA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1psdB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1sc6A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1sc6B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1sc6C01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1sc6D01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1psdA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 240;GLU 269;HIS 292
1psdB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 240;GLU 269;HIS 292
1sc6A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 240;;HIS 292 invisible 266-274, mutant W139G
1sc6B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 240;;HIS 292 invisible 266-274, mutant W139G
1sc6C02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 240; ; invisible 266-274/292-298 mutant W139G
1sc6D02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 240; ; invisible 266-274/292-295 mutant W139G
1psdA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1psdB03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1sc6A03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1sc6B03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1sc6C03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1sc6D03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[25]
p.3456-3458
[7]
p.73

References
[1]
Resource
Comments
Medline ID
PubMed ID 7049261
Journal Biosci Rep
Year 1981
Volume 1
Pages 733-41
Authors vGrant GA, Zapp ML
Title D-3-phosphoglycerate dehydrogenase from Escherichia coli: isolation by affinity chromatography and sequence comparison to other dehydrogenases.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 3800969
Journal Biochem J
Year 1986
Volume 238
Pages 919-22
Authors Lund K, Merrill DK, Guynn RW
Title Purification and subunit structure of phosphoglycerate dehydrogenase from rabbit liver.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 3017965
Journal J Biol Chem
Year 1986
Volume 261
Pages 12179-83
Authors Tobey KL, Grant GA
Title The nucleotide sequence of the serA gene of Escherichia coli and the amino acid sequence of the encoded protein, D-3-phosphoglycerate dehydrogenase.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 2692566
Journal Biochem Biophys Res Commun
Year 1989
Volume 165
Pages 1371-4
Authors Grant GA
Title A new family of 2-hydroxyacid dehydrogenases.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 2681152
Journal J Bacteriol
Year 1989
Volume 171
Pages 6084-92
Authors Schoenlein PV, Roa BB, Winkler ME
Title Divergent transcription of pdxB and homology between the pdxB and serA gene products in Escherichia coli K-12.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 1567457
Journal Biochem Biophys Res Commun
Year 1992
Volume 184
Pages 60-6
Authors Kochhar S, Hunziker PE, Leong-Morgenthaler P, Hottinger H
Title Evolutionary relationship of NAD(+)-dependent D-lactate dehydrogenase: comparison of primary structure of 2-hydroxy acid dehydrogenases.
Related PDB
Related UniProtKB
[7]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.75 ANGSTROMS).
Medline ID
PubMed ID 7719856
Journal Nat Struct Biol
Year 1995
Volume 2
Pages 69-76
Authors Schuller DJ, Grant GA, Banaszak LJ
Title The allosteric ligand site in the Vmax-type cooperative enzyme phosphoglycerate dehydrogenase.
Related PDB 1psd
Related UniProtKB P0A9T0
[8]
Resource
Comments
Medline ID
PubMed ID 8662776
Journal J Biol Chem
Year 1996
Volume 271
Pages 13013-7
Authors Al-Rabiee R, Lee EJ, Grant GA
Title The mechanism of velocity modulated allosteric regulation in D-3-phosphoglycerate dehydrogenase. Cross-linking adjacent regulatory domains with engineered disulfides mimics effector binding.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 8798520
Journal J Biol Chem
Year 1996
Volume 271
Pages 23235-8
Authors Al-Rabiee R, Zhang Y, Grant GA
Title The mechanism of velocity modulated allosteric regulation in D-3-phosphoglycerate dehydrogenase. Site-directed mutagenesis of effector binding site residues.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 8771194
Journal Protein Sci
Year 1996
Volume 5
Pages 34-41
Authors Grant GA, Schuller DJ, Banaszak LJ
Title A model for the regulation of D-3-phosphoglycerate dehydrogenase, a Vmax-type allosteric enzyme.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 9163325
Journal Biochem J
Year 1997
Volume 323
Pages 365-70
Authors Achouri Y, Rider MH, Schaftingen EV, Robbi M
Title Cloning, sequencing and expression of rat liver 3-phosphoglycerate dehydrogenase.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 9712860
Journal J Biol Chem
Year 1998
Volume 273
Pages 22389-94
Authors Grant GA, Xu XL
Title Probing the regulatory domain interface of D-3-phosphoglycerate dehydrogenase with engineered tryptophan residues.
Related PDB
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 10600116
Journal Biochemistry
Year 1999
Volume 38
Pages 16548-52
Authors Grant GA, Xu XL, Hu Z, Purvis AR
Title Phosphate ion partially relieves the cooperativity of effector binding in D-3-phosphoglycerate dehydrogenase without altering the cooperativity of inhibition.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 10026144
Journal J Biol Chem
Year 1999
Volume 274
Pages 5357-61
Authors Grant GA, Kim SJ, Xu XL, Hu Z
Title The contribution of adjacent subunits to the active sites of D-3-phosphoglycerate dehydrogenase.
Related PDB
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 10595555
Journal Protein Sci
Year 1999
Volume 8
Pages 2501-5
Authors Grant GA, Xu XL, Hu Z
Title The relationship between effector binding and inhibition of activity in D-3-phosphoglycerate dehydrogenase.
Related PDB
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 10683264
Journal Arch Biochem Biophys
Year 2000
Volume 375
Pages 171-4
Authors Grant GA, Xu XL, Hu Z
Title Removal of the tryptophan 139 side chain in Escherichia coli D-3-phosphoglycerate dehydrogenase produces a dimeric enzyme without cooperative effects.
Related PDB
Related UniProtKB
[17]
Resource
Comments
Medline ID
PubMed ID 10852732
Journal Biochemistry
Year 2000
Volume 39
Pages 7316-9
Authors Grant GA, Xu XL, Hu Z
Title Role of an interdomain Gly-Gly sequence at the regulatory-substrate domain interface in the regulation of Escherichia coli. D-3-phosphoglycerate dehydrogenase.
Related PDB
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 11155166
Journal Oral Microbiol Immunol
Year 2000
Volume 15
Pages 58-62
Authors Kawabata S, Terao Y, Hamada S
Title Molecular cloning, sequence and characterization of a novel streptococcal phosphoglycerate dehydrogenase gene.
Related PDB
Related UniProtKB
[19]
Resource
Comments
Medline ID
PubMed ID 11050089
Journal J Biol Chem
Year 2001
Volume 276
Pages 1078-83
Authors Grant GA, Hu Z, Xu XL
Title Specific interactions at the regulatory domain-substrate binding domain interface influence the cooperativity of inhibition and effector binding in Escherichia coli D-3-phosphoglycerate dehydrogenase.
Related PDB
Related UniProtKB
[20]
Resource
Comments
Medline ID
PubMed ID 11278587
Journal J Biol Chem
Year 2001
Volume 276
Pages 17844-50
Authors Grant GA, Hu Z, Xu XL
Title Amino acid residue mutations uncouple cooperative effects in Escherichia coli D-3-phosphoglycerate dehydrogenase.
Related PDB
Related UniProtKB
[21]
Resource
Comments
Medline ID
PubMed ID 12466884
Journal Appl Microbiol Biotechnol
Year 2002
Volume 60
Pages 437-41
Authors Peters-Wendisch P, Netzer R, Eggeling L, Sahm H
Title 3-Phosphoglycerate dehydrogenase from Corynebacterium glutamicum: the C-terminal domain is not essential for activity but is required for inhibition by L-serine.
Related PDB
Related UniProtKB
[22]
Resource
Comments
Medline ID
PubMed ID 12199695
Journal Eur J Biochem
Year 2002
Volume 269
Pages 4176-84
Authors Bell JK, Pease PJ, Bell JE, Grant GA, Banaszak LJ
Title De-regulation of D-3-phosphoglycerate dehydrogenase by domain removal. Eur J Biochem. 2002 Sep;269(17):4176-84.
Related PDB
Related UniProtKB
[23]
Resource
Comments
Medline ID
PubMed ID 12183470
Journal J Biol Chem
Year 2002
Volume 277
Pages 39548-53
Authors Grant GA, Hu Z, Xu XL
Title Cofactor binding to Escherichia coli D-3-phosphoglycerate dehydrogenase induces multiple conformations which alter effector binding.
Related PDB
Related UniProtKB
[24]
Resource
Comments
Medline ID
PubMed ID 12644455
Journal J Biol Chem
Year 2003
Volume 278
Pages 18170-6
Authors Grant GA, Hu Z, Xu XL
Title Hybrid tetramers reveal elements of cooperativity in Escherichia coli D-3-phosphoglycerate dehydrogenase.
Related PDB
Related UniProtKB
[25]
Resource
Comments
Medline ID
PubMed ID 15035616
Journal Biochemistry
Year 2004
Volume 43
Pages 3450-8
Authors Bell JK, Grant GA, Banaszak LJ
Title Multiconformational states in phosphoglycerate dehydrogenase.
Related PDB 1sc6
Related UniProtKB
[26]
Resource
Comments
Medline ID
PubMed ID 14718528
Journal J Biol Chem
Year 2004
Volume 279
Pages 13452-60
Authors Grant GA, Xu XL, Hu Z
Title Quantitative relationships of site to site interaction in Escherichia coli D-3-phosphoglycerate dehydrogenase revealed by asymmetric hybrid tetramers.
Related PDB
Related UniProtKB

Comments

Created Updated
2004-03-16 2009-02-26