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Catalytic Site Atlas Version 2.2.12
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CSA entry for 1psd
Original Entry
Title:
Oxidoreductase (nad(a))
Compound:
D-3-phosphoglycerate dehydrogenase (phosphoglycerate dehydrogenase) (e.c.1.1.1.95)
Mutant:
No
UniProt/Swiss-Prot:
P08328-SERA_ECOLI
EC Class:
1.1.1.95
Other CSA Entries:
Overview of all sites for 1psd
Homologues of 1psd
Entries for UniProt/Swiss-Prot: P08328
Entries for EC: 1.1.1.95
Other Databases:
PDB entry: 1psd
PDBsum entry: 1psd
UniProt/Swiss-Prot: P08328
IntEnz entry: 1.1.1.95
Literature Report:
Introduction:
3-phosphoglycerate dehydrogenase catalyses the oxidation of D-3-phosphoglycerate to 3-phosphohydroxypyruvate with concurrent reduction of NAD+ to NADH. This reaction is the first committed step in serine biosynthesis. In the following steps transamination of 3-phosphohydroxypyruvate with glutamate yields phosphoserine and the action of a phosphatase completes the biosynthesis. In prokaryotes and plants 3-phosphoglycerate dehydrogenase is inhibited by serine in an allosteric fashion.
Mechanism:
3-phosphoglycerate utilises a charge-relay system involving His 292 and Glu 269. His 292 deprotonates the C2 hydroxyl group of 3-phosphoglycerate as a hydride ion is transferred from C2 to NAD+. Glu 269 functions to modify the pKa of His 292, allowing it to carry out its catalytic role.
Sites:

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Found by:
Literature reference 

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
GLUA 269 0Sidechain
ElectrostaticResidue
Modifies the pKa of His 292, allowing it to carry out its role in catalysis.
Evidence from paper Evidence concerns Evidence type
PubMed ID 7719856 Current protein Conservation of residue
PubMed ID 7719856 Current protein Structural similarity to homologue of known mechanism
PubMed ID 7719856 Current protein Residue is positioned appropriately (ligand position known)

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
HISA 292 0Sidechain
Acid/baseSubstrate
Deprotonates the C2 hydroxyl group as hydride is transferred from C2 to NAD.
Evidence from paper Evidence concerns Evidence type
PubMed ID 7719856 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 7719856 Current protein Structural similarity to homologue of known mechanism
PubMed ID 14154 Current protein Kinetic studies
PubMed ID 7719856 Current protein Conservation of residue

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
NADA 450 0
Substrate
Accepts hydride from substrate.
Evidence from paper Evidence concerns Evidence type
PubMed ID 7719856 Current protein Structural similarity to homologue of known mechanism
PubMed ID 7719856 Current protein Residue is positioned appropriately (ligand position known)
References:
1
The allosteric ligand site in the Vmax-type cooperative enzyme phosphoglycerate dehydrogenase.
D. J. Schuller and G. A. Grant and L. J. Banaszak
Nat Struct Biol 2, (1) 69-76, (1995).
7719856
2
Transient kinetic and deuterium isotope effect studies on the catalytic mechanism of phosphoglycerate dehydrogenase.
R. Dubrow and L. I. Pizer
J Biol Chem 252, (5) 1539-51, (1977).
14154
3
The presence of a histidine-aspartic acid pair in the active site of 2-hydroxyacid dehydrogenases. X-ray refinement of cytoplasmic malate dehydrogenase.
J. J. Birktoft and L. J. Banaszak
J Biol Chem 258, (1) 472-82, (1983).
6848515
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