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Enzyme Nomenclature
Information on EC 1.1.1.95 - phosphoglycerate dehydrogenase
for references in articles please use BRENDA:EC1.1.1.95
Word Map on EC 1.1.1.95
- 1.1.1.95
- l-serine
- microcephaly
-
psychomotor
-
hydroxymethyltransferase
- hydroxypyruvate
-
2-hydroxyacid
- l-ser
-
neurometabolic
- synthesis
- biotechnology
- molecular biology
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The expected taxonomic range for this enzyme is: Eukaryota, Bacteria, Archaea
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EC NUMBER 
COMMENTARY 
1.1.1.95
-
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RECOMMENDED NAME
GeneOntology No.
phosphoglycerate dehydrogenase
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
3-phospho-D-glycerate + NAD+ = 3-phosphonooxypyruvate + NADH + H+
member of the 2-hydroxyacid dehydrogenases family, whereof only the enzymes from E. coli and Pisum sativum utilize phosphorylated substrates and transfer the hydride ion to the A-site of NAD+, uses also alpha-ketoglutarate as substrate
-
3-phospho-D-glycerate + NAD+ = 3-phosphonooxypyruvate + NADH + H+
regulation model with effector L-serine, member of the D-2-hydroxyacid dehydrogenases, D-isomer substrate specific, overview of related enzymes from other species
-
3-phospho-D-glycerate + NAD+ = 3-phosphonooxypyruvate + NADH + H+
model for catalytic mechanism
-
3-phospho-D-glycerate + NAD+ = 3-phosphonooxypyruvate + NADH + H+
-
-
-
-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
oxidation
-
-
-
-
redox reaction
-
-
-
-
reduction
-
-
-
-
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
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SYSTEMATIC NAME
IUBMB Comments
3-phospho-D-glycerate:NAD+ 2-oxidoreductase
This enzyme catalyses the first committed and rate-limiting step in the phosphoserine pathway of serine biosynthesis. The reaction occurs predominantly in the direction of reduction. The enzyme from the bacterium Escherichia coli also catalyses the activity of EC 1.1.1.399, 2-oxoglutarate reductase [6].
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CAS REGISTRY NUMBER
COMMENTARY
9075-29-0
-
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
malfunction
metabolism
physiological function
malfunction
-
mutations in the human PHGDH cause serine deficiency disorders characterized by severe neurological symptoms including congenital microcephaly and psychomotor retardation, growth retardation phenotypes seen in human patients suffering from SDD caused by PHGDH mutations, overview
malfunction
-
targeted disruption of Phgdh in mice causes overall growth retardation with severe brain microcephaly and leads to embryonic lethality
malfunction
3-PGDH deficiency is a rare recessive inborn error in the biosynthesis of the amino acid L-serine characterized clinically by congenital microcephaly, psychomotor retardation, and intractable seizures. The biochemical abnormalities associated with this disorder are low concentrations of L-serine, D-serine, and glycine in cerebrospinal fluid
malfunction
-
Phgdh null mice have markedly decreased free serine content in their tissues, which is associated with overall growth retardation, striking brain malformation, and embryonic lethality
malfunction
-
enzyme-depleted astrocytes accumulate 20fold less L-serine compared with controls
malfunction
PGDH1-silenced lines are inhibited in growth
malfunction
lacking of isoform EDA9 expression causes drastic developmental defects
metabolism
-
3-phosphoglycerate dehydrogenase catalyzes the first step of the phosphorylated pathway in the de novo synthesis of L-serine. Availability of L-serine within neural stem/progenitor cells may be a critical factor for neurogenesis in developing and adult brain
metabolism
the enzyme is required for the de novo biosynthesis of L-serine
metabolism
-
the enzyme catalyzes the first committed step of L-serine biosynthesis
physiological function
-
mutations in the human PHGDH cause serine deficiency disorders characterized by severe neurological symptoms including congenital microcephaly and psychomotor retardation
physiological function
-
Phgdh knockout mouse embryos demonstrate that free serine and glycine concentrations are decreased markedly in head samples
physiological function
3-PGDH deficiency is a rare recessive inborn error in the biosynthesis of the amino acid L-serine characterized clinically by congenital microcephaly, psychomotor retardation, and intractable seizures. The biochemical abnormalities associated with this disorder are low concentrations of L-serine, D-serine, and glycine in cerebrospinal fluid
physiological function
-
Phgdh null mice have markedly decreased free serine content in their tissues, which is associated with overall growth retardation, striking brain malformation, and embryonic lethality
physiological function
the gene EDA9 plays a crucial role in embryo and pollen development
physiological function
phosphoglycerate dehydrogenase isoform EDA9 is the essential gene for embryo and male gametophyte development in Arabidopsis thaliana
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
2-phospho-D-glycerate + NAD+
2-phosphohydroxypyruvate + NADH + H+
-
activity relative to 3-phospho-D-glycerate: 47%
-
-
?
3-phosphohydroxypyruvate + NADH
3-phosphoglycerate + NAD+
-
specific for
-
-
?
DL-glyceraldehyde 3-phosphate + NAD+
?
-
activity relative to 3-phospho-D-glycerate: 9%
-
-
?
3-phospho-D-glycerate + NAD+
3-phosphohydroxypyruvate + NADH
-
-
-
-
?
3-phospho-D-glycerate + NAD+
3-phosphohydroxypyruvate + NADH
-
first step in biosynthesis of L-serine, pathway regulation, overview
-
-
?
3-phospho-D-glycerate + NAD+
3-phosphohydroxypyruvate + NADH
-
-
-
-
-
3-phospho-D-glycerate + NAD+
3-phosphohydroxypyruvate + NADH
first step in biosynthesis of L-serine, the enzyme contains an ACT domain, which is involved in the allosteric regulation mechanism, residue W139 is involved
-
-
?
3-phospho-D-glycerate + NAD+
3-phosphohydroxypyruvate + NADH
-
first step in biosynthesis of L-serine, the enzyme contains an ACT domain, which is involved in the allosteric regulation mechanism, residue W139 is involved
-
-
?
3-phospho-D-glycerate + NAD+
3-phosphohydroxypyruvate + NADH
-
first step in biosynthesis of L-serine, Vmax regulation through domain and subunit changes, overview
-
-
?
3-phospho-D-glycerate + NAD+
3-phosphohydroxypyruvate + NADH
D-isomer-specific
-
-
?
3-phospho-D-glycerate + NAD+
3-phosphohydroxypyruvate + NADH
-
D-isomer-specific
-
-
?
3-phospho-D-glycerate + NAD+
3-phosphohydroxypyruvate + NADH + H+
-
-
-
-
r
3-phospho-D-glycerate + NAD+
3-phosphohydroxypyruvate + NADH + H+
-
-
-
?
3-phospho-D-glycerate + NAD+
3-phosphohydroxypyruvate + NADH + H+
-
highest activity
-
-
r
3-phospho-D-glycerate + NAD+
3-phosphonooxypyruvate + NADH + H+
-
-
-
?
3-phospho-D-glycerate + NAD+
3-phosphonooxypyruvate + NADH + H+
-
-
-
?
3-phospho-D-glycerate + NAD+
3-phosphonooxypyruvate + NADH + H+
-
-
-
?
3-phospho-D-glycerate + NAD+
3-phosphonooxypyruvate + NADH + H+
-
-
-
?
3-phospho-D-glycerate + NAD+
3-phosphonooxypyruvate + NADH + H+
-
-
-
-
?
3-phospho-D-glycerate + NAD+
3-phosphonooxypyruvate + NADH + H+
-
-
-
?
3-phospho-D-glycerate + NAD+
3-phosphonooxypyruvate + NADH + H+
-
-
-
?
3-phospho-D-glycerate + NAD+
3-phosphonooxypyruvate + NADH + H+
-
-
-
-
?
3-phospho-D-glycerate + NAD+
3-phosphonooxypyruvate + NADH + H+
-
-
-
-
?
3-phospho-D-glycerate + NAD+
3-phosphonooxypyruvate + NADH + H+
-
-
-
-
?
3-phospho-D-glycerate + NAD+
3-phosphonooxypyruvate + NADH + H+
-
-
-
-
?
3-phospho-D-glycerate + NAD+
3-phosphonooxypyruvate + NADH + H+
-
-
-
-
?
3-phospho-D-glycerate + NAD+
3-phosphonooxypyruvate + NADH + H+
-
-
-
-
?
3-phospho-D-glycerate + NAD+
3-phosphonooxypyruvate + NADH + H+
-
-
-
?
3-phospho-D-glycerate + NADP+
3-phosphohydroxypyruvate + NADPH + H+
-
-
-
-
3-phospho-D-glycerate + NADP+
3-phosphohydroxypyruvate + NADPH + H+
-
-
-
-
r
3-phosphoglycerate + NAD+
3-phosphohydroxypyruvate + NADH
-
-
-
r
3-phosphoglycerate + NAD+
3-phosphohydroxypyruvate + NADH
-
first enzyme in metabolic sequence of synthesis of serine from 3-phosphoglycerate
-
-
r
3-phosphoglycerate + NAD+
3-phosphohydroxypyruvate + NADH
-
-
-
r
3-phosphoglycerate + NAD+
3-phosphohydroxypyruvate + NADH
-
-
-
r
3-phosphoglycerate + NAD+
3-phosphohydroxypyruvate + NADH
-
reduction of hydroxypyruvate-phosphate is faster than oxidation of phosphoglycerate
-
r
3-phosphoglycerate + NAD+
3-phosphohydroxypyruvate + NADH
-
allosteric inhibition by L-serine, L-serine regulates the pathway of serine biosynthesis by end product inhibition interacting with His344, Asn346 and Asn364, 1 serine binds per subunit
-
r
3-phosphoglycerate + NAD+
3-phosphohydroxypyruvate + NADH
-
allosteric inhibition by L-serine, L-serine regulates the pathway of serine biosynthesis by end product inhibition interacting with His344, Asn346 and Asn364, 1 serine binds per subunit
-
-
r
3-phosphoglycerate + NAD+
3-phosphohydroxypyruvate + NADH
-
first enzyme in metabolic sequence of synthesis of serine from 3-phosphoglycerate
-
-
r
3-phosphoglycerate + NAD+
3-phosphohydroxypyruvate + NADH
-
first enzyme in metabolic sequence of synthesis of serine from 3-phosphoglycerate
-
-
-
3-phosphoglycerate + NAD+
3-phosphohydroxypyruvate + NADH
-
first enzyme in metabolic sequence of synthesis of serine from 3-phosphoglycerate
-
-
r
3-phosphoglycerate + NAD+
3-phosphohydroxypyruvate + NADH
-
-
-
r
3-phosphoglycerate + NAD+
3-phosphohydroxypyruvate + NADH
-
-
-
r
3-phosphoglycerate + NAD+
3-phosphohydroxypyruvate + NADH
-
-
-
r
3-phosphoglycerate + NAD+
3-phosphohydroxypyruvate + NADH
-
first enzyme in metabolic sequence of synthesis of serine from 3-phosphoglycerate
-
-
r
3-phosphoglycerate + NAD+
3-phosphohydroxypyruvate + NADH
-
the enzyme catalyzes the first reaction of serine and glycine biosynthesis. SER3 and SER33 encode phosphoglycerate dehydrogenases. The requirement for the SER-dependent phosphoglycerate pathway is conditional since the glyoxylate route of serine/glycine biosynthesis is glucose repressed. Ser33p is likely to be the main isoenzyme of the phosphoglycerate pathway during growth on glucose
-
-
?
3-phosphoglycerate + NAD+
3-phosphohydroxypyruvate + NADH
-
-
-
r
alpha-ketoglutarate + NADH
2-hydroxyglutaric acid + NAD+
-
-
both D- and L-isomer serve as substrate for the reverse reaction, but L-isomer is a poor substrate and probably due to contamination
r
phosphonooxypyruvate + NADH + H+
?
-
catalytic His280, active site, regulatory, and substrate binding site structures, overview
-
-
?
phosphonooxypyruvate + NADH + H+
?
-
very slow NADH binding in absence of substrate, productive NADH binding, that would support catalytic turnover, is dependent on the presence of substrate, active site structure with the catalytic His280, modelling of ligand-free and substrate-bound active site, overview
-
-
?
phosphonooxypyruvate + NADH + H+
?
-
catalytic His280, active site, regulatory, and substrate binding site structures, overview
-
-
?
additional information
?
-
no activity with 2-oxoglutarate
-
-
-
additional information
?
-
HOXA10 is required for enzyme regulation in the endometrium
-
-
-
additional information
?
-
-
enzyme is involved in de novo L-serine biosynthesis, in the peripheral nervous system and non-neuronal tissues of mice
-
-
-
additional information
?
-
-
HOXA10 is required for enzyme regulation in the endometrium
-
-
-
additional information
?
-
-
no activity with alpha-ketoglutarate
-
-
-
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NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
3-phospho-D-glycerate + NAD+
3-phosphohydroxypyruvate + NADH + H+
O49485
-
-
-
?
3-phospho-D-glycerate + NAD+
3-phosphohydroxypyruvate + NADH
-
first step in biosynthesis of L-serine, pathway regulation, overview
-
-
?
3-phospho-D-glycerate + NAD+
3-phosphohydroxypyruvate + NADH
P0A9T0
first step in biosynthesis of L-serine, the enzyme contains an ACT domain, which is involved in the allosteric regulation mechanism, residue W139 is involved
-
-
?
3-phospho-D-glycerate + NAD+
3-phosphohydroxypyruvate + NADH
-
first step in biosynthesis of L-serine, the enzyme contains an ACT domain, which is involved in the allosteric regulation mechanism, residue W139 is involved
-
-
?
3-phospho-D-glycerate + NAD+
3-phosphohydroxypyruvate + NADH
-
first step in biosynthesis of L-serine, Vmax regulation through domain and subunit changes, overview
-
-
?
3-phospho-D-glycerate + NAD+
3-phosphonooxypyruvate + NADH + H+
U3RH61
-
-
-
?
3-phospho-D-glycerate + NAD+
3-phosphonooxypyruvate + NADH + H+
U3RH61
-
-
-
?
3-phospho-D-glycerate + NAD+
3-phosphonooxypyruvate + NADH + H+
O04130, O49485, Q9LT69
-
-
-
?
3-phospho-D-glycerate + NAD+
3-phosphonooxypyruvate + NADH + H+
Q9LT69
-
-
-
?
3-phospho-D-glycerate + NAD+
3-phosphonooxypyruvate + NADH + H+
-
-
-
-
?
3-phospho-D-glycerate + NAD+
3-phosphonooxypyruvate + NADH + H+
F2X354
-
-
-
?
3-phospho-D-glycerate + NAD+
3-phosphonooxypyruvate + NADH + H+
F2X354
-
-
-
?
3-phospho-D-glycerate + NAD+
3-phosphonooxypyruvate + NADH + H+
-
-
-
-
?
3-phospho-D-glycerate + NAD+
3-phosphonooxypyruvate + NADH + H+
-
-
-
-
?
3-phospho-D-glycerate + NAD+
3-phosphonooxypyruvate + NADH + H+
-
-
-
-
?
3-phospho-D-glycerate + NAD+
3-phosphonooxypyruvate + NADH + H+
-
-
-
-
?
3-phospho-D-glycerate + NAD+
3-phosphonooxypyruvate + NADH + H+
-
-
-
-
?
3-phospho-D-glycerate + NAD+
3-phosphonooxypyruvate + NADH + H+
-
-
-
-
?
3-phospho-D-glycerate + NAD+
3-phosphonooxypyruvate + NADH + H+
Q9Z564
-
-
-
?
3-phosphoglycerate + NAD+
3-phosphohydroxypyruvate + NADH
-
first enzyme in metabolic sequence of synthesis of serine from 3-phosphoglycerate
-
-
r
3-phosphoglycerate + NAD+
3-phosphohydroxypyruvate + NADH
-
allosteric inhibition by L-serine, L-serine regulates the pathway of serine biosynthesis by end product inhibition interacting with His344, Asn346 and Asn364, 1 serine binds per subunit
-
r
3-phosphoglycerate + NAD+
3-phosphohydroxypyruvate + NADH
-
allosteric inhibition by L-serine, L-serine regulates the pathway of serine biosynthesis by end product inhibition interacting with His344, Asn346 and Asn364, 1 serine binds per subunit
-
-
r
3-phosphoglycerate + NAD+
3-phosphohydroxypyruvate + NADH
-
first enzyme in metabolic sequence of synthesis of serine from 3-phosphoglycerate
-
-
r
3-phosphoglycerate + NAD+
3-phosphohydroxypyruvate + NADH
-
first enzyme in metabolic sequence of synthesis of serine from 3-phosphoglycerate
-
-
-
3-phosphoglycerate + NAD+
3-phosphohydroxypyruvate + NADH
-
first enzyme in metabolic sequence of synthesis of serine from 3-phosphoglycerate
-
-
r
3-phosphoglycerate + NAD+
3-phosphohydroxypyruvate + NADH
-
first enzyme in metabolic sequence of synthesis of serine from 3-phosphoglycerate
-
-
r
3-phosphoglycerate + NAD+
3-phosphohydroxypyruvate + NADH
-
the enzyme catalyzes the first reaction of serine and glycine biosynthesis. SER3 and SER33 encode phosphoglycerate dehydrogenases. The requirement for the SER-dependent phosphoglycerate pathway is conditional since the glyoxylate route of serine/glycine biosynthesis is glucose repressed. Ser33p is likely to be the main isoenzyme of the phosphoglycerate pathway during growth on glucose
-
-
?
additional information
?
-
O43175
HOXA10 is required for enzyme regulation in the endometrium
-
-
-
additional information
?
-
-
enzyme is involved in de novo L-serine biosynthesis, in the peripheral nervous system and non-neuronal tissues of mice
-
-
-
additional information
?
-
-
HOXA10 is required for enzyme regulation in the endometrium
-
-
-
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
NAD+
-
-
NADH
-
binding of 4 NADH per tetrameric enzyme, negative cooperativity in NADH binding
NADH
-
cofactor binding site structure and binding mechanism, overview
NADH
-
-
NADP+
-
NADP utilization is not observed in the forward reaction even in the presence of high concentrations of 10 mM NADP and 10 mM 3-phospho-D-glycerate
NADPH
-
25% of activity with NADH, can not replace NADH in standard assay concentration
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Cl-
MgCl2
potassium phosphate
-
optimal activity at 75-100 mM, only about 30% of the optimal activity in 5 mM potassium phosphate
MgCl2
-
no effect on enzyme activity, but hinders enzyme inhibition by ATP and ADP
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INHIBITORS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
(NH4)2SO4
-
inhibitory effect on NADPH-dependent 3-phosphohydroxypyruvate reduction
2-methyl-N-(2-[[(2E)-2-[2-[(2-nitrobenzyl)oxy]benzylidene]hydrazinyl]carbonyl]phenyl)benzamide
-
-
4-(5-[(Z)-[1-(3,4-dimethylphenyl)-3,5-dioxopyrazolidin-4-ylidene]methyl]furan-2-yl)-N-(1,3-thiazol-2-yl)benzenesulfonamide
-
-
4-[(3,5-dioxo-1,2,6-thiadiazinan-4-ylidene)methyl]phenyl 2,3-diphenylquinoxaline-6-carboxylate
-
-
AMP
-
weak inhibitory effect on 3-phospho-D-glycerate oxidation, remaining activity: 75%
K2HPO4
-
inhibitory effect on NADPH-dependent 3-phosphohydroxypyruvate reduction. It appears that the phosphate ion PO43- exerts its inhibitory effect by binding to the free enzyme and NADPH-enzyme complex
ZnCl2
-
inhibitory effect on 3-phosphohydroxypyruvate reduction, remaining activity: 29%
3-phosphohydroxypyruvate
-
uncompetitive substrate inhibition at high substrate concentration
3-phosphohydroxypyruvate
-
product inhibition of 3-phospho-D-glycerate oxidation, variable substrate: 3-phospho-D-glycerate, inhibition pattern: competitive; product inhibition of 3-phospho-D-glycerate oxidation, variable substrate: NAD, inhibition pattern: non-competitive
ADP
-
weak inhibitory effect on 3-phospho-D-glycerate oxidation, remaining activity: 86%
ATP
-
weak inhibitory effect on 3-phospho-D-glycerate oxidation, remaining activity: 85%
L-Ser
-
mutant enzyme SerADELTA197, a C-terminally truncated mutant enzyme, shows inhibition
L-Ser
-
binding of the inhibitor to the apoenzyme displays positive cooperativity in the binding of the first two serine molecules and negative cooperativity in the binding of the last two serine molecules. At least two NADH-induced conformational forms of the enzyme bind the inhibitor in the physiological range. Successive binding of NADH to the enzyme results in an increase in the affinity for the first inhibitor ligand bound and a lessening of both the positive and negative cooperativity of inhibitor binding
L-serine
-
inhibition of enzyme from E. coli, Salmonella typhimurium and Haemophilus influenzae, not of mammalian enzyme, inhibition in both reaction directions
L-serine
-
allosteric inhibition, regulates the pathway of serine biosynthesis by end product inhibition interacting with His344, Asn346 and Asn364
L-serine
-
50% inhibition at 0.008 mM L-serine; allosteric inhibition, regulates the pathway of serine biosynthesis by end product inhibition interacting with His344, Asn346 and Asn364
L-serine
-
sigmoidal binding curve with mutant G294V/G336V, mutants with decreased sensitivity to serine
L-serine
-
feedback regulation, positive and negative cooperativity in absence of NADH, positive in presence of NADH, overview
L-serine
-
the enzyme contains an ACT regulatory domain which binds L-serine for feedback regulation, binding site lies around residues H344-N364
L-serine
-
physiological inhibitor, exerts its effect on at least two steps in the kinetic mechanism. There is a small but significant effect on the dissociation constant of NADH, increasing the Kd to 5 and 23 microM from 0.6 and 9 microM, respectively, for the two sets of sites in the enzyme. After the second substrate is added, serine reduces the amplitude of the signal without a significant effect on the observed rate constants for binding. The serine concentration that reduces the amplitude by 50% is equal to the K0.5 for serine inhibition. Serine binding eliminates a conformational change subsequent to substrate binding by formation of a dead-end quaternary complex consisting of enzyme, coenzyme, substrate, and effector. The rate data conform to a model in which serine can bind to two forms of the enzyme with different affinities
L-serine
-
I0.5: 0.03 mM. In presence of KCl, the binding and the inhibition of L-serine, are cooperative and in the absence of KCl they are not
L-serine
-
two serine molecules bound to the regulatory domain, anion- and serine-binding sites between two adjacent subunits
NADH
-
product inhibition of 3-phospho-D-glycerate oxidation, variable substrate: 3-phospho-D-glycerate, inhibition pattern: non-competitive; product inhibition of 3-phospho-D-glycerate oxidation, variable substrate: NAD, inhibition pattern: competitive
additional information
-
Ser, Tyr, Val, Gly, Trp, O-acetyl-L-Ser, and Cys have no effect on enzyme activity in both directions
-
additional information
-
the enzyme contains an ACT domain, which is involved in the allosteric regulation mechanism
-
additional information
substrate inhibition at concentrations above 0.1 mM
-
additional information
-
mechanism of substrate inhibition, linked to this pH-dependent depression in activity, overview
-
additional information
-
unlike the Escherichia coli PGDH no inhibition by L-serine
-
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
(NH4)2SO4
-
enhancing effect on NAD-dependent 3-phospho-D-glycerate oxidation and 3-phosphohydroxypyruvate reduction but inhibitory effect on NADPH-dependent 3-phosphohydroxypyruvate reduction
K2HPO4
-
enhancing effect on NAD-dependent 3-phospho-D-glycerate oxidation and 3-phosphohydroxypyruvate reduction but inhibitory effect on NADPH-dependent 3-phosphohydroxypyruvate reduction
NaCl
-
PGDH activity increase about 1.5-2.3fold upon the increase of salinity from 0.5 to 2.5 M NaCl
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.003
3-phospho-D-glycerate
-
in 50 mM MOPS buffer, pH 7.0, temperature not specified in the publication
0.004
3-phospho-D-glycerate
-
in 50 mM MOPS buffer, pH 7.0, temperature not specified in the publication
0.008
3-phospho-D-glycerate
-
in 50 mM MOPS buffer, pH 7.0, temperature not specified in the publication
0.014
3-phospho-D-glycerate
in 50 mM MOPS buffer, pH 7.0, temperature not specified in the publication
0.015
3-phospho-D-glycerate
-
in 50 mM MOPS buffer, pH 7.0, temperature not specified in the publication
0.025
3-phospho-D-glycerate
-
in 50 mM MOPS buffer, pH 7.0, temperature not specified in the publication
0.031
3-phospho-D-glycerate
-
in 200 mM KPO4 buffer, pH 7.0, temperature not specified in the publication
0.033
3-phospho-D-glycerate
-
value for 3-phospho-D-glycerate oxidation using NAD+ as a cofactor
0.041
3-phospho-D-glycerate
-
in 200 mM KPO4 buffer, pH 7.0, temperature not specified in the publication
0.049
3-phospho-D-glycerate
-
in 50 mM MOPS buffer, pH 7.0, temperature not specified in the publication
0.065
3-phospho-D-glycerate
-
in 200 mM KPO4 buffer, pH 7.0, temperature not specified in the publication
0.127
3-phospho-D-glycerate
-
in 200 mM KPO4 buffer, pH 7.0, temperature not specified in the publication
0.153
3-phospho-D-glycerate
-
in 200 mM KPO4 buffer, pH 7.0, temperature not specified in the publication
0.162
3-phospho-D-glycerate
in 200 mM KPO4 buffer, pH 7.0, temperature not specified in the publication
0.292
3-phospho-D-glycerate
-
in 200 mM KPO4 buffer, pH 7.0, temperature not specified in the publication
0.899
3-phospho-D-glycerate
isoform PGDH2, at pH 8.1 and 37°C
1.006
3-phospho-D-glycerate
isoform PGDH3, at pH 8.1 and 37°C
1.308
3-phospho-D-glycerate
isoform PGDH1, at pH 8.1 and 37°C
1.926
3-phospho-D-glycerate
isoform PGDH2, at pH 7.2 and 37°C
2.11
3-phospho-D-glycerate
isoform PGDH1, at pH 7.2 and 37°C
2.559
3-phospho-D-glycerate
isoform PGDH3, at pH 7.2 and 37°C
0.0096
3-phosphohydroxypyruvate
-
value for 3-phosphohydroxypyruvate reduction using NADH as a cofactor
0.015 - 0.02
3-phosphohydroxypyruvate
pH 7.1, 25°C, wild-type enzyme from fibroblasts
0.0216
3-phosphohydroxypyruvate
pH 7.1, 25°C, recombinant FLAG-tagged wild-type enzyme from HEK-293 cells
0.12
3-phosphohydroxypyruvate
-
value for 3-phosphohydroxypyruvate reduction using NADPH as a cofactor
0.0013
NADH
-
value for 3-phosphohydroxypyruvate reduction using NADH as a cofactor
0.004
NADH
-
with 2-oxoglutarate as cosubstrate, at pH 7.6 and 37°C; with oxaloacetate as cosubstrate, at pH 7.6 and 37°C
0.02
NADPH
-
value for 3-phosphohydroxypyruvate reduction using NADPH as a cofactor
additional information
additional information
-
stopped flow and steady-state kinetic analysis
-
additional information
additional information
-
kinetic analysis of wild-type and mutant enzymes
-
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
1.741
3-phospho-D-glycerate
isoform PGDH1, at pH 8.1 and 37°C
41
3-phospho-D-glycerate
-
in 50 mM MOPS buffer, pH 7.0, temperature not specified in the publication
97
3-phospho-D-glycerate
isoform PGDH3, at pH 7.2 and 37°C
115.1
3-phospho-D-glycerate
isoform PGDH1, at pH 7.2 and 37°C
119.7
3-phospho-D-glycerate
isoform PGDH2, at pH 7.2 and 37°C
142.4
3-phospho-D-glycerate
isoform PGDH3, at pH 8.1 and 37°C
147.4
3-phospho-D-glycerate
isoform PGDH2, at pH 8.1 and 37°C
194
3-phospho-D-glycerate
in 50 mM MOPS buffer, pH 7.0, temperature not specified in the publication
198
3-phospho-D-glycerate
-
in 50 mM MOPS buffer, pH 7.0, temperature not specified in the publication
311
3-phospho-D-glycerate
-
in 200 mM KPO4 buffer, pH 7.0, temperature not specified in the publication
341
3-phospho-D-glycerate
-
in 200 mM KPO4 buffer, pH 7.0, temperature not specified in the publication
350
3-phospho-D-glycerate
-
in 200 mM KPO4 buffer, pH 7.0, temperature not specified in the publication
464
3-phospho-D-glycerate
-
in 50 mM MOPS buffer, pH 7.0, temperature not specified in the publication
567
3-phospho-D-glycerate
-
in 200 mM KPO4 buffer, pH 7.0, temperature not specified in the publication
576
3-phospho-D-glycerate
in 200 mM KPO4 buffer, pH 7.0, temperature not specified in the publication
608
3-phospho-D-glycerate
-
in 50 mM MOPS buffer, pH 7.0, temperature not specified in the publication
1515
3-phospho-D-glycerate
-
in 50 mM MOPS buffer, pH 7.0, temperature not specified in the publication
1575
3-phospho-D-glycerate
-
in 50 mM MOPS buffer, pH 7.0, temperature not specified in the publication
2425
3-phospho-D-glycerate
-
in 200 mM KPO4 buffer, pH 7.0, temperature not specified in the publication
3850
3-phospho-D-glycerate
-
in 200 mM KPO4 buffer, pH 7.0, temperature not specified in the publication
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
37.91
3-phospho-D-glycerate
isoform PGDH3, at pH 7.2 and 37°C
54.57
3-phospho-D-glycerate
isoform PGDH2, at pH 8.1 and 37°C
62.16
3-phospho-D-glycerate
isoform PGDH1, at pH 7.2 and 37°C
133.1
3-phospho-D-glycerate
isoform PGDH1, at pH 8.1 and 37°C
141.6
3-phospho-D-glycerate
isoform PGDH2, at pH 7.2 and 37°C
154
3-phospho-D-glycerate
isoform PGDH3, at pH 8.1 and 37°C
1400
3-phospho-D-glycerate
in 50 mM MOPS buffer, pH 7.0, temperature not specified in the publication
2400
3-phospho-D-glycerate
-
in 200 mM KPO4 buffer, pH 7.0, temperature not specified in the publication
3200
3-phospho-D-glycerate
-
in 50 mM MOPS buffer, pH 7.0, temperature not specified in the publication
3600
3-phospho-D-glycerate
in 200 mM KPO4 buffer, pH 7.0, temperature not specified in the publication
5000
3-phospho-D-glycerate
-
in 50 mM MOPS buffer, pH 7.0, temperature not specified in the publication
5300
3-phospho-D-glycerate
-
in 200 mM KPO4 buffer, pH 7.0, temperature not specified in the publication
6100
3-phospho-D-glycerate
-
in 50 mM MOPS buffer, pH 7.0, temperature not specified in the publication
7600
3-phospho-D-glycerate
-
in 50 mM MOPS buffer, pH 7.0, temperature not specified in the publication
8300
3-phospho-D-glycerate
-
in 200 mM KPO4 buffer, pH 7.0, temperature not specified in the publication
13200
3-phospho-D-glycerate
-
in 200 mM KPO4 buffer, pH 7.0, temperature not specified in the publication
14000
3-phospho-D-glycerate
-
in 50 mM MOPS buffer, pH 7.0, temperature not specified in the publication
15800
3-phospho-D-glycerate
-
in 200 mM KPO4 buffer, pH 7.0, temperature not specified in the publication
18000
3-phospho-D-glycerate
-
in 200 mM KPO4 buffer, pH 7.0, temperature not specified in the publication
31000
3-phospho-D-glycerate
-
in 50 mM MOPS buffer, pH 7.0, temperature not specified in the publication
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Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.016
L-serine
-
in 50 mM MOPS buffer, pH 7.0, temperature not specified in the publication
0.038
L-serine
-
in 50 mM MOPS buffer, pH 7.0, temperature not specified in the publication
0.057
L-serine
-
in 200 mM KPO4 buffer, pH 7.0, temperature not specified in the publication
0.063
L-serine
-
in 50 mM MOPS buffer, pH 7.0, temperature not specified in the publication
0.066
L-serine
-
in 50 mM MOPS buffer, pH 7.0, temperature not specified in the publication
0.082
L-serine
-
in 50 mM MOPS buffer, pH 7.0, temperature not specified in the publication
0.115
L-serine
in 50 mM MOPS buffer, pH 7.0, temperature not specified in the publication
0.138
L-serine
-
in 50 mM MOPS buffer, pH 7.0, temperature not specified in the publication
0.255
L-serine
-
in 200 mM KPO4 buffer, pH 7.0, temperature not specified in the publication
0.581
L-serine
in 200 mM KPO4 buffer, pH 7.0, temperature not specified in the publication
0.628
L-serine
-
in 200 mM KPO4 buffer, pH 7.0, temperature not specified in the publication
1.065
L-serine
-
in 200 mM KPO4 buffer, pH 7.0, temperature not specified in the publication
4.539
L-serine
-
in 200 mM KPO4 buffer, pH 7.0, temperature not specified in the publication
5.898
L-serine
-
in 200 mM KPO4 buffer, pH 7.0, temperature not specified in the publication
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IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.131
2-methyl-N-(2-[[(2E)-2-[2-[(2-nitrobenzyl)oxy]benzylidene]hydrazinyl]carbonyl]phenyl)benzamide
Escherichia coli
-
at pH 7.5 and 25°C
0.058
4-(5-[(Z)-[1-(3,4-dimethylphenyl)-3,5-dioxopyrazolidin-4-ylidene]methyl]furan-2-yl)-N-(1,3-thiazol-2-yl)benzenesulfonamide
Escherichia coli
-
at pH 7.5 and 25°C
0.0348
4-[(3,5-dioxo-1,2,6-thiadiazinan-4-ylidene)methyl]phenyl 2,3-diphenylquinoxaline-6-carboxylate
Escherichia coli
-
at pH 7.5 and 25°C
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
-
during purification an unexpected decline in enzyme activity is observed if the enzyme is stored in plastic tubes, but not in glass ones
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
5.2
-
enzyme possess a dual pH optimum. A significant decrease in the Ki for substrate inhibition at pH values corresponding to the valley between these optima is responsible for this phenomenon
7.5
8
-
enzyme possess a dual pH optimum. A significant decrease in the Ki for substrate inhibition at pH values corresponding to the valley between these optima is responsible for this phenomenon
8.5
9.5
8.5
-
3-phosphohydroxypyruvate and alpha-ketoglutarate reduction, enzyme and substrate not stable, product inhibition
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
5.2 - 5.7
-
at approximately pH 5.7 the activity starts increasing again and reaches a new optimum at approximately pH 5.2 before decreasing once again
7.5 - 9.5
-
activity is relatively constant between pH 7.5-9.5. Above pH 9.5 and below pH 7.5 activity falls off rapidly
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
25
45 - 50
-
reduction, but enzyme is thermally unstable, therefore assay is performed at 37°C
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pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
-
satellite cell of the dorsal root ganglia and intestinal nerve plexuses
-
located in the rostral migratory stream, high enzyme expression level
-
satellite cell of the dorsal root ganglia and intestinal nerve plexuses
additional information
-
enzyme expression in the subventricular neural progenitor cells, but not in differentiated neurons. The subventricular neural progenitor cells also show a decline in Phgdh expression in type B and C cells in the aged brain
-
very high expression of Phgdh. It is shown that Phgdh is distributed highly in the renal papilla and inner layer of the outer zone and moderately in the cortex, whereas it is almost negative in the outer layer of the outer zone. This heterogeneous distribution is due to selective expression in distinct tubular segments, i.e., the Bowman's capsule, proximal tubule, and thin limbs of the Henle's loop
additional information
-
overview about distribution in animal tissues
additional information
-
tissue expression analysis, no expression in absent in committed neuronal precursors, type A cells, derived from type C cells
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
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PDB
SCOP
CATH
ORGANISM
UNIPROT
Lactobacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)
Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
35000
44000
-
4 * 44000, SDS-PAGE, each subunit is divided into 3 separate domains
55000
57000
57200
165000
207300
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SUBUNITS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
homodimer
homotetramer
tetramer
additional information
?
x * 47700, calculated from amino acid sequence; x * 50000, SDS-PAGE
?
-
x * 47700, calculated from amino acid sequence; x * 50000, SDS-PAGE
-
tetramer
-
4 * 44000, SDS-PAGE, each subunit is divided into 3 separate domains
tetramer
-
4 * 40000-43000, SDS-PAGE, sedimentation equilibrium studies in guanidine hydrochloride
tetramer
-
although the tetramer is composed of identical subunits, significant asymmetry is seen in the tertiary structure of the subunits
tetramer
-
intervening domains are the two four-stranded beta-sheet structures located next to the substrate binding domains and below the regulatory domains, structure model, overview
tetramer
-
intervening domains are the two four-stranded beta-sheet structures located next to the substrate binding domains and below the regulatory domains, structure model, overview
-
additional information
-
subunit structure with substrate binding domain, coenzyme binding domain and regulatory domain, active sites
additional information
-
the enzyme contains an ACT domain, which is involved in the allosteric regulation mechanism
additional information
-
the enzyme contains an ACT regulatory domain, enzyme domain structure
additional information
-
quarternary structure of the active enzyme, conformational changes through domain-domain reorientation, stereochemical model, overview
additional information
each subunit consists of three distinct domains: a cofactor or nucleotide binding domain, a substrate binding domain, and a regulatory domain. Structural molecular modeling of mutant enzymes, overview
additional information
-
the apo-enzyme shows an extreme asymmetry in the orientation of the domains from one subunit to another. The poly glycine stretch in the loop that contains the locus for the 160° rotation leads to subunit asymmetry, structure modelling, overview
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Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
in complexes with 3-phospho-D-glycerate and NAD+, hanging drop vapor diffusion method, using 20% (w/v) poly(ethylene glycol) 3350 in 100 mM Tris pH 7.0-8.5, 350 mM sodium formate and 5% (v/v) glycerol
-
purified recombinant selenomethionine-labeled enzyme, in presence of 2 mM NAD+ and 5 mM 2-ketoglutarate, euqilibration against precipitation solution containing 1.18-1.25 M ammonium sulfate and 100 mM potassium phosphate, pH 6.4, 18°C, 1-2 weeks, X-ray diffraction structure determination and analysis at 2.24 A resolution
-
D-3-phosphoglycerate dehydrogenase with bound effector L-serine or with bound substrate hydroxypyruvic acid phosphate, PGDH at 10 mg/ml is mixed with 5 mM hydroxypyruvic acid phosphate and 5 mM NAD+ analogue 3-acetyl pyridine adenine dinucleotide, or with 5 mM NADH and 5 mM L-serine, from 1 M Na K tartrate, 0.1 M MES, pH 6.5, cryoprotection in 25% propylene glycol, X-ray diffraction structure determination and analysis at resolutions of 2.7 A and 2.4 A, respectively
-
vapor diffusion in hanging drops, structure refined to 2.3 A resolution using SeMet multiwavelength anamolous dispersion
-
crystal structures is determined using X-ray diffraction to resolution of 1.95 A, crystals are grown at room temperature by sitting-drop method
crystal structure is determined using X-ray diffraction to resolution of 1.77 A, crystals are grown at room temperature by sitting-drop method
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pH STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
3.5 - 11.5
-
enzyme is stable over a wide range of pHs. No decrease in activity after 20 min incubation at 50°C
684698
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
50 - 80
-
enzyme is highly thermostable, retaining more than 90% of its activity after incubation for 1 h at 80°C
additional information
-
activity remains stable after incubation at 40°C for 7 min, but decreases to 50% when the enzyme is incubated at 50°C for 7 min
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GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
at low ionic strength the enzyme irreversibly loses activity with time. In 20 mM phosphate buffer, pH 7.5, most of the activity is lost within 24 h. The activity loss is prevented if the ionic strength is kept above approximately 100 mM salt
-
dilution inactivates
dithiothreitol increases stability
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OXIDATION STABILITY
ORGANISM
UNIPROT
LITERATURE
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-80°C, 50% glycerol, purified recombinant enzyme remains active after 1 month of storage
-
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
Ni-NTA column chromatography; Ni-NTA column chromatography; Ni-NTA column chromatography
nickel-Sepharose column chromatography and Superdex 200 gel filtration
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