Information on EC 1.1.1.95 - phosphoglycerate dehydrogenase

Word Map on EC 1.1.1.95
Please wait a moment until all data is loaded. This message will disappear when all data is loaded.
Specify your search results
Select one or more organisms in this record:
Show additional data
Do not include text mining results
Include (text mining) results (more...)
Include results (AMENDA + additional results, but less precise; more...)


The expected taxonomic range for this enzyme is: Eukaryota, Bacteria, Archaea

EC NUMBER
COMMENTARY hide
1.1.1.95
-
RECOMMENDED NAME
GeneOntology No.
phosphoglycerate dehydrogenase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
3-phospho-D-glycerate + NAD+ = 3-phosphonooxypyruvate + NADH + H+
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
oxidation
-
-
-
-
redox reaction
-
-
-
-
reduction
-
-
-
-
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Biosynthesis of antibiotics
-
-
Glycine, serine and threonine metabolism
-
-
L-serine biosynthesis
-
-
Metabolic pathways
-
-
Methane metabolism
-
-
Microbial metabolism in diverse environments
-
-
serine metabolism
-
-
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].
CAS REGISTRY NUMBER
COMMENTARY hide
9075-29-0
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
-
-
Manually annotated by BRENDA team
gene pgk
-
-
Manually annotated by BRENDA team
Frog
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
Nitrosolobus sp.
gene pgk, several strains, overview
-
-
Manually annotated by BRENDA team
gene pgk, several strains, overview
-
-
Manually annotated by BRENDA team
gene pgk or cbbK, strain ATCC 25196
SwissProt
Manually annotated by BRENDA team
gene pgk, several strains, overview
-
-
Manually annotated by BRENDA team
Nitrosovibrio sp.
gene pgk, several strains, overview
-
-
Manually annotated by BRENDA team
Pigeon
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
metabolism
physiological function
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
2-oxoglutarate + NADH + H+
2-hydroxyglutarate + NAD+
show the reaction diagram
-
-
-
-
?
2-oxoglutarate + NADH + H+
?
show the reaction diagram
2-oxoglutarate + NADH + H+
D-2-hydroxyglutarate + NAD+
show the reaction diagram
-
-
-
-
?
2-phospho-D-glycerate + NAD+
2-phosphohydroxypyruvate + NADH + H+
show the reaction diagram
-
activity relative to 3-phospho-D-glycerate: 47%
-
-
?
3-phospho-D-glycerate + NAD+
3-phosphohydroxypyruvate + NADH
show the reaction diagram
3-phospho-D-glycerate + NAD+
3-phosphohydroxypyruvate + NADH + H+
show the reaction diagram
3-phospho-D-glycerate + NAD+
3-phosphonooxypyruvate + NADH + H+
show the reaction diagram
3-phospho-D-glycerate + NADP+
3-phosphohydroxypyruvate + NADPH + H+
show the reaction diagram
3-phosphoglycerate + NAD+
3-phosphohydroxypyruvate + NADH
show the reaction diagram
3-phosphohydroxypyruvate + NAD+
?
show the reaction diagram
-
-
-
r
3-phosphohydroxypyruvate + NADH
3-phosphoglycerate + NAD+
show the reaction diagram
-
specific for
-
-
?
alpha-ketoglutarate + NADH
2-hydroxyglutaric acid + NAD+
show the reaction diagram
DL-glyceraldehyde 3-phosphate + NAD+
?
show the reaction diagram
-
activity relative to 3-phospho-D-glycerate: 9%
-
-
?
oxaloacetate + NADH + H+
malate + NAD+
show the reaction diagram
-
-
-
-
?
phosphonooxypyruvate + NADH + H+
?
show the reaction diagram
additional information
?
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
2-oxoglutarate + NADH + H+
D-2-hydroxyglutarate + NAD+
show the reaction diagram
-
-
-
-
?
3-phospho-D-glycerate + NAD+
3-phosphohydroxypyruvate + NADH
show the reaction diagram
3-phospho-D-glycerate + NAD+
3-phosphohydroxypyruvate + NADH + H+
show the reaction diagram
O49485
-
-
-
?
3-phospho-D-glycerate + NAD+
3-phosphonooxypyruvate + NADH + H+
show the reaction diagram
3-phosphoglycerate + NAD+
3-phosphohydroxypyruvate + NADH
show the reaction diagram
oxaloacetate + NADH + H+
malate + NAD+
show the reaction diagram
-
-
-
-
?
phosphonooxypyruvate + NADH + H+
?
show the reaction diagram
additional information
?
-
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
3-acetylpyridine-NAD+
3-acetylpyridine-NADH
deamino-NAD+
deamino-NADH
-
as effective as NADH
NADP+
NADPH
thio-NAD+
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
KCl
-
optimal salt concentration is 350-400 mM
NaCl
-
optimal salt concentration is 350-400 mM
potassium phosphate
-
optimal activity at 75-100 mM, only about 30% of the optimal activity in 5 mM potassium phosphate
SO42-
-
stimulates
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(NH4)2SO4
-
inhibitory effect on NADPH-dependent 3-phosphohydroxypyruvate reduction
(R)-2-amino-1-propanol
-
slightly
2-methyl-N-(2-[[(2E)-2-[2-[(2-nitrobenzyl)oxy]benzylidene]hydrazinyl]carbonyl]phenyl)benzamide
-
-
3-phosphoglycerate
3-phosphohydroxypyruvate
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
-
-
Ag+
-
inhibition can be overcome by addition of dithiothreitol
AMP
-
weak inhibitory effect on 3-phospho-D-glycerate oxidation, remaining activity: 75%
beta-Alanine
-
slightly
glycine
hydroxyglutarate
-
product inhibition of the alpha-ketoglutarate reduction
iodoacetate
-
-
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
L-alanine
L-allothreonine
-
-
L-homoserine
-
-
L-Ser
L-serine
L-threonine
-
-
Mercurials
-
inhibition can be overcome by addition of dithiothreitol
-
N-Butylmaleimide
-
-
N-ethylmaleimide
N-Heptylmaleimide
-
-
N-Pentylmaleimide
-
-
N-Phenylmaleimide
-
-
NAD+
-
product inhibition, competitive to NADH
p-chloromercuribenzoate
-
-
p-hydroxymercuribenzoate
-
-
pyridoxal 5'-phosphate
-
-
pyridoxamine 5'-phosphate
-
-
sulfhydryl reagents
-
-
ZnCl2
-
inhibitory effect on 3-phosphohydroxypyruvate reduction, remaining activity: 29%
additional information
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
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
HPO42-
-
-
K2HPO4
-
enhancing effect on NAD-dependent 3-phospho-D-glycerate oxidation and 3-phosphohydroxypyruvate reduction but inhibitory effect on NADPH-dependent 3-phosphohydroxypyruvate reduction
L-methionine
-
maximum activation at 10 mM
NaCl
-
PGDH activity increase about 1.5-2.3fold upon the increase of salinity from 0.5 to 2.5 M NaCl
SO42-
-
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
10.1
2-oxoglutarate
-
at pH 7.6 and 37C
0.00025 - 0.0054
3-acetylpyridine-NAD+
0.00016
3-acetylpyridine-NADH
-
25C
0.003 - 320
3-phospho-D-glycerate
0.212
3-phosphoglycerate
-
pH 9.0
0.00013 - 40.2
3-phosphohydroxypyruvate
0.038 - 0.088
alpha-ketoglutarate
0.05 - 1.35
D-3-phosphoglycerate
0.0078 - 0.551
NAD+
0.0005 - 12
NADH
0.02 - 0.15
NADPH
6.5
oxaloacetate
-
at pH 7.6 and 37C
0.015
phosphohydroxypyruvate
-
pH 6.5
additional information
additional information
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.078
2-oxoglutarate
Homo sapiens
-
at pH 7.6 and 37C
0.075 - 3850
3-phospho-D-glycerate
0.463 - 2461
3-phosphohydroxypyruvate
0.128 - 0.555
alpha-ketoglutarate
1.741 - 147.4
NAD+
603 - 2827
NADH
0.177
oxaloacetate
Homo sapiens
-
at pH 7.6 and 37C
additional information
additional information
Escherichia coli
-
-
-
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.216 - 31000
3-phospho-D-glycerate
201
176.1 - 780.1
NAD+
7
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.054 - 7.218
3-phosphohydroxypyruvate
2 - 10
K2HPO4
0.016 - 5.898
L-serine
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
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 25C
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 25C
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 25C
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.004
-
mutant enzyme K263A, at pH 9.0 and 25C
0.14
-
3-phosphoglycerate oxidation, recombinant protein
0.495
-
wild type enzyme, at pH 9.0 and 25C
8.7
-
3-phosphohydroxypyruvate reduction
9.7
-
alpha-ketoglutarate reduction
10.95
-
3-phosphohydroxypyruvate reduction, recombinant protein
21.3
-
-
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
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
5.5
-
NADH oxidation
6 - 6.5
-
reaction with 3-phosphohydroxypyruvate + NADH
6.1
-
NADH oxidation
7.1
assay at
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
9
-
reaction with 3-phosphoglycerate and NAD+
9.4
-
NAD+ reduction
10
-
3-phospho-D-glycerate oxidation
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5 - 7.8
-
about 50% of activity maximum at pH 5 and 7.8, NADH oxidation
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
5.5 - 8.5
-
Tris buffer and phosphate buffer
6 - 8.5
-
activity drops sharply above pH 8.5
6.5 - 8
-
enzymatic activity decreases below pH 6.5
7.5
-
3-phosphohydroxypyruvate reduction
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
8.5 - 10.3
-
about 50% of activity maximum at pH 8.5 and 10.3, NAD+ reduction
9
-
3-phospho-D-glycerate oxidation
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
45 - 50
-
reduction, but enzyme is thermally unstable, therefore assay is performed at 37C
50
-
assay at
53
-
optimum temperature for 3-phospho-D-glycerate oxidation
80
-
optimum for 3-phosphohydroxypyruvate reduction
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.9
-
calculation from nucleotide sequence
7.6
calculated from amino acid sequence
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
-
stellate cells
Manually annotated by BRENDA team
-
sustentacular cell
Manually annotated by BRENDA team
high expression levels in the proliferative phase
Manually annotated by BRENDA team
-
etiolated
Manually annotated by BRENDA team
skin-derived
Manually annotated by BRENDA team
-
satellite cell of the dorsal root ganglia and intestinal nerve plexuses
Manually annotated by BRENDA team
-
located in the rostral migratory stream, high enzyme expression level
Manually annotated by BRENDA team
-
epithelium
Manually annotated by BRENDA team
-
satellite cell of the dorsal root ganglia and intestinal nerve plexuses
Manually annotated by BRENDA team
-
primary culture
Manually annotated by BRENDA team
-
-
Manually annotated by BRENDA team
-
of the dorsal root ganglia and intestinal nerve plexuses
Manually annotated by BRENDA team
additional information
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
-
-
-
Manually annotated by BRENDA team
PDB
SCOP
CATH
ORGANISM
UNIPROT
Brucella abortus (strain 2308)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
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)
Ralstonia solanacearum (strain GMI1000)
Sulfolobus tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)
Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
33500
-
2 * 33500, calculation from nucleotide sequence
44000
-
4 * 44000, SDS-PAGE, each subunit is divided into 3 separate domains
55000
-
x * 55000, SDS-PAGE
56410
-
deduced from cDNA
56800
4 * 56800
60000
-
4 * 60000, SDS-PAGE
66453
-
x * 66453 and 90000, DNA sequence analysis and SDS-PAGE
70000 - 74000
-
gel filtration
70000
-
homodimer, gel filtration, pH 7
163000
-
sedimentation equilibrium analysis
165000
166000
-
gel filtration
207300
247000
-
HPLC gel filtration
250000
-
gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
homodimer
homotetramer
monomer
-
1 * 35000 at pH 5.0
tetramer
additional information
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, 18C, 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
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
3.5 - 11.5
-
enzyme is stable over a wide range of pHs. No decrease in activity after 20 min incubation at 50C
684698
5.5 - 7.5
-
stable
287525
8.5 - 9.5
-
unstable
287525
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
45
-
3 min, 40% loss of reductase activity
50 - 80
-
enzyme is highly thermostable, retaining more than 90% of its activity after incubation for 1 h at 80C
additional information
-
activity remains stable after incubation at 40C for 7 min, but decreases to 50% when the enzyme is incubated at 50C for 7 min
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
enzyme is highly thermostable
-
inorganic ions, i.e. Cl-, SO42-, HPO42-, essential for stability
-
OXIDATION STABILITY
ORGANISM
UNIPROT
LITERATURE
purified protein is extremly susceptible to oxidation at alkaline pH
-
287544
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-15C, stable for several weeks
-
-75C, 15% glycerol, purified stable for months
-
-80C, 20 mM sodium phosphate buffer, pH 7.2
-
-80C, 50% glycerol, purified recombinant enzyme remains active after 1 month of storage
-
2C, 40% loss of activity, 7 days
-
4C, purified stable for weeks
-
5C, 60% loss of activity, 24 h
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
diverse mutants expressed in Escherichia coli
-
Ni-NTA column chromatography and gel filtration
-
Ni-NTA column chromatography; Ni-NTA column chromatography; Ni-NTA column chromatography
nickel-Sepharose column chromatography and Superdex 200 gel filtration
-
partial
-
PGDH is expressed in Escherichia coli and purified using 5'-AMP-Sepharose affinity chromatography
-
recombinant selenomethionine-labeled enzyme from strain B834
-
recombinant tagged wild-type and mutant enzymes
-
Talon cobalt based immobilized metal affinity column chromatography
using a butyl Sepharose 4 Fast Flow column and a Superdex 200 gel filtration column. During purification an unexpected decline in enzyme activity is observed if the enzyme is stored in plastic tubes, but not in glass ones
-
using ammonium sulphate fractionation and ion exchange chromatography
-
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
diverse mutants expressed in Escherichia coli
-
DNA and amino sequence analysis, phylogenetic analysis, sequence comparisons
-
DNA and amino sequence analysis, phylogenetic analysis, sequence comparisons, expression in Escherichia coli strain JM109
expressed in Escherichia coli
expressed in Escherichia coli and Arabidopsis thaliana
-
expressed in Escherichia coli BL-21 cells; expressed in Escherichia coli BL-21 cells; expressed in Escherichia coli BL-21 cells