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Information on EC 1.1.1.95 - phosphoglycerate dehydrogenase and Organism(s) Entamoeba histolytica and UniProt Accession Q76KF5

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IUBMB Comments
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 .
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Entamoeba histolytica
UNIPROT: Q76KF5
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The taxonomic range for the selected organisms is: Entamoeba histolytica
The enzyme appears in selected viruses and cellular organisms
Synonyms
phgdh, phosphoglycerate dehydrogenase, 3-phosphoglycerate dehydrogenase, d-3-phosphoglycerate dehydrogenase, 3-pgdh, 3pgdh, pgdh3, pgdh1, ehpgdh, d-phosphoglycerate dehydrogenase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D-phosphoglycerate dehydrogenase
-
type III 3-phosphoglycerate dehydrogenase
-
3-PGDH
-
-
-
-
3-phosphoglycerate dehydrogenase
-
-
-
-
3-phosphoglyceric acid dehydrogenase
-
-
-
-
A10
-
-
-
-
alpha-phosphoglycerate dehydrogenase
-
-
-
-
D-3-phosphoglycerate dehydrogenase
-
-
-
-
D-3-phosphoglycerate:NAD oxidoreductase
-
-
-
-
D-phosphoglycerate dehydrogenase
-
-
dehydrogenase, phosphoglycerate
-
-
-
-
glycerate 3-phosphate dehydrogenase
-
-
-
-
glycerate-1,3-phosphate dehydrogenase
-
-
-
-
phosphoglycerate oxidoreductase
-
-
-
-
phosphoglyceric acid dehydrogenase
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
redox reaction
-
-
-
-
oxidation
-
-
-
-
reduction
-
-
-
-
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
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
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
-
-
-
r
3-phospho-D-glycerate + NAD+
3-phosphonooxypyruvate + NADH + H+
show the reaction diagram
-
-
-
-
?
additional information
?
-
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
3-phospho-D-glycerate + NAD+
3-phosphonooxypyruvate + NADH + H+
show the reaction diagram
-
-
-
?
3-phospho-D-glycerate + NAD+
3-phosphonooxypyruvate + NADH + H+
show the reaction diagram
-
-
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
NADPH
less efficiently than NADH
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
KCl
optimal salt concentration is 350-400 mM
NaCl
optimal salt concentration is 350-400 mM
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
3-phosphohydroxypyruvate
substrate inhibition
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.396 - 0.6
3-phospho-D-glycerate
0.212
3-phosphoglycerate
pH 9.0
0.0867
NAD+
pH 9.0
0.0177
NADH
pH 6.5
0.141
NADPH
pH 6.5
0.015
phosphohydroxypyruvate
pH 6.5
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.13 - 16.28
3-phospho-D-glycerate
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.216 - 4.2
3-phospho-D-glycerate
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.004
mutant enzyme K263A, at pH 9.0 and 25°C
0.495
wild type enzyme, at pH 9.0 and 25°C
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6 - 6.5
reaction with 3-phosphohydroxypyruvate + NADH
9
reaction with 3-phosphoglycerate and NAD+
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.5 - 8
-
enzymatic activity decreases below pH 6.5
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.9
calculation from nucleotide sequence
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
Q76KF5_ENTHI
299
0
33469
TrEMBL
other Location (Reliability: 1)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
33500
2 * 33500, calculation from nucleotide sequence
70000 - 74000
gel filtration
35000
70000
-
homodimer, gel filtration, pH 7
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dimer
2 * 33500, calculation from nucleotide sequence
homodimer
x-ray crystallography
homodimer
monomer
-
1 * 35000 at pH 5.0
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
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
K263A
the mutant shows strongly reduced activity compared to the wild type enzyme
E108A
-
in contrast to wild-type mutant existed as monomer even at pH 7
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-80°C, 50% glycerol, purified recombinant enzyme remains active after 1 month of storage
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
nickel-Sepharose column chromatography and Superdex 200 gel filtration
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli BL21(DE3) cells
expression in Escherichia coli
expressed in Escherichia coli
-
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Ali, V.; Hashimoto, T.; Shigeta, Y.; Nozaki, T.
Molecular and biochemical characterization of D-phosphoglycerate dehydrogenase from Entamoeba histolytica. A unique enteric protozoan parasite that possesses both phosphorylated and nonphosphorylated serine metabolic pathways
Eur. J. Biochem.
271
2670-2681
2004
Entamoeba histolytica (Q76KF5), Entamoeba histolytica
Manually annotated by BRENDA team
Mishra, V.; Kumar, A.; Ali, V.; Nozaki, T.; Zhang, K.Y.; Bhakuni, V.
Glu-108 is essential for subunit assembly and dimer stability of D-phosphoglycerate dehydrogenase from Entamoeba histolytica
Mol. Biochem. Parasitol.
181
117-124
2012
Entamoeba histolytica
Manually annotated by BRENDA team
Singh, R.K.; Raj, I.; Pujari, R.; Gourinath, S.
Crystal structures and kinetics of Type III 3-phosphoglycerate dehydrogenase reveal catalysis by lysine
FEBS J.
281
5498-5512
2014
Entamoeba histolytica (Q76KF5), Entamoeba histolytica
Manually annotated by BRENDA team
Mishra, V.; Kumar, A.; Ali, V.; Zhang, K.Y.; Nozaki, T.
Characterization of pH-induced transitions of Entamoeba histolytica D-phosphoglycerate dehydrogenase
Int. J. Biol. Macromol.
79
284-289
2015
Entamoeba histolytica
Manually annotated by BRENDA team