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Information on EC 1.1.1.95 - phosphoglycerate dehydrogenase and Organism(s) Sulfurisphaera tokodaii and UniProt Accession Q972A9

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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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This record set is specific for:
Sulfurisphaera tokodaii
UNIPROT: Q972A9
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Word Map
The taxonomic range for the selected organisms is: Sulfurisphaera tokodaii
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
NAD-dependent D-3-phosphoglycerate dehydrogenase
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3-PGDH
-
-
-
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3-phosphoglycerate dehydrogenase
-
-
-
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3-phosphoglyceric acid dehydrogenase
-
-
-
-
A10
-
-
-
-
alpha-phosphoglycerate dehydrogenase
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-
-
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D-3-phosphoglycerate dehydrogenase
D-3-phosphoglycerate:NAD oxidoreductase
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-
-
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dehydrogenase, phosphoglycerate
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-
-
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glycerate 3-phosphate dehydrogenase
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-
-
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glycerate-1,3-phosphate dehydrogenase
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-
-
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phosphoglycerate oxidoreductase
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-
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phosphoglyceric acid dehydrogenase
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-
-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
redox reaction
-
-
-
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oxidation
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-
-
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reduction
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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].
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
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 + H+
show the reaction diagram
-
highest activity
-
-
r
3-phospho-D-glycerate + NADP+
3-phosphohydroxypyruvate + NADPH + H+
show the reaction diagram
-
-
-
-
r
DL-glyceraldehyde 3-phosphate + NAD+
?
show the reaction diagram
-
activity relative to 3-phospho-D-glycerate: 9%
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
NADP+
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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
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(NH4)2SO4
-
inhibitory effect on NADPH-dependent 3-phosphohydroxypyruvate reduction
3-phosphohydroxypyruvate
ADP
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weak inhibitory effect on 3-phospho-D-glycerate oxidation, remaining activity: 86%
AMP
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weak inhibitory effect on 3-phospho-D-glycerate oxidation, remaining activity: 75%
ATP
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weak inhibitory effect on 3-phospho-D-glycerate oxidation, remaining activity: 85%
K2HPO4
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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
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inhibitory effect on 3-phosphohydroxypyruvate reduction, remaining activity: 29%
additional information
-
unlike the Escherichia coli PGDH no inhibition by L-serine
-
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
K2HPO4
-
enhancing effect on NAD-dependent 3-phospho-D-glycerate oxidation and 3-phosphohydroxypyruvate reduction but inhibitory effect on NADPH-dependent 3-phosphohydroxypyruvate reduction
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.033
3-phospho-D-glycerate
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value for 3-phospho-D-glycerate oxidation using NAD+ as a cofactor
0.0096 - 0.12
3-phosphohydroxypyruvate
0.04
NAD+
-
value for 3-phospho-D-glycerate oxidation
0.0013
NADH
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value for 3-phosphohydroxypyruvate reduction using NADH as a cofactor
0.02
NADPH
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value for 3-phosphohydroxypyruvate reduction using NADPH as a cofactor
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2 - 10
K2HPO4
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
10
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3-phospho-D-glycerate oxidation
7.5
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3-phosphohydroxypyruvate reduction
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
53
-
optimum temperature for 3-phospho-D-glycerate oxidation
80
-
optimum for 3-phosphohydroxypyruvate reduction
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
35000
-
SDS-PAGE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
homodimer
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gel filtration
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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
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enzyme is stable over a wide range of pHs. No decrease in activity after 20 min incubation at 50°C
684698
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
50 - 80
-
enzyme is highly thermostable, retaining more than 90% of its activity after incubation for 1 h at 80°C
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
enzyme is highly thermostable
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in Escheriochia coli BL21
expressed in Escherichia coli
-
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Shimizu, Y.; Sakuraba, H.; Doi, K.; Ohshima, T.
Molecular and functional characterization of D-3-phosphoglycerate dehydrogenase in the serine biosynthetic pathway of the hyperthermophilic archaeon Sulfolobus tokodaii
Arch. Biochem. Biophys.
470
120-128
2008
Sulfurisphaera tokodaii
Manually annotated by BRENDA team
Kumar, S.M.; Pampa, K.J.; Manjula, M.; Hemantha Kumar, G.; Kunishima, N.; Lokanath, N.K.
Crystal structures of type IIIH NAD-dependent D-3-phosphoglycerate dehydrogenase from two thermophiles
Biochem. Biophys. Res. Commun.
451
126-130
2014
Pyrococcus horikoshii (O58256), Pyrococcus horikoshii, Sulfurisphaera tokodaii (Q972A9), Sulfurisphaera tokodaii, Pyrococcus horikoshii DSM 12428 (O58256)
Manually annotated by BRENDA team