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Information on EC 1.1.1.95 - phosphoglycerate dehydrogenase and Organism(s) Arabidopsis thaliana and UniProt Accession O49485

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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:
Arabidopsis thaliana
UNIPROT: O49485
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Word Map
The taxonomic range for the selected organisms is: Arabidopsis thaliana
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
3-phosphoglycerate dehydrogenase
-
PGDH1
3-PGDH
3-phosphoglycerate dehydrogenase
3-phosphoglyceric acid dehydrogenase
-
-
-
-
A10
-
-
-
-
alpha-phosphoglycerate dehydrogenase
-
-
-
-
D-3-phosphoglycerate dehydrogenase
-
-
-
-
D-3-phosphoglycerate:NAD oxidoreductase
-
-
-
-
dehydrogenase, phosphoglycerate
-
-
-
-
glycerate 3-phosphate dehydrogenase
-
-
-
-
glycerate-1,3-phosphate dehydrogenase
-
-
-
-
PGDH2
PGDH3
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
2-oxoglutarate + NADH + H+
D-2-hydroxyglutarate + NAD+
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 + NAD+
3-phosphooxypyruvate + NADH + H+
show the reaction diagram
3-phosphooxypyruvate + NADH + H+
3-phospho-D-glycerate + NAD+
show the reaction diagram
-
-
-
r
oxaloacetate + NADH + H+
?
show the reaction diagram
-
-
-
?
2-oxoglutarate + NADH + H+
D-2-hydroxyglutarate + NAD+
show the reaction diagram
-
-
-
?
3-phospho-D-glycerate + NAD+
3-phosphonooxypyruvate + NADH + H+
show the reaction diagram
3-phospho-D-glycerate + NAD+
3-phosphooxypyruvate + NADH + H+
show the reaction diagram
3-phosphoglycerate + NAD+
3-phosphohydroxypyruvate + NADH
show the reaction diagram
3-phosphooxypyruvate + NADH + H+
3-phospho-D-glycerate + NAD+
show the reaction diagram
-
-
-
r
oxaloacetate + NADH + H+
?
show the reaction diagram
-
-
-
?
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-phosphohydroxypyruvate + NADH + H+
show the reaction diagram
-
-
-
?
3-phospho-D-glycerate + NAD+
3-phosphonooxypyruvate + NADH + H+
show the reaction diagram
-
-
-
?
3-phospho-D-glycerate + NAD+
3-phosphooxypyruvate + NADH + H+
show the reaction diagram
3-phospho-D-glycerate + NAD+
3-phosphonooxypyruvate + NADH + H+
show the reaction diagram
3-phospho-D-glycerate + NAD+
3-phosphooxypyruvate + NADH + H+
show the reaction diagram
3-phosphoglycerate + NAD+
3-phosphohydroxypyruvate + NADH
show the reaction diagram
-
first enzyme in metabolic sequence of synthesis of serine from 3-phosphoglycerate
-
-
r
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
L-serine
L-serine
additional information
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
L-alanine
10 mM, activates
L-cysteine
10 mM, activates
L-homocysteine
10 mM, activates
L-homoserine
10 mM, activates
L-methionine
10 mM, activates
L-valine
10 mM, activates
L-alanine
10 mM, activates
L-cysteine
10 mM, activates
L-homocysteine
10 mM, activates
L-homoserine
10 mM, activates
L-methionine
10 mM, activates
L-valine
10 mM, activates
additional information
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
7.6
2-oxoglutarate
pH 6.0, 25°C
0.5 - 2.11
3-phospho-D-glycerate
0.05 - 0.39
NAD+
11.2
oxaloacetate
pH 6.0, 25°C
3.7 - 10.7
2-oxoglutarate
0.77 - 2.559
3-phospho-D-glycerate
0.35
3-phosphohydroxypyruvate
-
pH 7.1
0.01 - 0.551
NAD+
0.12
NADH
-
pH 7.1
3.9 - 14.1
oxaloacetate
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.00015
2-oxoglutarate
pH 6.0, 25°C
1.741 - 115.1
3-phospho-D-glycerate
1.741 - 115.1
NAD+
0.00077
oxaloacetate
pH 6.0, 25°C
0.00018 - 0.0002
2-oxoglutarate
16 - 147.4
3-phospho-D-glycerate
16 - 147.4
NAD+
0.00051 - 0.00135
oxaloacetate
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.000019
2-oxoglutarate
pH 6.0, 25°C
30 - 133.1
3-phospho-D-glycerate
300 - 446.3
NAD+
0.000068
oxaloacetate
pH 6.0, 25°C
0.000017 - 0.000053
2-oxoglutarate
16 - 154
3-phospho-D-glycerate
130 - 780.1
NAD+
0.000131 - 0.000907
oxaloacetate
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.14
-
3-phosphoglycerate oxidation, recombinant protein
10.95
-
3-phosphohydroxypyruvate reduction, recombinant protein
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6
optimal pH for reduction of 2-oxoglutarate and oxaloacetate
9
substrate: 3-phospho-D-glycerate, AtPGDH1
10
substrate: 3-phospho-D-glycerate, AtPGDH2
6
optimal pH for reduction of 2-oxoglutarate and oxaloacetate
9.5
substrate: 3-phospho-D-glycerate, AtPGDH3
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
metabolism
physiological function
phosphoglycerate dehydrogenase isoform EDA9 is the essential gene for embryo and male gametophyte development in Arabidopsis thaliana
metabolism
physiological function
the gene EDA9 plays a crucial role in embryo and pollen development
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
SERA1_ARATH
603
0
63325
Swiss-Prot
Chloroplast (Reliability: 1)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
66453
-
x * 66453 and 90000, DNA sequence analysis and SDS-PAGE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
homotetramer
4 * 60000, SDS-PAGE
?
-
x * 66453 and 90000, DNA sequence analysis and SDS-PAGE
homooctamer
8 * 60000, SDS-PAGE, AtPGDH2 forms an equilibrium of homooctamers and homotetramers
homotetramer
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
-
expression of GFP-mutant enzyme in Arabidopsis to investigate the tissue distribution, complementation of Escherichia coli serA- mutant
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli BL-21 cells
expression in Escherichia coli
expressed in Escherichia coli BL-21 cells
expression in Escherichia coli
expression in Escherichia coli Rosetta (DE3) pLysS competent cells
overexpression in Escherichia coli strain AD494 (DE3), cloning of GFP-mutant with transit peptide, expression in plant
-
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
AtPGDH1 gene is coexpressed with genes of tryptophan biosynthesis. Activators of tryptophan biosynthesis MYB51 and MYB34 are involved in the expression of AtPGDH1
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Ho, C.L.; Noji, M.; Saito, M.; Saito, K.
Regulation of serine biosynthesis in Arabidopsis
J. Biol. Chem.
274
397-402
1999
Arabidopsis thaliana
Manually annotated by BRENDA team
Benstein, R.M.; Ludewig, K.; Wulfert, S.; Wittek, S.; Gigolashvili, T.; Frerigmann, H.; Gierth, M.; Fluegge, U.I.; Krueger, S.
Arabidopsis phosphoglycerate dehydrogenase1 of the phosphoserine pathway is essential for development and required for ammonium assimilation and tryptophan biosynthesis
Plant Cell
25
5011-5029
2013
Arabidopsis thaliana (O04130), Arabidopsis thaliana (O49485), Arabidopsis thaliana (Q9LT69), Arabidopsis thaliana
Manually annotated by BRENDA team
Toujani, W.; Munoz-Bertomeu, J.; Flores-Tornero, M.; Rosa-Tellez, S.; Anoman, A.D.; Alseekh, S.; Fernie, A.R.; Ros, R.
Functional characterization of the plastidial 3-phosphoglycerate dehydrogenase family in Arabidopsis
Plant Physiol.
163
1164-1178
2013
Arabidopsis thaliana (Q9LT69), Arabidopsis thaliana
Manually annotated by BRENDA team
Toujani, W.; Munoz-Bertomeu, J.; Flores-Tornero, M.; Rosa-Tellez, S.; Anoman, A.; Ros, R.
Identification of the phosphoglycerate dehydrogenase isoform EDA9 as the essential gene for embryo and male gametophyte development in Arabidopsis
Plant Signal. Behav.
8
e27207
2013
Arabidopsis thaliana (O49485)
Manually annotated by BRENDA team
Yoshida, K.; Ohtaka, K.; Hirai, M.Y.; Hisabori, T.
Biochemical insight into redox regulation of plastidial 3-phosphoglycerate dehydrogenase from Arabidopsis thaliana
J. Biol. Chem.
295
14906-14915
2020
Arabidopsis thaliana (O04130), Arabidopsis thaliana (O49485), Arabidopsis thaliana (Q9LT69), Arabidopsis thaliana
Manually annotated by BRENDA team
Okamura, E.; Hirai, M.Y.
Novel regulatory mechanism of serine biosynthesis associated with 3-phosphoglycerate dehydrogenase in Arabidopsis thaliana
Sci. Rep.
7
3533
2017
Arabidopsis thaliana (O04130), Arabidopsis thaliana (O49485), Arabidopsis thaliana (Q9LT69), Arabidopsis thaliana
Manually annotated by BRENDA team