Information on EC 1.1.1.290 - 4-phosphoerythronate dehydrogenase

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The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY hide
1.1.1.290
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RECOMMENDED NAME
GeneOntology No.
4-phosphoerythronate dehydrogenase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
4-phospho-D-erythronate + NAD+ = (3R)-3-hydroxy-2-oxo-4-phosphonooxybutanoate + NADH + H+
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
oxidation
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-
redox reaction
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reduction
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Metabolic pathways
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pyridoxal 5'-phosphate biosynthesis I
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Vitamin B6 metabolism
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vitamin B6 metabolism
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SYSTEMATIC NAME
IUBMB Comments
4-phospho-D-erythronate:NAD+ 2-oxidoreductase
This enzyme catalyses a step in a bacterial pathway for the biosynthesis of pyridoxal 5'-phosphate. The enzyme contains a tightly-bound NAD(H) cofactor that is not re-oxidized by free NAD+. In order to re-oxidize the cofactor and restore enzyme activity, the enzyme catalyses the reduction of a 2-oxo acid (such as 2-oxoglutarate, oxaloacetate, or pyruvate) to the respective (R)-hydroxy acid [6]. cf. EC 1.1.1.399, 2-oxoglutarate reductase.
CAS REGISTRY NUMBER
COMMENTARY hide
125858-75-5
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
metabolism
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 + NAD+
D-2-hydroxyglutaric acid + NADH + H+
show the reaction diagram
2-oxoglutarate + NADH + H+
L-2-hydroxyglutarate + NAD+
show the reaction diagram
-
stereospecific reaction
-
-
?
4-phospho-D-erythronate + NAD+
(3R)-3-hydroxy-2-oxo-4-phosphooxybutanoate + NADH
show the reaction diagram
4-phospho-D-erythronate + NAD+
2-oxo-3-hydroxy-4-phospho-butanoate + NADH
show the reaction diagram
4-phospho-D-erythronate + NAD+
2-oxo-3-hydroxy-4-phospho-butanoate + NADH + H+
show the reaction diagram
-
multiple turnovers requiring 2-oxo acids for re-oxidation of NADH bound to the enzyme PdxB a coupled assay with the enzymes SerC and PdxA following in the bioyntetic pathway, overview
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-
?
4-phospho-D-erythronate + NAD+
3-hydroxy-2-oxo-4-(phosphonooxy)butanoate + NADH + H+
show the reaction diagram
erythronate-4-phosphate + NAD+
(3R)-3-hydroxy-2-oxo-4-phosphonooxybutanoate + NADH
show the reaction diagram
reaction in pathway leading from erythrose-4-phosphate and glutamate to nitrogen 1 and carbon 5,5', and 6 of the pyridoxine ring
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-
?
erythronate-4-phosphate + NAD+
3-hydroxy-4-phospho-hydroxy-alpha-ketobutyrate + NADH
show the reaction diagram
-
-
-
-
?
oxaloacetic acid + NAD+
?
show the reaction diagram
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-
-
-
?
pyruvate + NAD+
?
show the reaction diagram
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-
-
-
?
additional information
?
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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 + NAD+
D-2-hydroxyglutaric acid + NADH + H+
show the reaction diagram
4-phospho-D-erythronate + NAD+
(3R)-3-hydroxy-2-oxo-4-phosphooxybutanoate + NADH
show the reaction diagram
Q9I3W9
the enzyme is involved in biosynthesis of pyridoxal-5'-phosphate
-
-
?
4-phospho-D-erythronate + NAD+
2-oxo-3-hydroxy-4-phospho-butanoate + NADH
show the reaction diagram
4-phospho-D-erythronate + NAD+
3-hydroxy-2-oxo-4-(phosphonooxy)butanoate + NADH + H+
show the reaction diagram
erythronate-4-phosphate + NAD+
(3R)-3-hydroxy-2-oxo-4-phosphonooxybutanoate + NADH
show the reaction diagram
P05459
reaction in pathway leading from erythrose-4-phosphate and glutamate to nitrogen 1 and carbon 5,5', and 6 of the pyridoxine ring
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-
?
oxaloacetic acid + NAD+
?
show the reaction diagram
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-
-
-
?
pyruvate + NAD+
?
show the reaction diagram
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-
-
-
?
additional information
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
NADH
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specific for; the enzyme contains a tightly bound NADH, the released cofactor is 10% NAD+ and 90% NADH
additional information
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PdxB contains tightly bound NAD+ and/or NADH that cannot be removed by extensive dialysis
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INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
D-2-hydroxyglutarate
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competitive versus 4-phospho-D-erythronate, noncompetitive versus 2-oxoglutarate
D-2-hydroxyglutaric acid
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competitive inhibitor vs. 4-phospho-D-erythronate and a noncompetitive inhibitor vs. alpha-oxoglutarate
L-2-hydroxyglutaric acid
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.093
2-oxoglutarate
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in 50 mM Tris-HCl (pH 8.0) with 50 mM NaCl, 1 mM dithiothreitol, at 22°C
0.0029
4-phospho-D-erythronate
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in 50 mM Tris-HCl (pH 8.0) with 50 mM NaCl, 1 mM dithiothreitol, at 22°C; pH 8.0, 22°C, recombinant enzyme
0.086
oxaloacetic acid
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in 50 mM Tris-HCl (pH 8.0) with 50 mM NaCl, 1 mM dithiothreitol, at 22°C
0.128
pyruvate
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in 50 mM Tris-HCl (pH 8.0) with 50 mM NaCl, 1 mM dithiothreitol, at 22°C
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1
2-oxoglutarate
Escherichia coli
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in 50 mM Tris-HCl (pH 8.0) with 50 mM NaCl, 1 mM dithiothreitol, at 22°C
1.4
4-phospho-D-erythronate
Escherichia coli
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in 50 mM Tris-HCl (pH 8.0) with 50 mM NaCl, 1 mM dithiothreitol, at 22°C; pH 8.0, 22°C, recombinant enzyme
1.1
oxaloacetic acid
Escherichia coli
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in 50 mM Tris-HCl (pH 8.0) with 50 mM NaCl, 1 mM dithiothreitol, at 22°C
1.3
pyruvate
Escherichia coli
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in 50 mM Tris-HCl (pH 8.0) with 50 mM NaCl, 1 mM dithiothreitol, at 22°C
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
11
2-oxoglutarate
Escherichia coli
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in 50 mM Tris-HCl (pH 8.0) with 50 mM NaCl, 1 mM dithiothreitol, at 22°C
34
6700
4-phospho-D-erythronate
Escherichia coli
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in 50 mM Tris-HCl (pH 8.0) with 50 mM NaCl, 1 mM dithiothreitol, at 22°C; pH 8.0, 22°C, recombinant enzyme
2613
13
oxaloacetic acid
Escherichia coli
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in 50 mM Tris-HCl (pH 8.0) with 50 mM NaCl, 1 mM dithiothreitol, at 22°C
2862
9.9
pyruvate
Escherichia coli
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in 50 mM Tris-HCl (pH 8.0) with 50 mM NaCl, 1 mM dithiothreitol, at 22°C
31
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.017 - 0.03
D-2-hydroxyglutarate
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.102
D-2-hydroxyglutaric acid
Escherichia coli
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in 50 mM Tris-HCl (pH 8.0) with 50 mM NaCl, 1 mM dithiothreitol, at 22°C
2
L-2-hydroxyglutaric acid
Escherichia coli
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in 50 mM Tris-HCl (pH 8.0) with 50 mM NaCl, 1 mM dithiothreitol, at 22°C
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
8
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assay at
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
22
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assay at room temperature
PDB
SCOP
CATH
ORGANISM
UNIPROT
Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
83000
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estimated by dynamic light-scattering analysis
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dimer
homodimer, each subunit consists of three structural domains: the lid domain, the nucleotide-binding domain, and the C-terminal dimerization domain with a unique fold responsible for the dimerization, crystal structure analysis, overview
homodimer
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2 * 42 067, enzyme including a C-terminal tag, enzyme consists of two identical 380-residue subunits
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
hanging-drop vapour diffusion at 24°C K using 0.7 M ammonium dihydrogen phosphate, 0.4 M ammonium tartrate, 0.1 M sodium citrate pH 5.6 and 10 mM cupric chloride
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purified recombinant C-terminally His8-tagged and selenomethionine-labeled enzyme, subunit A is bound with NAD+ and a phosphate ion, while subunit B, with a more open active site cleft, is bound with NAD+ and L(+)-tartrate, cryoprotection by 30% glycerol, X-ray diffraction structure determination and analysis at 2.3 A resolution, asymmetric subunit conformation and strucure comparison, overview
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
metal-chelate chromatography on Ni-NTA resin and size exclusion chromatography
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Ni-agarose column chromatography; recombinant His-tagged PdxB from Escherichia coli stran BL21(DE3) by nickel affinity chromatography and ultrafiltration
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
coexpression of His-tagged PdxB, SerC, and PdxA in Escherichia coli stran BL21(DE3); expressed in Escherichia coli BL21(DE3) cells
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expressed in Escherichia coli
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Show AA Sequence (4117 entries)
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