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EC Tree
IUBMB Comments 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 . cf. EC 1.1.1.399, 2-oxoglutarate reductase.
The taxonomic range for the selected organisms is: Escherichia coli The expected taxonomic range for this enzyme is: Bacteria, Archaea, Eukaryota
Synonyms
erythronate-4-phosphate dehydrogenase, 4-phosphoerythronate dehydrogenase,
more
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4-O-phosphoerythronate dehydrogenase
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erythronate-4-phosphate dehydrogenase
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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.
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erythronate-4-phosphate + NAD+
(3R)-3-hydroxy-2-oxo-4-phosphonooxybutanoate + NADH
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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2-oxoglutarate + NAD+
D-2-hydroxyglutaric acid + NADH + H+
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2-oxoglutarate + NADH + H+
L-2-hydroxyglutarate + NAD+
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stereospecific reaction
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-
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4-phospho-D-erythronate + NAD+
2-oxo-3-hydroxy-4-phospho-butanoate + NADH
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?
4-phospho-D-erythronate + NAD+
2-oxo-3-hydroxy-4-phospho-butanoate + NADH + H+
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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+
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r
oxaloacetic acid + NAD+
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pyruvate + NAD+
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?
additional information
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additional information
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pdxB is the first gene in the pdxB-hisT operon
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additional information
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the enzyme mediates a step in the biosynthesis of the coenzyme pyridoxal 5'-phosphate. Transcription of pdxB gene is positively growth rate regulated. PdxB-specific transcript remains unchanged during amino acid starvation in wild-type and relA mutant strains
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additional information
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2,6-dichloroindolphenol, N-nitrosodimethylamine, and methylene blue cannot be reduced in the presence of the enzyme and 4-phospho-D-erythronate
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additional information
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2-oxoglutarate, oxaloacetic acid, and pyruvate are equally good subtrates for the enzyme
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erythronate-4-phosphate + NAD+
(3R)-3-hydroxy-2-oxo-4-phosphonooxybutanoate + NADH
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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-
?
2-oxoglutarate + NAD+
D-2-hydroxyglutaric acid + NADH + H+
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?
4-phospho-D-erythronate + NAD+
2-oxo-3-hydroxy-4-phospho-butanoate + NADH
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?
4-phospho-D-erythronate + NAD+
3-hydroxy-2-oxo-4-(phosphonooxy)butanoate + NADH + H+
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r
oxaloacetic acid + NAD+
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pyruvate + NAD+
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additional information
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additional information
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pdxB is the first gene in the pdxB-hisT operon
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additional information
?
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the enzyme mediates a step in the biosynthesis of the coenzyme pyridoxal 5'-phosphate. Transcription of pdxB gene is positively growth rate regulated. PdxB-specific transcript remains unchanged during amino acid starvation in wild-type and relA mutant strains
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?
additional information
?
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2,6-dichloroindolphenol, N-nitrosodimethylamine, and methylene blue cannot be reduced in the presence of the enzyme and 4-phospho-D-erythronate
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?
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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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NAD+
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specific for
NAD+
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the released cofactor is 10% NAD+ and 90% NADH
NADH
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specific for
NADH
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the enzyme contains a tightly bound NADH, the released cofactor is 10% NAD+ and 90% NADH
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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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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
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
0.0029
4-phospho-D-erythronate
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pH 8.0, 22°C, recombinant enzyme
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
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1
2-oxoglutarate
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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
1.1
oxaloacetic acid
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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
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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
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pH 8.0, 22°C, recombinant enzyme
1.4
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
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11
2-oxoglutarate
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in 50 mM Tris-HCl (pH 8.0) with 50 mM NaCl, 1 mM dithiothreitol, at 22°C
6700
4-phospho-D-erythronate
13
oxaloacetic acid
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in 50 mM Tris-HCl (pH 8.0) with 50 mM NaCl, 1 mM dithiothreitol, at 22°C
9.9
pyruvate
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in 50 mM Tris-HCl (pH 8.0) with 50 mM NaCl, 1 mM dithiothreitol, at 22°C
6700
4-phospho-D-erythronate
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pH 8.0, 22°C, recombinant enzyme
6700
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
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0.017 - 0.03
D-2-hydroxyglutarate
0.017
D-2-hydroxyglutarate
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pH 8.0, 22°C, recombinant enzyme, versus 2-oxoglutarate
0.03
D-2-hydroxyglutarate
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pH 8.0, 22°C, recombinant enzyme, versus 4-phospho-D-erythronate
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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
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22
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assay at room temperature
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SwissProt
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K-12
SwissProt
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metabolism
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pyridoxal phosphate biosynthesis in Escherichia coli is quite different from the more widely used Pdx1/Pdx2-dependent pathway. Escherichia coli uses seven enzymes in a bifurcated pathway that converts pyruvate, glyceraldehyde-3-phosphate, and erythrose-4-phosphate to pyridoxal phosphate via the intermediates 1-deoxy-D-xylulose 5-phosphate and 1-amino-propan-2-one-3-phosphate. PdxB catalyzes the second step in the biosynthesis of pyridoxal phosphate by oxidizing 4-phospho-D-erythronate to 2-oxo-3-hydroxy-4-phospho-butanoate with concomitant reduction
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Ni-agarose column chromatography
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recombinant His-tagged PdxB from Escherichia coli stran BL21(DE3) by nickel affinity chromatography and ultrafiltration
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coexpression of His-tagged PdxB, SerC, and PdxA in Escherichia coli stran BL21(DE3)
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expressed in Escherichia coli BL21(DE3) cells
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Grant, G.A.
A new family of 2-hydroxyacid dehydrogenases
Biochem. Biophys. Res. Commun.
165
1371-1374
1989
Escherichia coli
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Schoenlein, P.V.; Roa, B.B.; Winkler, M.E.
Divergent transcription of pdxB and homology between the pdxB and serA gene products in Escherichia coli K-12
J. Bacteriol.
171
6084-6092
1989
Escherichia coli (P05459)
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Lam, H.M.; Winkler, M.E.
Metabolic relationships between pyridoxine (vitamin B6) and serine biosynthesis in Escherichia coli K-12
J. Bacteriol.
172
6518-6528
1990
Escherichia coli (P05459)
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Pease, A.J.; Roa, B.R.; Luo, W.; Winkler, M.E.
Positive growth rate-dependent regulation of the pdxA, ksgA, and pdxB genes of Escherichia coli K-12
J. Bacteriol.
184
1359-1369
2002
Escherichia coli (P05459)
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Rudolph, J.; Kim, J.; Copley, S.D.
Multiple turnovers of the nicotino-enzyme PdxB require alpha-keto acids as cosubstrates
Biochemistry
49
9249-9255
2010
Escherichia coli, Escherichia coli JW2317
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