BRENDA - Enzyme Database

Multiple turnovers of the nicotino-enzyme PdxB require alpha-keto acids as cosubstrates

Rudolph, J.; Kim, J.; Copley, S.D.; Biochemistry 49, 9249-9255 (2010)

Data extracted from this reference:

Cloned(Commentary)
EC Number
Commentary
Organism
1.1.1.290
coexpression of His-tagged PdxB, SerC, and PdxA in Escherichia coli stran BL21(DE3); expressed in Escherichia coli BL21(DE3) cells
Escherichia coli
Inhibitors
EC Number
Inhibitors
Commentary
Organism
Structure
1.1.1.290
D-2-hydroxyglutarate
competitive versus 4-phospho-D-erythronate, noncompetitive versus 2-oxoglutarate
Escherichia coli
1.1.1.290
D-2-hydroxyglutaric acid
competitive inhibitor vs. 4-phospho-D-erythronate and a noncompetitive inhibitor vs. alpha-oxoglutarate
Escherichia coli
1.1.1.290
L-2-hydroxyglutaric acid
-
Escherichia coli
KM Value [mM]
EC Number
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
1.1.1.290
0.0029
-
4-phospho-D-erythronate
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
Escherichia coli
1.1.1.290
0.086
-
oxaloacetic acid
in 50 mM Tris-HCl (pH 8.0) with 50 mM NaCl, 1 mM dithiothreitol, at 22°C
Escherichia coli
1.1.1.290
0.093
-
2-oxoglutarate
in 50 mM Tris-HCl (pH 8.0) with 50 mM NaCl, 1 mM dithiothreitol, at 22°C
Escherichia coli
1.1.1.290
0.128
-
pyruvate
in 50 mM Tris-HCl (pH 8.0) with 50 mM NaCl, 1 mM dithiothreitol, at 22°C
Escherichia coli
Natural Substrates/ Products (Substrates)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
1.1.1.290
2-oxoglutarate + NAD+
Escherichia coli
-
D-2-hydroxyglutaric acid + NADH + H+
-
-
?
1.1.1.290
2-oxoglutarate + NAD+
Escherichia coli JW2317
-
D-2-hydroxyglutaric acid + NADH + H+
-
-
?
1.1.1.290
4-phospho-D-erythronate + NAD+
Escherichia coli
-
2-oxo-3-hydroxy-4-phospho-butanoate + NADH
-
-
?
1.1.1.290
4-phospho-D-erythronate + NAD+
Escherichia coli
-
3-hydroxy-2-oxo-4-(phosphonooxy)butanoate + NADH + H+
-
-
r
1.1.1.290
4-phospho-D-erythronate + NAD+
Escherichia coli JW2317
-
2-oxo-3-hydroxy-4-phospho-butanoate + NADH
-
-
?
1.1.1.290
4-phospho-D-erythronate + NAD+
Escherichia coli JW2317
-
3-hydroxy-2-oxo-4-(phosphonooxy)butanoate + NADH + H+
-
-
r
1.1.1.290
additional information
Escherichia coli
2,6-dichloroindolphenol, N-nitrosodimethylamine, and methylene blue cannot be reduced in the presence of the enzyme and 4-phospho-D-erythronate
?
-
-
-
1.1.1.290
additional information
Escherichia coli JW2317
2,6-dichloroindolphenol, N-nitrosodimethylamine, and methylene blue cannot be reduced in the presence of the enzyme and 4-phospho-D-erythronate
?
-
-
-
1.1.1.290
oxaloacetic acid + NAD+
Escherichia coli
-
?
-
-
?
1.1.1.290
pyruvate + NAD+
Escherichia coli
-
?
-
-
?
Organism
EC Number
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
1.1.1.290
Escherichia coli
-
-
-
1.1.1.290
Escherichia coli JW2317
-
-
-
Purification (Commentary)
EC Number
Commentary
Organism
1.1.1.290
Ni-agarose column chromatography; recombinant His-tagged PdxB from Escherichia coli stran BL21(DE3) by nickel affinity chromatography and ultrafiltration
Escherichia coli
Substrates and Products (Substrate)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
1.1.1.290
2-oxoglutarate + NAD+
-
724295
Escherichia coli
D-2-hydroxyglutaric acid + NADH + H+
-
-
-
?
1.1.1.290
2-oxoglutarate + NAD+
-
724295
Escherichia coli JW2317
D-2-hydroxyglutaric acid + NADH + H+
-
-
-
?
1.1.1.290
2-oxoglutarate + NADH + H+
stereospecific reaction
724295
Escherichia coli
L-2-hydroxyglutarate + NAD+
-
-
-
?
1.1.1.290
4-phospho-D-erythronate + NAD+
-
724295
Escherichia coli
2-oxo-3-hydroxy-4-phospho-butanoate + NADH
-
-
-
?
1.1.1.290
4-phospho-D-erythronate + NAD+
-
724295
Escherichia coli JW2317
2-oxo-3-hydroxy-4-phospho-butanoate + NADH
-
-
-
?
1.1.1.290
4-phospho-D-erythronate + NAD+
-
724295
Escherichia coli
3-hydroxy-2-oxo-4-(phosphonooxy)butanoate + NADH + H+
-
-
-
r
1.1.1.290
4-phospho-D-erythronate + NAD+
-
724295
Escherichia coli JW2317
3-hydroxy-2-oxo-4-(phosphonooxy)butanoate + NADH + H+
-
-
-
r
1.1.1.290
4-phospho-D-erythronate + NAD+
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
724295
Escherichia coli
2-oxo-3-hydroxy-4-phospho-butanoate + NADH + H+
-
-
-
?
1.1.1.290
additional information
2,6-dichloroindolphenol, N-nitrosodimethylamine, and methylene blue cannot be reduced in the presence of the enzyme and 4-phospho-D-erythronate
724295
Escherichia coli
?
-
-
-
-
1.1.1.290
additional information
2-oxoglutarate, oxaloacetic acid, and pyruvate are equally good subtrates for the enzyme
724295
Escherichia coli
?
-
-
-
-
1.1.1.290
additional information
2,6-dichloroindolphenol, N-nitrosodimethylamine, and methylene blue cannot be reduced in the presence of the enzyme and 4-phospho-D-erythronate
724295
Escherichia coli JW2317
?
-
-
-
-
1.1.1.290
additional information
2-oxoglutarate, oxaloacetic acid, and pyruvate are equally good subtrates for the enzyme
724295
Escherichia coli JW2317
?
-
-
-
-
1.1.1.290
oxaloacetic acid + NAD+
-
724295
Escherichia coli
?
-
-
-
?
1.1.1.290
pyruvate + NAD+
-
724295
Escherichia coli
?
-
-
-
?
Temperature Optimum [°C]
EC Number
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
1.1.1.290
22
-
assay at room temperature
Escherichia coli
Turnover Number [1/s]
EC Number
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
1.1.1.290
1
-
2-oxoglutarate
in 50 mM Tris-HCl (pH 8.0) with 50 mM NaCl, 1 mM dithiothreitol, at 22°C
Escherichia coli
1.1.1.290
1.1
-
oxaloacetic acid
in 50 mM Tris-HCl (pH 8.0) with 50 mM NaCl, 1 mM dithiothreitol, at 22°C
Escherichia coli
1.1.1.290
1.3
-
pyruvate
in 50 mM Tris-HCl (pH 8.0) with 50 mM NaCl, 1 mM dithiothreitol, at 22°C
Escherichia coli
1.1.1.290
1.4
-
4-phospho-D-erythronate
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
Escherichia coli
pH Optimum
EC Number
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
1.1.1.290
8
-
assay at
Escherichia coli
Cofactor
EC Number
Cofactor
Commentary
Organism
Structure
1.1.1.290
additional information
PdxB contains tightly bound NAD+ and/or NADH that cannot be removed by extensive dialysis
Escherichia coli
1.1.1.290
NAD+
specific for; the released cofactor is 10% NAD+ and 90% NADH
Escherichia coli
1.1.1.290
NADH
specific for; the enzyme contains a tightly bound NADH, the released cofactor is 10% NAD+ and 90% NADH
Escherichia coli
Ki Value [mM]
EC Number
Ki Value [mM]
Ki Value maximum [mM]
Inhibitor
Commentary
Organism
Structure
1.1.1.290
0.017
-
D-2-hydroxyglutarate
pH 8.0, 22°C, recombinant enzyme, versus 2-oxoglutarate
Escherichia coli
1.1.1.290
0.03
-
D-2-hydroxyglutarate
pH 8.0, 22°C, recombinant enzyme, versus 4-phospho-D-erythronate
Escherichia coli
IC50 Value
EC Number
IC50 Value
IC50 Value Maximum
Commentary
Organism
Inhibitor
Structure
1.1.1.290
0.102
-
in 50 mM Tris-HCl (pH 8.0) with 50 mM NaCl, 1 mM dithiothreitol, at 22°C
Escherichia coli
D-2-hydroxyglutaric acid
1.1.1.290
2
-
in 50 mM Tris-HCl (pH 8.0) with 50 mM NaCl, 1 mM dithiothreitol, at 22°C
Escherichia coli
L-2-hydroxyglutaric acid
Cloned(Commentary) (protein specific)
EC Number
Commentary
Organism
1.1.1.290
coexpression of His-tagged PdxB, SerC, and PdxA in Escherichia coli stran BL21(DE3); expressed in Escherichia coli BL21(DE3) cells
Escherichia coli
Cofactor (protein specific)
EC Number
Cofactor
Commentary
Organism
Structure
1.1.1.290
additional information
PdxB contains tightly bound NAD+ and/or NADH that cannot be removed by extensive dialysis
Escherichia coli
1.1.1.290
NAD+
specific for; the released cofactor is 10% NAD+ and 90% NADH
Escherichia coli
1.1.1.290
NADH
specific for; the enzyme contains a tightly bound NADH, the released cofactor is 10% NAD+ and 90% NADH
Escherichia coli
IC50 Value (protein specific)
EC Number
IC50 Value
IC50 Value Maximum
Commentary
Organism
Inhibitor
Structure
1.1.1.290
0.102
-
in 50 mM Tris-HCl (pH 8.0) with 50 mM NaCl, 1 mM dithiothreitol, at 22°C
Escherichia coli
D-2-hydroxyglutaric acid
1.1.1.290
2
-
in 50 mM Tris-HCl (pH 8.0) with 50 mM NaCl, 1 mM dithiothreitol, at 22°C
Escherichia coli
L-2-hydroxyglutaric acid
Inhibitors (protein specific)
EC Number
Inhibitors
Commentary
Organism
Structure
1.1.1.290
D-2-hydroxyglutarate
competitive versus 4-phospho-D-erythronate, noncompetitive versus 2-oxoglutarate
Escherichia coli
1.1.1.290
D-2-hydroxyglutaric acid
competitive inhibitor vs. 4-phospho-D-erythronate and a noncompetitive inhibitor vs. alpha-oxoglutarate
Escherichia coli
1.1.1.290
L-2-hydroxyglutaric acid
-
Escherichia coli
Ki Value [mM] (protein specific)
EC Number
Ki Value [mM]
Ki Value maximum [mM]
Inhibitor
Commentary
Organism
Structure
1.1.1.290
0.017
-
D-2-hydroxyglutarate
pH 8.0, 22°C, recombinant enzyme, versus 2-oxoglutarate
Escherichia coli
1.1.1.290
0.03
-
D-2-hydroxyglutarate
pH 8.0, 22°C, recombinant enzyme, versus 4-phospho-D-erythronate
Escherichia coli
KM Value [mM] (protein specific)
EC Number
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
1.1.1.290
0.0029
-
4-phospho-D-erythronate
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
Escherichia coli
1.1.1.290
0.086
-
oxaloacetic acid
in 50 mM Tris-HCl (pH 8.0) with 50 mM NaCl, 1 mM dithiothreitol, at 22°C
Escherichia coli
1.1.1.290
0.093
-
2-oxoglutarate
in 50 mM Tris-HCl (pH 8.0) with 50 mM NaCl, 1 mM dithiothreitol, at 22°C
Escherichia coli
1.1.1.290
0.128
-
pyruvate
in 50 mM Tris-HCl (pH 8.0) with 50 mM NaCl, 1 mM dithiothreitol, at 22°C
Escherichia coli
Natural Substrates/ Products (Substrates) (protein specific)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
1.1.1.290
2-oxoglutarate + NAD+
Escherichia coli
-
D-2-hydroxyglutaric acid + NADH + H+
-
-
?
1.1.1.290
2-oxoglutarate + NAD+
Escherichia coli JW2317
-
D-2-hydroxyglutaric acid + NADH + H+
-
-
?
1.1.1.290
4-phospho-D-erythronate + NAD+
Escherichia coli
-
2-oxo-3-hydroxy-4-phospho-butanoate + NADH
-
-
?
1.1.1.290
4-phospho-D-erythronate + NAD+
Escherichia coli
-
3-hydroxy-2-oxo-4-(phosphonooxy)butanoate + NADH + H+
-
-
r
1.1.1.290
4-phospho-D-erythronate + NAD+
Escherichia coli JW2317
-
2-oxo-3-hydroxy-4-phospho-butanoate + NADH
-
-
?
1.1.1.290
4-phospho-D-erythronate + NAD+
Escherichia coli JW2317
-
3-hydroxy-2-oxo-4-(phosphonooxy)butanoate + NADH + H+
-
-
r
1.1.1.290
additional information
Escherichia coli
2,6-dichloroindolphenol, N-nitrosodimethylamine, and methylene blue cannot be reduced in the presence of the enzyme and 4-phospho-D-erythronate
?
-
-
-
1.1.1.290
additional information
Escherichia coli JW2317
2,6-dichloroindolphenol, N-nitrosodimethylamine, and methylene blue cannot be reduced in the presence of the enzyme and 4-phospho-D-erythronate
?
-
-
-
1.1.1.290
oxaloacetic acid + NAD+
Escherichia coli
-
?
-
-
?
1.1.1.290
pyruvate + NAD+
Escherichia coli
-
?
-
-
?
Purification (Commentary) (protein specific)
EC Number
Commentary
Organism
1.1.1.290
Ni-agarose column chromatography; recombinant His-tagged PdxB from Escherichia coli stran BL21(DE3) by nickel affinity chromatography and ultrafiltration
Escherichia coli
Substrates and Products (Substrate) (protein specific)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
1.1.1.290
2-oxoglutarate + NAD+
-
724295
Escherichia coli
D-2-hydroxyglutaric acid + NADH + H+
-
-
-
?
1.1.1.290
2-oxoglutarate + NAD+
-
724295
Escherichia coli JW2317
D-2-hydroxyglutaric acid + NADH + H+
-
-
-
?
1.1.1.290
2-oxoglutarate + NADH + H+
stereospecific reaction
724295
Escherichia coli
L-2-hydroxyglutarate + NAD+
-
-
-
?
1.1.1.290
4-phospho-D-erythronate + NAD+
-
724295
Escherichia coli
2-oxo-3-hydroxy-4-phospho-butanoate + NADH
-
-
-
?
1.1.1.290
4-phospho-D-erythronate + NAD+
-
724295
Escherichia coli JW2317
2-oxo-3-hydroxy-4-phospho-butanoate + NADH
-
-
-
?
1.1.1.290
4-phospho-D-erythronate + NAD+
-
724295
Escherichia coli
3-hydroxy-2-oxo-4-(phosphonooxy)butanoate + NADH + H+
-
-
-
r
1.1.1.290
4-phospho-D-erythronate + NAD+
-
724295
Escherichia coli JW2317
3-hydroxy-2-oxo-4-(phosphonooxy)butanoate + NADH + H+
-
-
-
r
1.1.1.290
4-phospho-D-erythronate + NAD+
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
724295
Escherichia coli
2-oxo-3-hydroxy-4-phospho-butanoate + NADH + H+
-
-
-
?
1.1.1.290
additional information
2,6-dichloroindolphenol, N-nitrosodimethylamine, and methylene blue cannot be reduced in the presence of the enzyme and 4-phospho-D-erythronate
724295
Escherichia coli
?
-
-
-
-
1.1.1.290
additional information
2-oxoglutarate, oxaloacetic acid, and pyruvate are equally good subtrates for the enzyme
724295
Escherichia coli
?
-
-
-
-
1.1.1.290
additional information
2,6-dichloroindolphenol, N-nitrosodimethylamine, and methylene blue cannot be reduced in the presence of the enzyme and 4-phospho-D-erythronate
724295
Escherichia coli JW2317
?
-
-
-
-
1.1.1.290
additional information
2-oxoglutarate, oxaloacetic acid, and pyruvate are equally good subtrates for the enzyme
724295
Escherichia coli JW2317
?
-
-
-
-
1.1.1.290
oxaloacetic acid + NAD+
-
724295
Escherichia coli
?
-
-
-
?
1.1.1.290
pyruvate + NAD+
-
724295
Escherichia coli
?
-
-
-
?
Temperature Optimum [°C] (protein specific)
EC Number
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
1.1.1.290
22
-
assay at room temperature
Escherichia coli
Turnover Number [1/s] (protein specific)
EC Number
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
1.1.1.290
1
-
2-oxoglutarate
in 50 mM Tris-HCl (pH 8.0) with 50 mM NaCl, 1 mM dithiothreitol, at 22°C
Escherichia coli
1.1.1.290
1.1
-
oxaloacetic acid
in 50 mM Tris-HCl (pH 8.0) with 50 mM NaCl, 1 mM dithiothreitol, at 22°C
Escherichia coli
1.1.1.290
1.3
-
pyruvate
in 50 mM Tris-HCl (pH 8.0) with 50 mM NaCl, 1 mM dithiothreitol, at 22°C
Escherichia coli
1.1.1.290
1.4
-
4-phospho-D-erythronate
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
Escherichia coli
pH Optimum (protein specific)
EC Number
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
1.1.1.290
8
-
assay at
Escherichia coli
General Information
EC Number
General Information
Commentary
Organism
1.1.1.290
metabolism
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
Escherichia coli
General Information (protein specific)
EC Number
General Information
Commentary
Organism
1.1.1.290
metabolism
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
Escherichia coli
KCat/KM [mM/s]
EC Number
kcat/KM Value [1/mMs-1]
kcat/KM Value Maximum [1/mMs-1]
Substrate
Commentary
Organism
Structure
1.1.1.290
9.9
-
pyruvate
in 50 mM Tris-HCl (pH 8.0) with 50 mM NaCl, 1 mM dithiothreitol, at 22°C
Escherichia coli
1.1.1.290
11
-
2-oxoglutarate
in 50 mM Tris-HCl (pH 8.0) with 50 mM NaCl, 1 mM dithiothreitol, at 22°C
Escherichia coli
1.1.1.290
13
-
oxaloacetic acid
in 50 mM Tris-HCl (pH 8.0) with 50 mM NaCl, 1 mM dithiothreitol, at 22°C
Escherichia coli
1.1.1.290
6700
-
4-phospho-D-erythronate
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
Escherichia coli
KCat/KM [mM/s] (protein specific)
EC Number
KCat/KM Value [1/mMs-1]
KCat/KM Value Maximum [1/mMs-1]
Substrate
Commentary
Organism
Structure
1.1.1.290
9.9
-
pyruvate
in 50 mM Tris-HCl (pH 8.0) with 50 mM NaCl, 1 mM dithiothreitol, at 22°C
Escherichia coli
1.1.1.290
11
-
2-oxoglutarate
in 50 mM Tris-HCl (pH 8.0) with 50 mM NaCl, 1 mM dithiothreitol, at 22°C
Escherichia coli
1.1.1.290
13
-
oxaloacetic acid
in 50 mM Tris-HCl (pH 8.0) with 50 mM NaCl, 1 mM dithiothreitol, at 22°C
Escherichia coli
1.1.1.290
6700
-
4-phospho-D-erythronate
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
Escherichia coli