Cloned (Comment) | Organism |
---|---|
coexpression of His-tagged PdxB, SerC, and PdxA in Escherichia coli stran BL21(DE3) | Escherichia coli |
expressed in Escherichia coli BL21(DE3) cells | Escherichia coli |
Inhibitors | Comment | Organism | Structure |
---|---|---|---|
D-2-hydroxyglutarate | competitive versus 4-phospho-D-erythronate, noncompetitive versus 2-oxoglutarate | Escherichia coli | |
D-2-hydroxyglutaric acid | competitive inhibitor vs. 4-phospho-D-erythronate and a noncompetitive inhibitor vs. alpha-oxoglutarate | Escherichia coli | |
L-2-hydroxyglutaric acid | - |
Escherichia coli |
KM Value [mM] | KM Value Maximum [mM] | Substrate | Comment | Organism | Structure |
---|---|---|---|---|---|
0.0029 | - |
4-phospho-D-erythronate | pH 8.0, 22°C, recombinant enzyme | Escherichia coli | |
0.0029 | - |
4-phospho-D-erythronate | in 50 mM Tris-HCl (pH 8.0) with 50 mM NaCl, 1 mM dithiothreitol, at 22°C | Escherichia coli | |
0.086 | - |
oxaloacetic acid | in 50 mM Tris-HCl (pH 8.0) with 50 mM NaCl, 1 mM dithiothreitol, at 22°C | Escherichia coli | |
0.093 | - |
2-oxoglutarate | in 50 mM Tris-HCl (pH 8.0) with 50 mM NaCl, 1 mM dithiothreitol, at 22°C | Escherichia coli | |
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 | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
---|---|---|---|---|---|---|
2-oxoglutarate + NAD+ | Escherichia coli | - |
D-2-hydroxyglutaric acid + NADH + H+ | - |
? | |
2-oxoglutarate + NAD+ | Escherichia coli JW2317 | - |
D-2-hydroxyglutaric acid + NADH + H+ | - |
? | |
4-phospho-D-erythronate + NAD+ | Escherichia coli | - |
2-oxo-3-hydroxy-4-phospho-butanoate + NADH | - |
? | |
4-phospho-D-erythronate + NAD+ | Escherichia coli | - |
3-hydroxy-2-oxo-4-(phosphonooxy)butanoate + NADH + H+ | - |
r | |
4-phospho-D-erythronate + NAD+ | Escherichia coli JW2317 | - |
2-oxo-3-hydroxy-4-phospho-butanoate + NADH | - |
? | |
4-phospho-D-erythronate + NAD+ | Escherichia coli JW2317 | - |
3-hydroxy-2-oxo-4-(phosphonooxy)butanoate + NADH + H+ | - |
r | |
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 | ? | - |
? | |
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 | ? | - |
? | |
oxaloacetic acid + NAD+ | Escherichia coli | - |
? | - |
? | |
pyruvate + NAD+ | Escherichia coli | - |
? | - |
? |
Organism | UniProt | Comment | Textmining |
---|---|---|---|
Escherichia coli | - |
- |
- |
Escherichia coli JW2317 | - |
- |
- |
Purification (Comment) | Organism |
---|---|
Ni-agarose column chromatography | Escherichia coli |
recombinant His-tagged PdxB from Escherichia coli stran BL21(DE3) by nickel affinity chromatography and ultrafiltration | Escherichia coli |
Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
---|---|---|---|---|---|---|
2-oxoglutarate + NAD+ | - |
Escherichia coli | D-2-hydroxyglutaric acid + NADH + H+ | - |
? | |
2-oxoglutarate + NAD+ | - |
Escherichia coli JW2317 | D-2-hydroxyglutaric acid + NADH + H+ | - |
? | |
2-oxoglutarate + NADH + H+ | stereospecific reaction | Escherichia coli | L-2-hydroxyglutarate + NAD+ | - |
? | |
4-phospho-D-erythronate + NAD+ | - |
Escherichia coli | 2-oxo-3-hydroxy-4-phospho-butanoate + NADH | - |
? | |
4-phospho-D-erythronate + NAD+ | - |
Escherichia coli JW2317 | 2-oxo-3-hydroxy-4-phospho-butanoate + NADH | - |
? | |
4-phospho-D-erythronate + NAD+ | - |
Escherichia coli | 3-hydroxy-2-oxo-4-(phosphonooxy)butanoate + NADH + H+ | - |
r | |
4-phospho-D-erythronate + NAD+ | - |
Escherichia coli JW2317 | 3-hydroxy-2-oxo-4-(phosphonooxy)butanoate + NADH + H+ | - |
r | |
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 | Escherichia coli | 2-oxo-3-hydroxy-4-phospho-butanoate + NADH + H+ | - |
? | |
additional information | 2,6-dichloroindolphenol, N-nitrosodimethylamine, and methylene blue cannot be reduced in the presence of the enzyme and 4-phospho-D-erythronate | Escherichia coli | ? | - |
? | |
additional information | 2-oxoglutarate, oxaloacetic acid, and pyruvate are equally good subtrates for the enzyme | Escherichia coli | ? | - |
? | |
additional information | 2,6-dichloroindolphenol, N-nitrosodimethylamine, and methylene blue cannot be reduced in the presence of the enzyme and 4-phospho-D-erythronate | Escherichia coli JW2317 | ? | - |
? | |
additional information | 2-oxoglutarate, oxaloacetic acid, and pyruvate are equally good subtrates for the enzyme | Escherichia coli JW2317 | ? | - |
? | |
oxaloacetic acid + NAD+ | - |
Escherichia coli | ? | - |
? | |
pyruvate + NAD+ | - |
Escherichia coli | ? | - |
? |
Synonyms | Comment | Organism |
---|---|---|
PDXB | - |
Escherichia coli |
Temperature Optimum [°C] | Temperature Optimum Maximum [°C] | Comment | Organism |
---|---|---|---|
22 | - |
assay at room temperature | Escherichia coli |
Turnover Number Minimum [1/s] | Turnover Number Maximum [1/s] | Substrate | Comment | Organism | Structure |
---|---|---|---|---|---|
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 | - |
oxaloacetic acid | in 50 mM Tris-HCl (pH 8.0) with 50 mM NaCl, 1 mM dithiothreitol, at 22°C | Escherichia coli | |
1.3 | - |
pyruvate | in 50 mM Tris-HCl (pH 8.0) with 50 mM NaCl, 1 mM dithiothreitol, at 22°C | Escherichia coli | |
1.4 | - |
4-phospho-D-erythronate | pH 8.0, 22°C, recombinant enzyme | Escherichia coli | |
1.4 | - |
4-phospho-D-erythronate | in 50 mM Tris-HCl (pH 8.0) with 50 mM NaCl, 1 mM dithiothreitol, at 22°C | Escherichia coli |
pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
---|---|---|---|
8 | - |
assay at | Escherichia coli |
Cofactor | Comment | Organism | Structure |
---|---|---|---|
additional information | PdxB contains tightly bound NAD+ and/or NADH that cannot be removed by extensive dialysis | Escherichia coli | |
NAD+ | specific for | Escherichia coli | |
NAD+ | the released cofactor is 10% NAD+ and 90% NADH | Escherichia coli | |
NADH | specific for | Escherichia coli | |
NADH | the enzyme contains a tightly bound NADH, the released cofactor is 10% NAD+ and 90% NADH | Escherichia coli |
Ki Value [mM] | Ki Value maximum [mM] | Inhibitor | Comment | Organism | Structure |
---|---|---|---|---|---|
0.017 | - |
D-2-hydroxyglutarate | pH 8.0, 22°C, recombinant enzyme, versus 2-oxoglutarate | Escherichia coli | |
0.03 | - |
D-2-hydroxyglutarate | pH 8.0, 22°C, recombinant enzyme, versus 4-phospho-D-erythronate | Escherichia coli |
IC50 Value | IC50 Value Maximum | Comment | Organism | Inhibitor | Structure |
---|---|---|---|---|---|
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 | |
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 |
General Information | Comment | Organism |
---|---|---|
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 Value [1/mMs-1] | kcat/KM Value Maximum [1/mMs-1] | Substrate | Comment | Organism | Structure |
---|---|---|---|---|---|
9.9 | - |
pyruvate | in 50 mM Tris-HCl (pH 8.0) with 50 mM NaCl, 1 mM dithiothreitol, at 22°C | Escherichia coli | |
11 | - |
2-oxoglutarate | in 50 mM Tris-HCl (pH 8.0) with 50 mM NaCl, 1 mM dithiothreitol, at 22°C | Escherichia coli | |
13 | - |
oxaloacetic acid | in 50 mM Tris-HCl (pH 8.0) with 50 mM NaCl, 1 mM dithiothreitol, at 22°C | Escherichia coli | |
6700 | - |
4-phospho-D-erythronate | pH 8.0, 22°C, recombinant enzyme | Escherichia coli | |
6700 | - |
4-phospho-D-erythronate | in 50 mM Tris-HCl (pH 8.0) with 50 mM NaCl, 1 mM dithiothreitol, at 22°C | Escherichia coli |