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Literature summary extracted from

  • Rudolph, J.; Kim, J.; Copley, S.D.
    Multiple turnovers of the nicotino-enzyme PdxB require alpha-keto acids as cosubstrates (2010), Biochemistry, 49, 9249-9255.
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

EC Number Cloned (Comment) Organism
1.1.1.290 coexpression of His-tagged PdxB, SerC, and PdxA in Escherichia coli stran BL21(DE3) Escherichia coli
1.1.1.290 expressed in Escherichia coli BL21(DE3) cells Escherichia coli

Inhibitors

EC Number Inhibitors Comment 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 Comment Organism Structure
1.1.1.290 0.0029
-
 4-phospho-D-erythronate pH 8.0, 22°C, recombinant enzyme Escherichia coli
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 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 Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
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 UniProt Comment Textmining
1.1.1.290 Escherichia coli
-
-
-
1.1.1.290 Escherichia coli JW2317
-
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
1.1.1.290 Ni-agarose column chromatography Escherichia coli
1.1.1.290 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 Comment Substrates Organism Products Comment (Products) Rev. Reac.
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 2-oxoglutarate + NADH + H+ stereospecific reaction Escherichia coli L-2-hydroxyglutarate + NAD+
-
 ?
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 JW2317 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 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 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 Escherichia coli ?
-
 ?
1.1.1.290 additional information 2-oxoglutarate, oxaloacetic acid, and pyruvate are equally good subtrates for the enzyme 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 Escherichia coli JW2317 ?
-
 ?
1.1.1.290 additional information 2-oxoglutarate, oxaloacetic acid, and pyruvate are equally good subtrates for the enzyme Escherichia coli JW2317 ?
-
 ?
1.1.1.290 oxaloacetic acid + NAD+
-
 Escherichia coli ?
-
 ?
1.1.1.290 pyruvate + NAD+
-
 Escherichia coli ?
-
 ?

Synonyms

EC Number Synonyms Comment Organism
1.1.1.290 PDXB
-
 Escherichia coli

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment 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 Comment 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 pH 8.0, 22°C, recombinant enzyme 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 Escherichia coli

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
1.1.1.290 8
-
 assay at Escherichia coli

Cofactor

EC Number Cofactor Comment 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 Escherichia coli
1.1.1.290 NAD+ the released cofactor is 10% NAD+ and 90% NADH Escherichia coli
1.1.1.290 NADH specific for Escherichia coli
1.1.1.290 NADH 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 Comment 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 Comment 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

General Information

EC Number General Information Comment 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 Comment 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 pH 8.0, 22°C, recombinant enzyme 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 Escherichia coli