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show all sequences of 1.1.1.290

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)
Commentary
Organism
coexpression of His-tagged PdxB, SerC, and PdxA in Escherichia coli stran BL21(DE3); expressed in Escherichia coli BL21(DE3) cells
Escherichia coli
Inhibitors
Inhibitors
Commentary
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 [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
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
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/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
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
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Escherichia coli
-
-
-
Escherichia coli JW2317
-
-
-
Purification (Commentary)
Commentary
Organism
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)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
2-oxoglutarate + NAD+
-
724295
Escherichia coli
D-2-hydroxyglutaric acid + NADH + H+
-
-
-
?
2-oxoglutarate + NAD+
-
724295
Escherichia coli JW2317
D-2-hydroxyglutaric acid + NADH + H+
-
-
-
?
2-oxoglutarate + NADH + H+
stereospecific reaction
724295
Escherichia coli
L-2-hydroxyglutarate + NAD+
-
-
-
?
4-phospho-D-erythronate + NAD+
-
724295
Escherichia coli
2-oxo-3-hydroxy-4-phospho-butanoate + NADH
-
-
-
?
4-phospho-D-erythronate + NAD+
-
724295
Escherichia coli JW2317
2-oxo-3-hydroxy-4-phospho-butanoate + NADH
-
-
-
?
4-phospho-D-erythronate + NAD+
-
724295
Escherichia coli
3-hydroxy-2-oxo-4-(phosphonooxy)butanoate + NADH + H+
-
-
-
r
4-phospho-D-erythronate + NAD+
-
724295
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
724295
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
724295
Escherichia coli
?
-
-
-
-
additional information
2-oxoglutarate, oxaloacetic acid, and pyruvate are equally good subtrates for the enzyme
724295
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
724295
Escherichia coli JW2317
?
-
-
-
-
additional information
2-oxoglutarate, oxaloacetic acid, and pyruvate are equally good subtrates for the enzyme
724295
Escherichia coli JW2317
?
-
-
-
-
oxaloacetic acid + NAD+
-
724295
Escherichia coli
?
-
-
-
?
pyruvate + NAD+
-
724295
Escherichia coli
?
-
-
-
?
Temperature Optimum [°C]
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
22
-
assay at room temperature
Escherichia coli
Turnover Number [1/s]
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
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
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
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
8
-
assay at
Escherichia coli
Cofactor
Cofactor
Commentary
Organism
Structure
additional information
PdxB contains tightly bound NAD+ and/or NADH that cannot be removed by extensive dialysis
Escherichia coli
NAD+
specific for; the released cofactor is 10% NAD+ and 90% NADH
Escherichia coli
NADH
specific for; the enzyme contains a tightly bound NADH, the released cofactor is 10% NAD+ and 90% NADH
Escherichia coli
Ki Value [mM]
Ki Value [mM]
Ki Value maximum [mM]
Inhibitor
Commentary
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
IC50 Value Maximum
Commentary
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
Cloned(Commentary) (protein specific)
Commentary
Organism
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)
Cofactor
Commentary
Organism
Structure
additional information
PdxB contains tightly bound NAD+ and/or NADH that cannot be removed by extensive dialysis
Escherichia coli
NAD+
specific for; the released cofactor is 10% NAD+ and 90% NADH
Escherichia coli
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)
IC50 Value
IC50 Value Maximum
Commentary
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
Inhibitors (protein specific)
Inhibitors
Commentary
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
Ki Value [mM] (protein specific)
Ki Value [mM]
Ki Value maximum [mM]
Inhibitor
Commentary
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
KM Value [mM] (protein specific)
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
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
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/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
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
-
?
-
-
?
Purification (Commentary) (protein specific)
Commentary
Organism
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)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
2-oxoglutarate + NAD+
-
724295
Escherichia coli
D-2-hydroxyglutaric acid + NADH + H+
-
-
-
?
2-oxoglutarate + NAD+
-
724295
Escherichia coli JW2317
D-2-hydroxyglutaric acid + NADH + H+
-
-
-
?
2-oxoglutarate + NADH + H+
stereospecific reaction
724295
Escherichia coli
L-2-hydroxyglutarate + NAD+
-
-
-
?
4-phospho-D-erythronate + NAD+
-
724295
Escherichia coli
2-oxo-3-hydroxy-4-phospho-butanoate + NADH
-
-
-
?
4-phospho-D-erythronate + NAD+
-
724295
Escherichia coli JW2317
2-oxo-3-hydroxy-4-phospho-butanoate + NADH
-
-
-
?
4-phospho-D-erythronate + NAD+
-
724295
Escherichia coli
3-hydroxy-2-oxo-4-(phosphonooxy)butanoate + NADH + H+
-
-
-
r
4-phospho-D-erythronate + NAD+
-
724295
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
724295
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
724295
Escherichia coli
?
-
-
-
-
additional information
2-oxoglutarate, oxaloacetic acid, and pyruvate are equally good subtrates for the enzyme
724295
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
724295
Escherichia coli JW2317
?
-
-
-
-
additional information
2-oxoglutarate, oxaloacetic acid, and pyruvate are equally good subtrates for the enzyme
724295
Escherichia coli JW2317
?
-
-
-
-
oxaloacetic acid + NAD+
-
724295
Escherichia coli
?
-
-
-
?
pyruvate + NAD+
-
724295
Escherichia coli
?
-
-
-
?
Temperature Optimum [°C] (protein specific)
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
22
-
assay at room temperature
Escherichia coli
Turnover Number [1/s] (protein specific)
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
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
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)
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
8
-
assay at
Escherichia coli
General Information
General Information
Commentary
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
General Information (protein specific)
General Information
Commentary
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 [mM/s]
kcat/KM Value [1/mMs-1]
kcat/KM Value Maximum [1/mMs-1]
Substrate
Commentary
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
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)
KCat/KM Value [1/mMs-1]
KCat/KM Value Maximum [1/mMs-1]
Substrate
Commentary
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
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
Other publictions for EC 1.1.1.290
No.
1st author
Pub Med
title
organims
journal
volume
pages
year
Activating Compound
Application
Cloned(Commentary)
Crystallization (Commentary)
Engineering
General Stability
Inhibitors
KM Value [mM]
Localization
Metals/Ions
Molecular Weight [Da]
Natural Substrates/ Products (Substrates)
Organic Solvent Stability
Organism
Oxidation Stability
Posttranslational Modification
Purification (Commentary)
Reaction
Renatured (Commentary)
Source Tissue
Specific Activity [micromol/min/mg]
Storage Stability
Substrates and Products (Substrate)
Subunits
Temperature Optimum [°C]
Temperature Range [°C]
Temperature Stability [°C]
Turnover Number [1/s]
pH Optimum
pH Range
pH Stability
Cofactor
Ki Value [mM]
pI Value
IC50 Value
Activating Compound (protein specific)
Application (protein specific)
Cloned(Commentary) (protein specific)
Cofactor (protein specific)
Crystallization (Commentary) (protein specific)
Engineering (protein specific)
General Stability (protein specific)
IC50 Value (protein specific)
Inhibitors (protein specific)
Ki Value [mM] (protein specific)
KM Value [mM] (protein specific)
Localization (protein specific)
Metals/Ions (protein specific)
Molecular Weight [Da] (protein specific)
Natural Substrates/ Products (Substrates) (protein specific)
Organic Solvent Stability (protein specific)
Oxidation Stability (protein specific)
Posttranslational Modification (protein specific)
Purification (Commentary) (protein specific)
Renatured (Commentary) (protein specific)
Source Tissue (protein specific)
Specific Activity [micromol/min/mg] (protein specific)
Storage Stability (protein specific)
Substrates and Products (Substrate) (protein specific)
Subunits (protein specific)
Temperature Optimum [°C] (protein specific)
Temperature Range [°C] (protein specific)
Temperature Stability [°C] (protein specific)
Turnover Number [1/s] (protein specific)
pH Optimum (protein specific)
pH Range (protein specific)
pH Stability (protein specific)
pI Value (protein specific)
Expression
General Information
General Information (protein specific)
Expression (protein specific)
KCat/KM [mM/s]
KCat/KM [mM/s] (protein specific)
739912
Sato
Involvement of vitamin B6 bios ...
Photorhabdus luminescens, Photorhabdus luminescens DSM 15139
Appl. Environ. Microbiol.
82
3546-3553
2016
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724295
Rudolph
Multiple turnovers of the nico ...
Escherichia coli, Escherichia coli JW2317
Biochemistry
49
9249-9255
2010
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688340
Ha
Crystal structure of D-erythro ...
Pseudomonas aeruginosa
J. Mol. Biol.
366
1294-1304
2007
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