BRENDA - Enzyme Database
show all sequences of 1.1.1.262

Crystal structure of Escherichia coli PdxA, an enzyme involved in the pyridoxal phosphate biosynthesis pathway

Sivaraman, J.; Li, Y.; Banks, J.; Cane, D.E.; Matte, A.; Cygler, M.; J. Biol. Chem. 278, 43682-43690 (2003)

Data extracted from this reference:

Cloned(Commentary)
Cloned (Commentary)
Organism
gene pdxA, expression of the His-tagged enzyme with a thrombin cleavage site in Escherichia coli
Escherichia coli
Crystallization (Commentary)
Crystallization (Commentary)
Organism
8.1 mg/ml purified recombinant enzyme in complex with substrate 4-(phosphonooxy)threonine and Zn2+ in 20 mM Tris-HCl, pH 8.0, 0.2 M NaCl, 10 mM DTT, 5% w/v glycerol, hanging drop vapour diffusion method, 0.002 ml protein solution with 0.004 ml reservoir solution, usage of 2 reservoir solution variants resulting in 2 differen crystal forms, solution 1 contains 7.5% w/v PEG 8000, 0.1 M NaOAc, pH 5.5, 10 mM MgCl2, 10 mM NaKHPO4, pH 5.9, solution 2 contains 20% w/v PEG 8000, 100 mM HEPES, pH 7.5, 75 mM citrate, and 100 mM MgCl2, suspension over reservoir solution, X-ray diffraction structure determination and analysis at 2,0 and 2.45 A resolution, respectively
Escherichia coli
Metals/Ions
Metals/Ions
Commentary
Organism
Structure
Zn2+
divalent metal ion-dependent enzyme, Zn2+ is bound to the active site of each monomer coordinated by 3 histidine residues from both monomer
Escherichia coli
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
ID
4-(phosphonooxy)threonine + NAD(P)+
Escherichia coli
fourth step of the pyridoxal 5'-phosphate biosynthesis
2-amino-3-oxo-4-phosphonooxybutyrate + NAD(P)H
-
-
?
Organism
Organism
UniProt
Commentary
Textmining
Escherichia coli
P19624
-
-
Purification (Commentary)
Purification (Commentary)
Organism
recombinant His-tagged enzyme from Escherichia coli by nickel affinity chromatography, cleavage by thrombin
Escherichia coli
Reaction
Reaction
Commentary
Organism
Reaction ID
4-phosphooxy-L-threonine + NAD+ = 3-amino-2-oxopropyl phosphate + CO2 + NADH + H+
Asp247 and Asp267 are involved in formation and maintaining of the integrity of the active site
Escherichia coli
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
Substrate Product ID
2-amino-3-oxo-4-phosphonooxybutyrate + H2O
step 2 of the overall reaction
656172
Escherichia coli
3-amino-1-hydroxyacetone 1-phosphate + CO2
i.e. AHAP
-
-
?
4-(phosphonooxy)threonine + NAD(P)+
fourth step of the pyridoxal 5'-phosphate biosynthesis
656172
Escherichia coli
2-amino-3-oxo-4-phosphonooxybutyrate + NAD(P)H
-
-
-
?
4-(phosphonooxy)threonine + NAD(P)+
i.e. 4-hydroxy-L-threonine phosphate or HTP, enzyme strictly requires the phosphate ester form of the substrate, interaction between enzyme and substrate via phosphate group, step 1 of the overall reaction
656172
Escherichia coli
2-amino-3-oxo-4-phosphonooxybutyrate + NAD(P)H
reaction intermediate
-
-
?
Subunits
Subunits
Commentary
Organism
dimer
tightly bound, monomer fold is alpha/beta/alpha divided into 2 subdomains, the active site is located at the dimer interface
Escherichia coli
Synonyms
Synonyms
Commentary
Organism
PdxA
-
Escherichia coli
Cofactor
Cofactor
Commentary
Organism
Structure
NAD(P)+
putative binding site structure
Escherichia coli
Cloned(Commentary) (protein specific)
Commentary
Organism
gene pdxA, expression of the His-tagged enzyme with a thrombin cleavage site in Escherichia coli
Escherichia coli
Cofactor (protein specific)
Cofactor
Commentary
Organism
Structure
NAD(P)+
putative binding site structure
Escherichia coli
Crystallization (Commentary) (protein specific)
Crystallization
Organism
8.1 mg/ml purified recombinant enzyme in complex with substrate 4-(phosphonooxy)threonine and Zn2+ in 20 mM Tris-HCl, pH 8.0, 0.2 M NaCl, 10 mM DTT, 5% w/v glycerol, hanging drop vapour diffusion method, 0.002 ml protein solution with 0.004 ml reservoir solution, usage of 2 reservoir solution variants resulting in 2 differen crystal forms, solution 1 contains 7.5% w/v PEG 8000, 0.1 M NaOAc, pH 5.5, 10 mM MgCl2, 10 mM NaKHPO4, pH 5.9, solution 2 contains 20% w/v PEG 8000, 100 mM HEPES, pH 7.5, 75 mM citrate, and 100 mM MgCl2, suspension over reservoir solution, X-ray diffraction structure determination and analysis at 2,0 and 2.45 A resolution, respectively
Escherichia coli
Metals/Ions (protein specific)
Metals/Ions
Commentary
Organism
Structure
Zn2+
divalent metal ion-dependent enzyme, Zn2+ is bound to the active site of each monomer coordinated by 3 histidine residues from both monomer
Escherichia coli
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
ID
4-(phosphonooxy)threonine + NAD(P)+
Escherichia coli
fourth step of the pyridoxal 5'-phosphate biosynthesis
2-amino-3-oxo-4-phosphonooxybutyrate + NAD(P)H
-
-
?
Purification (Commentary) (protein specific)
Commentary
Organism
recombinant His-tagged enzyme from Escherichia coli by nickel affinity chromatography, cleavage by thrombin
Escherichia coli
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
ID
2-amino-3-oxo-4-phosphonooxybutyrate + H2O
step 2 of the overall reaction
656172
Escherichia coli
3-amino-1-hydroxyacetone 1-phosphate + CO2
i.e. AHAP
-
-
?
4-(phosphonooxy)threonine + NAD(P)+
fourth step of the pyridoxal 5'-phosphate biosynthesis
656172
Escherichia coli
2-amino-3-oxo-4-phosphonooxybutyrate + NAD(P)H
-
-
-
?
4-(phosphonooxy)threonine + NAD(P)+
i.e. 4-hydroxy-L-threonine phosphate or HTP, enzyme strictly requires the phosphate ester form of the substrate, interaction between enzyme and substrate via phosphate group, step 1 of the overall reaction
656172
Escherichia coli
2-amino-3-oxo-4-phosphonooxybutyrate + NAD(P)H
reaction intermediate
-
-
?
Subunits (protein specific)
Subunits
Commentary
Organism
dimer
tightly bound, monomer fold is alpha/beta/alpha divided into 2 subdomains, the active site is located at the dimer interface
Escherichia coli
Other publictions for EC 1.1.1.262
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
Synonyms
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)
654972
Banks
Biosynthesis of vitamin B6: di ...
Escherichia coli
Bioorg. Med. Chem. Lett.
14
1633-16367
2004
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656172
Sivaraman
Crystal structure of Escherich ...
Escherichia coli
J. Biol. Chem.
278
43682-43690
2003
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207962
Laber
Vitamin B6 biosynthesis: forma ...
Escherichia coli
FEBS Lett.
449
45-48
1999
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207963
Cane
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Biosynthesis of vitamin B6: en ...
Escherichia coli
J. Am. Chem. Soc.
121
7722-7723
1999
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207964
Cane
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Biosynthesis of vitamin B6: th ...
Escherichia coli
J. Am. Chem. Soc.
120
1936-1937
1998
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