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Literature summary extracted from

  • Sivaraman, J.; Li, Y.; Banks, J.; Cane, D.E.; Matte, A.; Cygler, M.
    Crystal structure of Escherichia coli PdxA, an enzyme involved in the pyridoxal phosphate biosynthesis pathway (2003), J. Biol. Chem., 278, 43682-43690.
    View publication on PubMed

Cloned(Commentary)

EC Number Cloned (Comment) Organism
1.1.1.262 gene pdxA, expression of the His-tagged enzyme with a thrombin cleavage site in Escherichia coli Escherichia coli

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
1.1.1.262 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

EC Number Metals/Ions Comment Organism Structure
1.1.1.262 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)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
1.1.1.262 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

EC Number Organism UniProt Comment Textmining
1.1.1.262 Escherichia coli P19624
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
1.1.1.262 recombinant His-tagged enzyme from Escherichia coli by nickel affinity chromatography, cleavage by thrombin Escherichia coli

Reaction

EC Number Reaction Comment Organism Reaction ID
1.1.1.262 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
a

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
1.1.1.262 2-amino-3-oxo-4-phosphonooxybutyrate + H2O step 2 of the overall reaction Escherichia coli 3-amino-1-hydroxyacetone 1-phosphate + CO2 i.e. AHAP ?
1.1.1.262 4-(phosphonooxy)threonine + NAD(P)+ fourth step of the pyridoxal 5'-phosphate biosynthesis Escherichia coli 2-amino-3-oxo-4-phosphonooxybutyrate + NAD(P)H
-
 ?
1.1.1.262 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 Escherichia coli 2-amino-3-oxo-4-phosphonooxybutyrate + NAD(P)H reaction intermediate ?

Subunits

EC Number Subunits Comment Organism
1.1.1.262 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

EC Number Synonyms Comment Organism
1.1.1.262 PdxA
-
 Escherichia coli

Cofactor

EC Number Cofactor Comment Organism Structure
1.1.1.262 NAD(P)+ putative binding site structure Escherichia coli