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Catalytic Site Atlas Version 2.2.12
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CSA entry for 1g79
Original Entry
Title:
Oxidoreductase
Compound:
Pyridoxine 5'-phosphate oxidase
Mutant:
No
UniProt/Swiss-Prot:
P28225-PDXH_ECOLI
EC Class:
1.4.3.5
Other CSA Entries:
Overview of all sites for 1g79
Homologues of 1g79
Entries for UniProt/Swiss-Prot: P28225
Entries for EC: 1.4.3.5
Other Databases:
PDB entry: 1g79
PDBsum entry: 1g79
UniProt/Swiss-Prot: P28225
IntEnz entry: 1.4.3.5
Literature Report:
Introduction:
E. coli pyridoxine 5'-phosphate oxidase is the enzyme catalysing the final step in the synthesis of pyridoxal 5'-phosphate, a vital cofactor in many metabolic processes including amino acid metabolism. This means that the synthetic pathway is of great importance to the survival of the bacteria. The enzyme is also present in higher organisms, and the E. coli form is expected to show significant sequence and structural homology to the mammalian form. Of particular interest is the second binding site of PLP which protects the product of the reaction from release into the cell so it can be transferred directly onto the enzymes that require it.
Mechanism:
The reaction involves the oxidation of PNP to PLP using the cofactor FMN. It proceeds through hydride transfer from the 4'Carbon to the N7 of FMN, with steric strain from Arg 197 acting to place the substrate and cofactor in correct orientation for this to occur. This forms an electron deficient transition state; the oxygen lone pair then forms a bond to the 4'Carbon to result in the product.
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Found by:
Literature reference 

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
250 0
Substrate
Acts as a recipient for hydride transfer from PNP, thus is an electrophile. This means that it accepts electrons, so is reduced, allowing oxidation of the PNP to PLP.
Evidence from paper Evidence concerns Evidence type
PubMed ID 11786019 Current protein Ligand is essential for catalysis
PubMed ID 15858270 Current protein Residue is positioned appropriately

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
ARGA 197 197Sidechain
Steric strainCofactor
Steric strain between the Arg 197 and the FMN forces the FMN into position where it can accept a hydride ion from the PNP substrate, thus allowing the formation of PLP.
Evidence from paper Evidence concerns Evidence type
PubMed ID 12686112 Current protein Mutagenesis of residue
PubMed ID 15858270 Current protein Residue is positioned appropriately (ligand position known)
References:
1
Active site structure and stereospecificity of Escherichia coli pyridoxine-5'-phosphate oxidase.
M. L. di Salvo and T. P. Ko and F. N. Musayev and S. Raboni and V. Schirch and M. K. Safo
J Mol Biol 315, (3) 385-97, (2002).
11786019
2
A preliminary time-of-flight neutron diffraction study on amicyanin from Paracoccus denitrificans.
N. Sukumar and P. Langan and F. S. Mathews and L. H. Jones and P. Thiyagarajan and B. P. Schoenborn and V. L. Davidson
Acta Crystallogr D Biol Crystallogr 61, (Pt 5) 640-2, (2005).
15858270
3
Structure and mechanism of Escherichia coli pyridoxine 5'-phosphate oxidase.
M. L. di Salvo and M. K. Safo and F. N. Musayev and F. Bossa and V. Schirch
Biochim Biophys Acta 1647, (1-2) 76-82, (2003).
12686112
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