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Catalytic Site Atlas

CSA LITERATURE entry for 1g79

E.C. namepyridoxal 5'-phosphate synthase
SpeciesEscherichia coli (Bacteria)
E.C. Number (IntEnz) 1.4.3.5
CSA Homologues of 1g79There are 13 Homologs
CSA Entries With UniProtID P0AFI7
CSA Entries With EC Number 1.4.3.5
PDBe Entry 1g79
PDBSum Entry 1g79
MACiE Entry 1g79

Literature Report

IntroductionE. 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.
MechansimThe 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.
Reaction

Catalytic Sites for 1g79

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
ArgA197197macie:sideChainSteric 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.

Literature References

Notes:
di Salvo ML
Active site structure and stereospecificity of Escherichia coli pyridoxine-5'-phosphate oxidase.
J Mol Biol 2002 315 385-397
PubMed: 11786019
Safo MK
Structure of Escherichia coli pyridoxine 5'-phosphate oxidase in a tetragonal crystal form: insights into the mechanistic pathway of the enzyme.
Acta Crystallogr D Biol Crystallogr 2005 61 599-604
PubMed: 15858270
di Salvo ML
Structure and mechanism of Escherichia coli pyridoxine 5'-phosphate oxidase.
Biochim Biophys Acta 2003 1647 76-82
PubMed: 12686112
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