Pyridoxal 5'-phosphate synthase

 

Escherichia 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 Escherichia 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.

 

Reference Protein and Structure

Sequence
P0AFI7 UniProt (1.4.3.5) IPR000659 (Sequence Homologues) (PDB Homologues)
Biological species
Escherichia coli K-12 (Bacteria) Uniprot
PDB
1g79 - X-RAY STRUCTURE OF ESCHERICHIA COLI PYRIDOXINE 5'-PHOSPHATE OXIDASE COMPLEXED WITH PYRIDOXAL 5'-PHOSPHATE AT 2.0 A RESOLUTION (2.0 Å) PDBe PDBsum 1g79
Catalytic CATH Domains
2.30.110.10 CATHdb (see all for 1g79)
Cofactors
Fmnh2(2-) (1)
Click To Show Structure

Enzyme Reaction (EC:1.4.3.5)

dioxygen
CHEBI:15379ChEBI
+
water
CHEBI:15377ChEBI
+
pyridoxamine 5'-phosphate(1-)
CHEBI:58451ChEBI
→
hydrogen peroxide
CHEBI:16240ChEBI
+
ammonium
CHEBI:28938ChEBI
+
pyridoxal 5'-phosphate(2-)
CHEBI:597326ChEBI
Alternative enzyme names: PMP oxidase, Pyridoxamine 5'-phosphate oxidase, Pyridoxamine phosphate oxidase, Pyridoxaminephosphate oxidase (EC 1.4.3.5: deaminating), Pyridoxine (pyridoxamine) 5'-phosphate oxidase, Pyridoxine (pyridoxamine)phosphate oxidase, Pyridoxol-5'-phosphate:oxygen oxidoreductase (deaminating), Pyridoxamine-phosphate oxidase, PdxH,

Enzyme Mechanism

Introduction

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.

Catalytic Residues Roles

UniProt PDB* (1g79)
Arg197 Arg197A 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. steric role
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

References

  1. di Salvo ML et al. (2003), Biochim Biophys Acta, 1647, 76-82. Structure and mechanism of Escherichia coli pyridoxine 5′-phosphate oxidase. DOI:10.1016/s1570-9639(03)00060-8. PMID:12686112.
  2. Safo MK et al. (2005), Acta Crystallogr D Biol Crystallogr, 61, 599-604. Structure ofEscherichia colipyridoxine 5′-phosphate oxidase in a tetragonal crystal form: insights into the mechanistic pathway of the enzyme. DOI:10.1107/s0907444905005512. PMID:15858270.
  3. di Salvo ML et al. (2002), J Mol Biol, 315, 385-397. Active site structure and stereospecificity of Escherichia coli pyridoxine-5′-phosphate oxidase. DOI:10.1006/jmbi.2001.5254. PMID:11786019.

Step 1.

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Catalytic Residues Roles

Residue Roles
Arg197A steric role

Chemical Components

Step 1.

Contributors

Peter Sarkies, Gemma L. Holliday