Structure and inhibition of orotidine 5'-monophosphate decarboxylase from Plasmodium falciparum

Biochemistry. 2008 Mar 25;47(12):3842-54. doi: 10.1021/bi702390k. Epub 2008 Feb 28.

Abstract

Orotidine 5'-monophosphate (OMP) decarboxylase from Plasmodium falciparum (PfODCase, EC 4.1.1.23) has been overexpressed, purified, subjected to kinetic and biochemical analysis, and crystallized. The native enzyme is a homodimer with a subunit molecular mass of 38 kDa. The saturation curve for OMP as a substrate conformed to Michaelis-Menten kinetics with K m = 350 +/- 60 nM and V max = 2.70 +/- 0.10 micromol/min/mg protein. Inhibition patterns for nucleoside 5'-monophosphate analogues were linear competitive with respect to OMP with a decreasing potency of inhibition of PfODCase in the order: pyrazofurin 5'-monophosphate ( K i = 3.6 +/- 0.7 nM) > xanthosine 5'-monophosphate (XMP, K i = 4.4 +/- 0.7 nM) > 6-azauridine 5'-monophosphate (AzaUMP, K i = 12 +/- 3 nM) > allopurinol-3-riboside 5'-monophosphate ( K i = 240 +/- 20 nM). XMP is an approximately 150-fold more potent inhibitor of PfODCase compared with the human enzyme. The structure of PfODCase was solved in the absence of ligand and displays a classic TIM-barrel fold characteristic of the enzyme. Both the phosphate-binding loop and the betaalpha5-loop have conformational flexibility, which may be associated with substrate capture and product release along the reaction pathway.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Binding Sites
  • Crystallization
  • Crystallography, X-Ray
  • Dimerization
  • Escherichia coli / metabolism
  • Humans
  • Kinetics
  • Models, Molecular
  • Molecular Weight
  • Orotidine-5'-Phosphate Decarboxylase / antagonists & inhibitors*
  • Orotidine-5'-Phosphate Decarboxylase / chemistry*
  • Plasmodium falciparum / enzymology
  • Recombinant Proteins / antagonists & inhibitors
  • Recombinant Proteins / chemistry
  • Ribonucleotides / pharmacology
  • Species Specificity
  • Uridine Monophosphate / analogs & derivatives
  • Uridine Monophosphate / pharmacology

Substances

  • Recombinant Proteins
  • Ribonucleotides
  • allopurinol riboside 5'-monophosphate
  • 1-(5'-phospho-beta-D-ribofuranosyl)barbituric acid
  • Uridine Monophosphate
  • Orotidine-5'-Phosphate Decarboxylase

Associated data

  • PDB/2F84
  • PDB/2Q8L
  • PDB/2ZCG