The crystal structure and mechanism of orotidine 5 '-monophosphate decarboxylase

The crystal structure of Bacillus subtilis orotidine 5'-monophosphate (OMP) decarboxylase with bound uridine 5'-monophosphate has been determined by m ultiple wavelength anomalous diffraction phasing techniques and refined to an R-factor of 19.3% at 2.4 Angstrom resolution. OMP decarboxylase is a dim er of two identical subunits. Each monomer consists of a triosephosphate is omerase barrel and contains an active site that is located across one end o f the barrel and near the dimer interface. For each active site, most of th e residues are contributed by one monomer with a few residues contributed f rom the adjacent monomer, The most highly conserved residues are located in the active site and suggest a novel catalytic mechanism for decarboxylatio n that is different from any previously proposed OMP decarboxylase mechanis m, The uridine 5'-monophosphate molecule is bound to the active site such t hat the phosphate group is most exposed and the C5-C6 edge of the pyrimidin e base is most buried. In the proposed catalytic mechanism, the ground stat e of the substrate is destabilized by electrostatic repulsion between the c arboxylate of the substrate and the carboxylate of Asp60. This repulsion is reduced in the transition state by shifting negative charge from the carbo xylate to C6 of the pyrimidine, which is close to the protonated amine of L ys62, We propose that the decarboxylation of OMP proceeds by an electrophil ic substitution mechanism in which decarboxylation and carbon-carbon bond p rotonation by Lys62 occur in a concerted reaction.