title: Quantum and classical simulations of orotidine monophosphate decarboxylase: support for a direct decarboxylation mechanism.
abstract: Orotidine 5'-monophosphate (OMP) decarboxylase (ODCase) catalyzes the decarboxylation of OMP to uridine 5'-monophosphate (UMP). Numerous studies of this reaction have suggested a plethora of mechanisms including covalent addition, ylide or carbene formation, and concerted or stepwise protonation. Recent experiments and simulations present strong evidence for a direct decarboxylation mechanism, although direct comparison between experiment and theory is still lacking. In the current work we present hybrid quantum mechanics-molecular mechanics simulations that address the detailed decarboxylation mechanisms for OMP and 5-fluoro-OMP by ODCase. Multidimensional potentials of mean force are computed as functions of structural progress coordinates for the Methanobacterium thermoautotrophicum ODCase reaction: the decarboxylation reaction coordinate, an orbital rehybridization coordinate, and the proton transfer coordinate between Lys72 and the substrate. The computed free energy profiles are in accord with the available experimental data. To facilitate further direct comparison with experiment, we compute the kinetic isotope effects (KIEs) for the enzyme-catalyzed reactions using a mass-perturbation-based path-integral method. The computed KIE provide further support for a direct decarboxylation mechanism. In agreement with experiment, the data suggest a role for Lys72 in stabilizing the transition state in the catalysis of OMP and, to a somewhat lesser extent, in 5-fluoro-OMP.
authors.affiliation: Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel.
authors.forename: Alexandra
authors.initials: A
authors.lastname: Vardi-Kilshtain
authors.forename: Dvir
authors.initials: D
authors.lastname: Doron
authors.forename: Dan Thomas
authors.initials: DT
authors.lastname: Major
mesh_terms: D003198:Computer Simulation; D018360:Crystallography, X-Ray; D003653:Decarboxylation; D017014:Methanobacterium / Q000201:enzymology; D009964:Orotidine-5'-Phosphate Decarboxylase / Q000737:chemistry* / Q000378:metabolism* / Q000493:pharmacokinetics; D011789:Quantum Theory
chemical_list: D009964:Orotidine-5'-Phosphate Decarboxylase