Density Functional Calculations on Class III Ribonucleotide Reductase: Substrate Reaction Mechanism with Two Formates

The substrate reaction mechanism for class III anaerobic ribonucleotide reductase has been studied by density functional theory on a charged system involving two formates. Previous studies on small charge-neutral models yielded a rate-limiting barrier of 19.9 kcal/mol, compared to the experimental value of approximately 17 kcal/mol. The current study involves a larger model with four amino acid residues (Cys290, Asn78, Cys79, and Asn311) present in the active site, in addition to the two formates and the substrate model. All steps starting from the Cys290 radical have been considered here in contrast to only the rate-limiting part considered before. The rate-limiting step is again found to be the oxidation of formate to carbon dioxide. The highest barrier is now calculated to be as low as 11.7 kcal/mol, suggesting that a step outside of the substrate reactions is rate limiting. The model used for the substrate is a simple ribonucleotide ring, but preliminary results using the full substrate model (with a guanine base and a triphosphate chain) are also reported. These calculations show an overall agreement with the smaller substrate model calculations. The reaction mechanism presented here is highly consistent with existing experimental information.