Molecular basis of the substrate specificity of the Pd-PTE phosphotriesterase: a combined QM/MM MD and electron density study

The increase of organophosphorus compounds, pesticides and flame-retardants, in wastes is an emerging ecological problem. Bacterial phosphotriesterases are capable for hydrolysis of some of them. We utilize modern molecular modeling tools to study hydrolysis mechanism of organophosphorus compounds with different leaving groups by phosphotriesterase from Pseudomonas diminuta (Pd-PTE). We compute Gibbs energy profiles for enzymes with different cations in the active site: native Zn2+ cations; Co2+ cations that increase the steady-state rate constant. A high-spin state of the cobalt-containing active site catalyzes hydrolysis. Reaction happens with two elementary steps via formation of the pentacoordinated intermediate. For substrates with good leaving groups the reaction proceeds with low energy barriers with both Zn2+ and Co2+ cations in the active site, thus the product release is likely to be a limiting step. For substrates with poor leaving groups, reaction products are destabilized relative to the ES complex that suppresses the reaction. Electron density and geometry analysis of the QM/MM MD trajectories of the intermediate states with all considered compounds allow us to discriminate substrates by their ability to be hydrolyzed by the Pd-PTE. These criteria is can be utilized to predict whether novel organophosphorus compounds can be hydrolyzed by the Pd-PTE.