Credit: © 2010 ACS

Structural similarity and related substrate promiscuity are tell-tale signs of evolutionary links between enzymes. The enzymes alkaline phosphatase and nucleotide pyrophosphatase/phosphodiesterase (NPP) share such links. Their active sites share many similarities but alkaline phosphatase primarily catalyses phosphate monoester hydrolysis and shows secondary activity for the hydrolysis of diesters, whereas NPP, although also catalysing both processes, does so with the opposite activity. Detailed understanding of their mechanisms of action could help understand their evolutionary changes since they deviated from a common ancestor.

Now, a team of chemists from Spain led by Iñaki Tuñón and Vincent Moliner have carried out a theoretical study1 on the reaction mechanisms of phosphodiester hydrolysis, either catalysed by NPP or uncatalysed in aqueous solution, to understand environmental effects. Such reactions can occur through mechanisms that range from an SN1-like dissociative reaction (where the leaving group detaches before nucleophillic attack) to an associative reaction (where no bond breaking occurs as the nucelophile–phosphorus bond forms).

Tuñón, Moliner and colleagues investigated the energetics and transition state structures of both the catalysed and uncatalysed reactions using hybrid quantum mechanics/molecular mechanics methods. By examining the lengths of the bonds in the transition states between both the nucleophile and phosphorus and the leaving group and phosphorus, they found that the catalysed reaction proceeds through a dissociative mechanism, whereas the uncatalysed reaction proceeds through an associative one. The electrostatics of the NPP active site stabilize dissociative transition-state structures, causing the observed mechanistic differences and leading to the suggestion that the related enzymes of this family may have evolved to stabilize substrates in this way.