A 5000-Fold Increase in the Specificity of a Bacterial Phosphotriesterase for Malathion through Combinatorial Active Site Mutagenesis

Phosphotriesterases (PTEs) have been isolated from a range of bacterial species, including Agrobcaterium radiobacter (PTE(Ar)), and are efficient enzymes with broad substrate ranges. The turnover rate of PTE(Ar) for the common organophosphorous insecticide malathion is lower than expected based on its physical properties; principally the pk(a) of its leaving group. In this study, we rationalise the turnover rate of PTE(Ar) for malathion using computational docking of the substrate into a high resolution crystal structure of the enzyme, suggesting that malathion is too large for the PTE(Ar) binding pocket. Protein engineering through combinatorial active site saturation testing (CASTing) was then used to increase the rate of malathion turnover. Variants from a CASTing library in which Ser308 and Tyr309 were mutated yielded variants with increased activity towards malathion. The most active PTE(Ar) variant carried Ser308Leu and Tyr309Ala substitutions, which resulted in a ca. 5000-fold increase in k (cat)/K (M) for malathion. X-ray crystal structures for the PTE(Ar) Ser308Leu\Tyr309Ala variant demonstrate that the access to the binding pocket was enhanced by the replacement of the bulky Tyr309 residue with the smaller alanine residue.