Dock & design: engineering specificity for an alternative pimaradiene outcome with the ent-kaurene synthase from Bradyrhizobium japonicum.

Abstract

The complexity of the reactions catalyzed by terpene synthases has hindered enzymatic engineering. In most cases such efforts result in non-specific product outcome, with the targeted compound being produced alongside others, hindering further use. Previous work with the structurally characterized ent-kaurene synthase from Bradyrhizobium japonicum (BjKS) identified a serine for alanine substitution (A167S) that led to premature deprotonation, yielding a pair of ent-pimaradiene double-bond isomers, with retrospective analysis by the TerDockin computational approach indicating that the introduced hydroxyl acts as a catalytic base for both. Here this route to 'short-circuiting' the BjKS catalyzed reaction for ent-pimaradiene production was further explored, with prospective application of TerDockin, via design-build-test cycles, enabling specific production of a novel pimaradiene isomer via introduction of a water molecule as the catalytic base. The resulting mutants, BjKS:F72S and particularly BjKS:F72Y/Y280S specifically yield the targeted ent-pimara-8,15-diene with reasonable catalytic efficiency, demonstrating the applicability of this computationally inexpensive approach to engineering terpene synthase product outcomes.