Computational Investigation of the PazB-Catalyzed Cyclopropanation Reaction: Role of Active-Site Water in S_N2 Mechanism

We investigated the mechanism of PazB, a PLP-dependent enzyme involved in the biosynthesis of the cyclopropyl group in Pazamine, using DFT calculations, classical MD, and QM(GFN2-xTB)/MM/MD simulations. We found that two active-site water molecules selectively stabilize the rate-determining SN2 transition state over the reactant and product states by forming hydrogen bonds with the leaving chloride. Our studies reveal the structure and function of active site water molecules. Additionally, we found that PazB significantly enhanced the population of the reactive conformation, increasing its population from 29.6% in water to 92.4% in the enzyme’s active site.