Computational Exploration of How Enzyme XimE Converts Natural S‑Epoxide to Pyran and R‑Epoxide to Furan

Enzymes have long been characterized for their specificity and efficiency in catalyzing one substrate to one product. However, a SnoaL-like cyclase (XimE) that was originally discovered in xiamenmycin biosynthesis not only catalyzes the pyran-forming cyclization of the natural epoxide metabolites generated by XimD, but also enhances the furan-forming cyclization of the unnatural epoxide isomer. We have investigated and elucidated the reaction mechanism for this potentially unique substrate control of enzyme function. We explored the plausible pathways occurring at the hydrophobic active sites with a combination of theozyme (a small cluster model) calculations, pre- and post-reaction molecular dynamics (MD) simulations, ONIOM­(ωB97X-D/6-31G­(d):AMBER) transition state searching, and QM/SCRF­(VS) dielectric constant scanning. Both the pyran and furan pathways share similar general acid–base catalytic mechanisms in which E136 and H102 act as proton donor and acceptor, respectively; pyran is generated by a fused-TS that proceeds via a general-acid-catalyzed mode, while furan is generated via a spiro-TS catalyzed by a general-base-catalyzed mode. The relative energies of the four possible transition states were found by ONIOM calculations to be Fused-S ≲ Spiro-S Spiro-R Fused-R. The regiochemical preference of the XimE-catalyzed pyran formation from S-epoxide and furan formation from R-epoxide stems from the induced-fit interaction between the enzyme and its transition states, which carries over to products. XimE apparently evolved along with the natural S-epoxide substrate generated by the upstream XimD epoxidase, and accidentally is also able to catalyze a different reaction of the enantiomeric R-epoxide via a similar catalytic mechanism.