QM/MM study on the catalytic mechanism of heme-containing aliphatic aldoxime dehydratase

Aliphatic aldoxime dehydratase (Oxd) catalyzes the dehydration of aliphatic aldoximes (R-CH═N-OH) to the corresponding nitriles (R-C≡N). Quantum mechanics/molecular mechanics (QM/MM) calculations are performed to elucidate the catalytic mechanism of the enzyme on the basis of the X-ray crystal structure of the Michaelis complex. On the basis of the calculations, we propose a complete catalytic cycle of Oxd in which the distal histidine (His320) acts as a general acid/base. In the Michaelis complex, the elimination of the hydroxyl group of aldoxime is facilitated by His320 donating a proton to the hydroxyl group in a concerted way, which is the rate-limiting step. The formed intermediate has a ferric heme iron and an unpaired electron on the nitrogen atom of the substrate coupled to a singlet state. The second step is the deprotonation of the β-hydrogen of the substrate by His320 after the substrate rotates about the Fe-N bond for ∼180° to yield the neutral product. In the meantime, the heme iron goes back to ferrous state by a one-electron transfer from the substrate to the ferric heme iron, and His320 goes back to the protonated state to proceed with the following reaction. The functions of the protein environment and the active site residues are also discussed.