Insights into the Chemical Reactivity in Acetyl-CoA Synthase

The biological synthesis of acetyl-coenzyme A (acetyl-CoA), catalyzed by acetyl-CoA synthase (ACS), is of biological significance and chemical interest acting as a source of energy and carbon. The catalyst contains an unusual hexa-metal cluster with two nickel ions and a [Fe₄S₄] cluster. DFT calculations have been performed to investigate the ACS reaction mechanism starting from three different oxidation states (+2, +1, and 0) of Ni_p, the nickel proximal to [Fe₄S₄]. The results indicate that the ACS reaction proceeds first through a methyl radical transfer from cobalamin (Cbl) to Ni_p randomly accompanying with the CO binding. After that, C-C bond formation occurs between the Ni_p-bound methyl and CO, forming Ni_p-acetyl. The substrate CoA-S^- then binds to Ni_p, allowing C-S bond formation between the Ni_p-bound acetyl and CoA-S^-. Methyl transfer is rate-limiting with a barrier of ∼14 kcal/mol, which does not depend on the presence or absence of CO. Both the Ni_p²⁺ and Ni_p¹⁺ states are chemically capable of catalyzing the ACS reaction independent of the state (+2 or +1) of the [Fe₄S₄] cluster. The [Fe₄S₄] cluster is not found to affect the steps of methyl transfer and C-C bond formation but may be involved in the C-S bond formation depending on the detailed mechanism chosen. An ACS active site containing a Ni_p(0) state could not be obtained. Optimizations always led to a Ni_p¹⁺ state coupled with [Fe₄S₄]¹⁺. The calculations show a comparable activity for Ni_p¹⁺/[Fe₄S₄]¹⁺, Ni_p¹⁺/[Fe₄S₄]²⁺, and Ni_p²⁺/[Fe₄S₄]²⁺. The results here give significant insights into the chemistry of the important ACS reaction.