Human Fatty Acid Synthase: A Computational Study of the Transfer of the Acyl Moieties from MAT to the ACP Domain

Abstract

Human Fatty Acid Synthase (hFAS) is a multidomain enzyme responsible for the biosynthesis of saturated fatty acids, which are crucial for numerous biological processes. During the biosynthetic reaction, hFAS incorporates acetyl and malonyl moieties through the action of its malonyl‐acetyl transferase (MAT) domain. These precursor molecules are transferred from CoA to the acyl‐carrier protein (ACP) domain by a two‐stage ping‐pong catalytic mechanism. The first stage, during which the acyl moieties are relocated from CoA to the MAT domain, has been elucidated in a previous work of ours. In this study, we employ QM/MM calculations at the DLPNO‐CCSD(T)/CBS:AMBER level of theory to understand the catalytic machinery behind the transfer of the acyl moieties from MAT to the ACP domain. The results show that the acyl transfer to the ACP's phosphopantetheine (PNS) occurs in two sequential events: Step 3) asynchronous concerted reaction that combines the deprotonation of the PNS's thiol group and the nucleophilic attack on the acyl‐Ser581 ester carbon; Step 4) tetrahedral intermediate breakdown and regeneration of the catalytic Ser581/His683 dyad. The energy barriers of these two steps are inferior to those reported for the first catalytic stage, suggesting that the rate‐limiting step of the MAT mechanism lies on Stage 1, particularly on the concerted nucleophilic attack that starts the reaction. The oxyanion hole, formed by the backbone amines of Met499 and Leu582, was reported to transiently stabilize the tetrahedral intermediate and to play a favorable catalytic effect on the overall MAT reaction, particularly through the reduction of the energetic span. The knowledge gathered in this work complements previous experimental and theoretical studies and instigates further investigations that explore the therapeutic potential of hFAS.

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“…The computational analysis identified the first step as rate-limiting for the full MAT-mediated reaction. [135] Type I and II ATs from FASs and PKSs show similar folds. [3,41,69,99,136,137] They comprise a core domain with an ↵/ -hydrolase-like structure and a smaller subdomain with a ferrodoxin-like structure (Fig.…”

“…[41] Recently, P. Paiva and co-workers analyzed the reactions mediated by the human MAT in mechanistic detail using quantum mechanics/molecular mechanics (QM/MM) calculations. [134,135] They showed that both steps, the AT-loading ping and the ACP-loading pong step, occur in two sequential steps. The first step consists of the concerted deprotonation of Ser581 by His683 and the nuceophilic attack of the substrate thioester carbonyl carbon by the deprotonated Ser581, leading to a tetrahedral intermediate.…”

“…The third step, the first step of the pong step, consists of the concerted deprotonation of the holo-ACP thiol group by His683 and the nucleophilic attack of the MAT-bound substrate carbonyl carbon by the deprotonated thiol group. [135] The resulting tetrahedral intermediate is stabilized by the oxyanion hole. The fourth step is the breakdown of the intermediate and the deprotonation of the protonated His683 by the MAT active site Ser581 yielding acyl-loaded ACP.…”