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A Description of Enzymatic Catalysis in N‑Acetylhexosamine 1‑Kinase: Concerted Mechanism of Two-Magnesium-Ion-Assisted GlcNAc Phosphorylation, Flexibility Behavior of Lid Motif upon Substrate Recognition, and Water-Assisted GlcNAc-1‑P Release

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journal contribution
posted on 04.04.2018, 00:00 by Yuan Zhao, Nai She, Yiming Ma, Chaojie Wang, Zexing Cao
The N-acetylhexosamine 1-kinase (NahK) is the typical example of anomeric kinases acting on gluco-type substrate, which catalyzes the phosphorylation of GlcNAc or GalNAc at anomeric C1 position with ATP, playing a crucial role in bifidobacteria metabolic pathway and biosynthesis of sugar 1-phosphates and oligosaccharides. Herein, by using state-of-the art ab initio QM/MM MD and MM MD simulations, one-dimensional and two-dimensional free energy profiles to descript catalytic process have been explored. A concerted mechanism has been recognized for the delivery of phosphate group and proton to product ADP and GlcNAc-1-P with the free energy barrier of ∼7.0 kcal/mol. The chemical reaction is assisted by two Mg2+ ions with a standing six coordination structure during the enzymatic process. The deficiency of Mg2+ bridging β–γ phosphates of ATP may alter the catalytic mechanism and brings higher free energy barriers. The protonation of GlcNAc-1-P is beneficial because its eliminates the Mg2+ ion binding. The water-assisted GlcNAc-1-P cleavage from binding of Mg2+ requires ∼9.4 kcal/mol at least, which means that the π–π bond breaking in the chemical reaction step is probably not the rate-limiting step in the entire enzymatic process. A strongly exothermic phenomenon and an open-closed structural change of lid motif have been observed upon the GlcNAc binding. The exothermic trend is strongly dependent on the quantity and quality of the hydrogen bond network around the ligand.