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,ACS Catalysis

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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
ACS Catalysis ( IF 11.3 ) Pub Date : 2018-04-04 00:00:00 , DOI: 10.1021/acscatal.8b00006
Yuan Zhao ₁ , Nai She ₁ , Yiming Ma ₂ , Chaojie Wang ₁ , Zexing Cao ₃

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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.

中文翻译：

N-乙酰己糖胺1-激酶中酶催化的描述：两种镁离子辅助的GlcNAc磷酸化的协同机制，底物识别后盖基序的柔韧性和水辅助的GlcNAc-1-P释放

所述Ñ -acetylhexosamine 1激酶（NahK）是端基异构体的激酶作用于葡糖型衬底，其催化的GlcNAc或半乳糖胺的磷酸化在与ATP异头C1的位置，在双歧杆菌代谢途径和生物合成发挥关键作用的典型例子糖1磷酸盐和寡糖。在本文中，通过使用最先进的从头开始的QM / MM MD和MM MD模拟，探索了一维和二维自由能曲线来描述催化过程。公认的协同机制可以将磷酸基团和质子传递到产物ADP和GlcNAc-1-P中，其自由能垒约为7.0 kcal / mol。两个Mg ²⁺辅助化学反应离子在酶促过程中具有六个配位结构。Mg ²⁺桥接ATP的β-γ磷酸的缺乏可能会改变催化机理，并带来更高的自由能垒。GlcNAc-1-P的质子化是有益的，因为它消除了Mg ²⁺离子的结合。水辅助的GlcNAc-1-P从Mg ^2+的结合中裂解至少需要约9.4 kcal / mol，这意味着在化学反应步骤中断开π-π键可能不是整个酶促过程中的限速步骤。在GlcNAc结合后，观察到强烈的放热现象和盖基序的开-闭结构变化。放热趋势强烈取决于配体周围氢键网络的数量和质量。

更新日期：2018-04-04

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