Transimination Reaction at the Active Site of Aspartate Aminotransferase: A Proton Hopping Mechanism through Pyridoxal 5′-Phosphate,ACS Catalysis

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Transimination Reaction at the Active Site of Aspartate Aminotransferase: A Proton Hopping Mechanism through Pyridoxal 5′-Phosphate
ACS Catalysis ( IF 11.3 ) Pub Date : 2019-05-30 00:00:00 , DOI: 10.1021/acscatal.9b00834
Kumari Soniya ₁ , Shalini Awasthi ₁ , Nisanth N. Nair ₁ , Amalendu Chandra ₁

Affiliation

The transimination reaction involves conversion of an internal aldimine involving pyridoxal 5′-phosphate (PLP) and an enzyme to an external aldimine involving PLP and a substrate amino acid and it constitutes an essential step in many biological processes catalyzed by PLP-dependent enzymes. We have investigated the free energy landscape and mechanistic pathways of the transimination process at the active site of aspartate aminotransferase by means of hybrid quantum–classical molecular dynamics simulations combined with various enhanced sampling techniques. It is found that, after a geminal diamine is formed in the first step of the process, the reaction proceeds through a path where a proton from the amine nitrogen of the substrate amino acid is transferred first to the phenolic oxygen of the PLP ring, and from there, it is transferred to the imine nitrogen of the active site lysine in the next step of the reaction. Both of these proton transfer events are found to be assisted by relative rotation of the PLP ring which brings the phenolic oxygen of PLP closer to the amine and imine nitrogens of the substrate and lysine, respectively. The transfer of the proton from the phenolic oxygen of PLP to the active site lysine residue is found to be the rate-determining step with an effective barrier of only 4 kcal/mol. Neither any direct proton transfer from lysine to the substrate nor any indirect proton transfer involving any active site residue or water is found.

中文翻译：

天冬氨酸转氨酶活性位点的转氨反应：通过吡P醛5'-磷酸的质子跳跃机制。

氨基转移反应包括将涉及吡咯醛5'-磷酸（PLP）的内部醛亚胺和一种酶转化为涉及PLP和底物氨基酸的外部醛亚胺，它构成了许多由PLP依赖性酶催化的生物学过程中的重要步骤。我们研究了天冬氨酸转氨酶活性位点上的转移过程中自由能态势和机制途径，方法是通过混合经典的量子经典分子动力学模拟和各种增强的采样技术。已发现，在该方法的第一步中形成双链双胺之后，反应通过一条路径进行，在该路径中，来自底物氨基酸的胺氮的质子首先被转移至PLP环的酚氧，并且从那里，在下一步反应中，将其转移到活性位点赖氨酸的亚胺氮上。发现这两个质子转移事件均通过PLP环的相对旋转来辅助，这使PLP的酚氧分别更接近底物和赖氨酸的胺和亚胺氮。发现质子从PLP的酚氧到活性位点赖氨酸残基的转移是确定速率的步骤，有效屏障仅为4kcal / mol。既没有发现任何从赖氨酸到底物的直接质子转移，也没有发现涉及任何活性位点残基或水的任何间接质子转移。发现这两个质子转移事件均通过PLP环的相对旋转来辅助，这使PLP的酚氧分别更接近底物和赖氨酸的胺和亚胺氮。发现质子从PLP的酚氧到活性位点赖氨酸残基的转移是决定速率的步骤，有效屏障仅为4kcal / mol。既没有发现任何从赖氨酸到底物的直接质子转移，也没有发现涉及任何活性位点残基或水的任何间接质子转移。发现这两个质子转移事件均通过PLP环的相对旋转来辅助，这使PLP的酚氧分别更接近底物和赖氨酸的胺和亚胺氮。发现质子从PLP的酚氧到活性位点赖氨酸残基的转移是确定速率的步骤，有效屏障仅为4kcal / mol。既没有发现任何从赖氨酸到底物的直接质子转移，也没有发现涉及任何活性位点残基或水的任何间接质子转移。

更新日期：2019-05-30

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