Computational Mutation Design of Diol Dehydratase: Catalytic Ability toward Glycerol beyond the Wild-Type Enzyme
Computational Mutation Design of Diol Dehydratase: Catalytic Ability toward Glycerol beyond the Wild-Type Enzyme
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DOI：
10.1246/bcsj.20140115
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发表时间：
2014-09-15
影响因子：
4
通讯作者：
Yoshizawa, Kazunari
中科院分区：
文献类型：
--
作者：
Doitomi, Kazuki;Tanaka, Hiromasa;Yoshizawa, Kazunari
基于量子力学/分子力学（QM/MM）计算，对甘油脱水生成3-羟基丙醛过程中二醇脱氢酶活性中心氨基酸残基的催化功能进行了计算突变分析.虽然野生型二醇脱氢酶在脱水过程中受到自杀失活，但突变体Gln 336 Ala和Ser 301 Ala对甘油的失活更具抗性（Yamanishi等人，FEBS 2012，279，793）。在本研究中的突变的影响进行了讨论的基础上的能量分布的两个反应途径的甘油脱水和失活的酶。这两种突变体有效地区分两种可能的结合构象的甘油，GS和GR的构象，其中前者是已知的，主要有助于失活的酶。观察到的突变体的失活的改善的阻力可以解释由甘油和Ser 301的OH基团之间的氢键相互作用，以及甘油和Val 300之间的空间排斥。计算突变分析首先揭示了Val 300在GS和GR构象的区分中的重要作用，这在野生型酶中并不清楚。目前的研究结果将鼓励应用计算突变的方法来优化所需的有机合成酶的合理设计。
A computational mutation analysis based on quantum mechanical/molecular mechanical (QM/MM) calculations is performed for the elucidation of catalytic functions of amino acid residues at the active site of diol dehydratase in the dehydration of glycerol to afford 3-hydroxypropionaldehyde. While the wild-type diol dehydratase is subject to suicide inactivation in the dehydration process, mutants Gln336Ala and Ser301Ala are more resistant to the inactivation by glycerol (Yamanishi et al., FEBS 2012, 279, 793). In the present study the impact of the mutation is discussed on the basis of energy profiles of two reaction pathways for the dehydration of glycerol and the inactivation of the enzyme. Both the mutants efficiently distinguish between two possible binding conformations of glycerol, the GS and GR conformations, where the former is known to mainly contribute to the inactivation of the enzyme. The improved resistance to the inactivation observed for the mutants can be explained by a hydrogen-bonding interaction between an OH group of glycerol and Ser301 as well as steric repulsion between glycerol and Val300. The computational mutation analysis first unveils the vital role of Val300 in the discrimination of the GS and GR conformations, which was not clearly viewed in the wild-type enzyme. The present findings will encourage the application of computational mutation approach to the rational design of enzymes optimized for desired organic synthesis.