A significant role of Arg41 residue in the enzymatic reaction of haloacid dehalogenase L-DEX YL studied by QM/MM method
A significant role of Arg41 residue in the enzymatic reaction of haloacid dehalogenase L-DEX YL studied by QM/MM method
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DOI：
10.1016/j.molcatb.2014.09.006
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发表时间：
2014-12-01
影响因子：
--
通讯作者：
Tanaka, Shigenori
中科院分区：
文献类型：
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作者：
Kondo, hirotaka;Nakamura, Takashi;Tanaka, Shigenori
L-2-卤酸脱卤酶（L-DEX）是一类降解L-2-氯丙酸（L-CPA）等环境污染物的酶家族。这种酶特异性地从L-2-卤代酸产生D-2-羟基酸，并且迄今为止，已经提出一些残基在这种酶促反应中是重要的。本文采用量子力学/分子力学方法对假单胞菌YL（L-DEX YL）2-CPA复合物进行了研究，以阐明该酶促反应的过渡态结构和能量分布。使用ONIOM（PM 3：Amber）方法的QM/MM模拟显示，脱卤反应的活化能为约9.0 kcal/mol，并且酯中间体形成步骤中最重要的残基之一是Arg 41，发现与不存在Arg 41的情况相比，Arg 41使活化能降低约40 kcal/mol。另一方面，Arg 41的这种稳定作用被Asnl 77的存在显著抵消。在Arg 41处突变的酶的模拟表明，在Arg 41位置附近具有正电荷的突变体也将允许脱卤反应。具体地说，我们的模拟表明，Arg 41的高赖氨酸（homK）突变体（与赖氨酸相比，其在侧链中含有多一个亚甲基）可能与野生型酶一样具有活性。从氯离子到受体正电荷位置的距离似乎决定了活化能。(C)2014爱思唯尔有限公司版权所有。
L-2-Haloacid dehalogenase (L-DEX) is one of a family of enzymes that decompose a variety of environmental pollutants such as L-2-chloropropionate (L-2-CPA). This enzyme specifically produces a D-2-hydroxy acid from a L-2-haloacid, and, to date, some residues have been suggested as important in this enzymatic reaction. Here, quantum-mechanical (QM)/molecular-mechanical (MM) calculations for the L-DEX from Pseudomonas sp. YL (L-DEX YL) 2-CPA complex were performed to elucidate the structure of transition state and the energy profile in this enzymatic reaction. QM/MM simulations using the ONIOM (PM3:Amber) method revealed that the activation energy of dehalogenation reaction was around 9.0 kcal/mol and that one of the most important residues in the ester intermediate formation step was Arg41, which was found to decrease the activation energy by about 40 kcal/mol compared to the case of its absence. On the other hand, this stabilization effect by Arg41 was significantly counterbalanced by the presence of Asnl 77. Simulations of enzymes mutated at Arg41 indicated that mutants possessing a positive charge near the Arg41 position would allow the dehalogenation reaction as well. Specifically, it was suggested by our simulations that homolysine (homK) mutant of Arg41, which contains one more methylene group in the side chain compared to lysine, could be active as well as the wild-type enzyme. The distance from the chloride ion to the position of the positive charge of the acceptor seems to dictate the activation energy. (C) 2014 Elsevier B.V. All rights reserved.