Nylon-Oligomer Hydrolase Promoting Cleavage Reactions in Unnatural Amide Compounds
Nylon-Oligomer Hydrolase Promoting Cleavage Reactions in Unnatural Amide Compounds
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尼龙低聚物水解酶促进非天然酰胺化合物中的裂解反应
DOI：
10.1021/jz500323y
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发表时间：
2014
期刊：
影响因子：
--
通讯作者：
and Yasuteru Shigeta
中科院分区：
文献类型：
--
作者：
Katsumasa Kamiya;Takeshi Baba;Mauro Boero;Toru Matsui;Seiji Negoro;and Yasuteru Shigeta
6-氨基己酸二聚体水解酶是一种具有β-内酰胺酶折叠的尼龙-6副产物降解酶，其活性部位具有Ser112/Lys115/Tyr215催化三联体，类似于青霉素识别丝氨酸反应性水解酶家族的催化三联体，但包含一个独特的Tyr170残基。通过反应量子力学/分子力学(QM/MM)方法，我们研究了其催化机理和相关的功能/结构特性。与其他肽酶不同的是，我们发现Tyr170参与酶-底物相互作用是底物结合状态结构变化的原因。通过四面体中间体的酰化反应是限速步骤，其自由能垒为∼21千卡/摩尔，由催化三联体Ser112、Lys115和Tyr215驱动，分别作为亲核剂、总碱和总酸。Tyr170与这个三联体的功能相互作用导致四面体中间体的有效破坏，促进了有利于质子从总酸中给出的底物的构象变化。
The active site of 6-aminohexanoate-dimer hydrolase, a nylon-6 byproduct-degrading enzyme with a β-lactamase fold, possesses a Ser112/Lys115/Tyr215 catalytic triad similar to the one of penicillin-recognizing family of serine-reactive hydrolases but includes a unique Tyr170 residue. By using a reactive quantum mechanics/molecular mechanics (QM/MM) approach, we work out its catalytic mechanism and related functional/structural specificities. At variance with other peptidases, we show that the involvement of Tyr170 in the enzyme–substrate interactions is responsible for a structural variation in the substrate-binding state. The acylation via a tetrahedral intermediate is the rate-limiting step, with a free-energy barrier of ∼21 kcal/mol, driven by the catalytic triad Ser112, Lys115, and Tyr215, acting as a nucleophile, general base, and general acid, respectively. The functional interaction of Tyr170 with this triad leads to an efficient disruption of the tetrahedral intermediate, promoting a conformational change of the substrate favorable for proton donation from the general acid.