Theoretical study on substrate recognition and catalytic mechanisms of gephyronic acid dehydratase DH1
Theoretical study on substrate recognition and catalytic mechanisms of gephyronic acid dehydratase DH1
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吉菲膦酸脱水酶DH1底物识别及催化机制的理论研究
DOI：
10.1039/d0cy01776k
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发表时间：
2021
影响因子：
5
通讯作者：
Shi Ting
中科院分区：
文献类型：
--
作者：
Liu Lei;Yu Qian;Zhang Haoqing;Tao Wentao;Wang Rufan;Bai Linquan;Zhao Yi-Lei;Shi Ting
脱水酶（DH）是聚酮合成酶（PKS）模块中的一个结构域，可以催化β-羟基脱水成α，β-不饱和酰基中间体。作为PDB数据库中发现的首个双功能（脱水酶/异构酶）DH结构域，PKS生物合成途径中的gephyronic acid (GphF) DH1结构域备受关注。然而，I型PKS的脱水和异构化机制仍不清楚。本研究将MD模拟和QM/MM计算相结合，阐明GphF DH1的分子机制。结果表明，GphF DH1对(2R,3R)-底物具有较好的识别效果，且倾向于提前形成α -β双键而不是直接形成β -γ双键。通过计算结合能，突出了活性袋附近的一些关键残基。伞式取样结果表明，非甲基化底物比α-甲基底物更容易形成分子内氢键。采用M062X/6-311+G**//M062X/6-31G*方法进行的QM/MM计算和SMD溶剂化校正均支持单碱脱水和单碱异构化机制，能垒分别为27.0 kcal mol - 1和17.2 kcal mol - 1。这些结果可以为进一步研究PKS DHs的催化机理和合理设计典型DHs提供参考。
Dehydratase (DH), a domain in polyketide synthase (PKS) modules, can catalyze the dehydration of β-hydroxy to an α,β-unsaturated acyl intermediate. As the first dual-function (dehydratase/isomerase) DH domain accessible in the PDB database, the gephyronic acid (GphF) DH1 domain from the PKS biosynthetic pathway attracts great attention from researchers. However, the mechanisms of dehydration and isomerization in type I PKS still remain unclear. In this study, MD simulations and QM/MM calculations were combined to elucidate the molecular mechanism of GphF DH1. The results indicated that GphF DH1 had better recognition effect towards the (2R,3R)-substrate and preferred forming the α–β double bond in advance to the β–γ double bond directly. By calculating the binding energy, some key residues near the active pocket were highlighted. Umbrella sampling results showed that non-methylated substrates could form intra-molecular hydrogen bonds more easily than α-methyl substrates. The QM/MM calculations with the M062X/6-311+G**//M062X/6-31G* method and SMD solvation correction supported the one-base dehydration and one-base isomerization mechanism with energy barriers of 27.0 kcal mol−1 and 17.2 kcal mol−1, respectively. These results can encourage future studies for the comprehensive understanding of the catalytic mechanism of PKS DHs and for the rational design of typical DHs.