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首页> 外文期刊>Chemistry: A European journal >The Catalytic Mechanism of the Pyridoxal-5'-phosphate-Dependent Enzyme, Histidine Decarboxylase: A Computational Study
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The Catalytic Mechanism of the Pyridoxal-5'-phosphate-Dependent Enzyme, Histidine Decarboxylase: A Computational Study

机译：吡哆醛-5'-磷酸酯依赖性酶，组氨酸脱羧酶的催化机制：计算研究

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摘要

The catalytic mechanism of histidine decarboxylase (HDC), a pyridoxal-5'-phosphate (PLP)-dependent enzyme, was studied by using a computational QM/MM approach following the scheme M06-2X/6-311++ G(3df,2pd):Amber. The reaction involves two sequential steps: the decarboxylation of l-histidine and the protonation of the generated intermediate from which results histamine. The rate-limiting step is the first one (DG*=17.6 kcal mol-1; DGr=13.7 kcalmol-1) and agrees closely with the available experimental kcat (1.73 s-1), which corresponds to an activation barrier of 17.9 kcalmol-1. In contrast, the second step is very fast (DG*=1.9 kcalmol-1) and exergonic (DGr= -33.2 kcalmol-1). Our results agree with the available experimental data and allow us to explain the role played by several active site residues that are considered relevant according to site-directed mutagenesis studies, namely Tyr334B, Asp273A, Lys305A, and Ser354B. These results can provide insights regarding the catalytic mechanism of other enzymes belonging to family II of PLP-dependent decarboxylases.
机译：通过使用在该方案M06-2X / 6-311 ++ G（3DF，3DF， 2PD）：琥珀色。反应涉及两个顺序步骤：L-组氨酸的脱羧和产生的中间体的质子化来自哪个结果组胺。速率限制步骤是第一个（DG * = 17.6kcal Mol-1; DGR = 13.7 kcalmol-1），并与可用的实验kcat（1.73 s-1）密切地同意，其对应于17.9 kcalmol的活化屏障-1。相反，第二步骤非常快（DG * = 1.9 kcalmol-1）和出现（DGR = -33.2 kcalmol-1）。我们的业绩达成了可用的实验数据，并允许我们解释几种活性位点残留物的作用，该角度根据现场导向的诱变研究，即TYR334B，ASP273A，LYS305A和SER354B。这些结果可以提供关于属于PLP依赖性脱羧酶的族II的其他酶的催化机制的见解。

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