UCIBIO-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências s/n, Universidade do Porto, 4169-007, Porto, Portugal.
Chemistry. 2017 Jul 6;23(38):9162-9173. doi: 10.1002/chem.201701375. Epub 2017 Jun 14.
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 (ΔG =17.6 kcal mol ; ΔG =13.7 kcal mol ) and agrees closely with the available experimental k (1.73 s ), which corresponds to an activation barrier of 17.9 kcal mol . In contrast, the second step is very fast (ΔG =1.9 kcal mol ) and exergonic (ΔG =-33.2 kcal mol ). 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.
组氨酸脱羧酶（HDC）是一种依赖于吡哆醛-5'-磷酸（PLP）的酶，其催化机制采用 M06-2X/6-311++G（3df,2pd）：Amber 的计算 QM/MM 方法进行了研究。该反应涉及两个连续的步骤：l-组氨酸的脱羧和生成的中间产物的质子化，由此产生组胺。限速步骤是第一步（ΔG =17.6 kcal mol；ΔG =13.7 kcal mol），与可用的实验 k（1.73 s）非常接近，这对应于 17.9 kcal mol 的活化能垒。相比之下，第二步非常快（ΔG =1.9 kcal mol）且是放能的（ΔG =-33.2 kcal mol）。我们的结果与可用的实验数据一致，并允许我们解释几个活性位点残基的作用，这些残基根据定点突变研究被认为是相关的，即 Tyr334B、Asp273A、Lys305A 和 Ser354B。这些结果可以为属于 PLP 依赖脱羧酶家族 II 的其他酶的催化机制提供深入了解。
