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The Catalytic Mechanism of the Pyridoxal‐5′‐phosphate‐Dependent Enzyme, Histidine Decarboxylase: A Computational Study
Author(s) -
Fernandes Henrique Silva,
Ramos Maria João,
Cerqueira Nuno M. F. S. A.
Publication year - 2017
Publication title -
chemistry – a european journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.687
H-Index - 242
eISSN - 1521-3765
pISSN - 0947-6539
DOI - 10.1002/chem.201701375
Subject(s) - histidine decarboxylase , histidine , exergonic reaction , decarboxylation , chemistry , protonation , stereochemistry , enzyme , catalysis , pyridoxal , reaction mechanism , active site , biochemistry , organic chemistry , ion
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 (Δ G ≠ =17.6 kcal mol −1 ; Δ G r =13.7 kcal mol −1 ) and agrees closely with the available experimental k cat (1.73 s −1 ), which corresponds to an activation barrier of 17.9 kcal mol −1 . In contrast, the second step is very fast (Δ G ≠ =1.9 kcal mol −1 ) and exergonic (Δ G r =−33.2 kcal mol −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.