title: Theoretical study of the reaction mechanism of phenolic acid decarboxylase.
abstract: The cofactor-free phenolic acid decarboxylases (PADs) catalyze the non-oxidative decarboxylation of phenolic acids to their corresponding p-vinyl derivatives. Phenolic acids are toxic to some organisms, and a number of them have evolved the ability to transform these compounds, including PAD-catalyzed reactions. Since the vinyl derivative products can be used as polymer precursors and are also of interest in the food-processing industry, PADs might have potential applications as biocatalysts. We have investigated the detailed reaction mechanism of PAD from Bacillus subtilis using quantum chemical methodology. A number of different mechanistic scenarios have been considered and evaluated on the basis of their energy profiles. The calculations support a mechanism in which a quinone methide intermediate is formed by protonation of the substrate double bond, followed by C-C bond cleavage. A different substrate orientation in the active site is suggested compared to the literature proposal. This suggestion is analogous to other enzymes with p-hydroxylated aromatic compounds as substrates, such as hydroxycinnamoyl-CoA hydratase-lyase and vanillyl alcohol oxidase. Furthermore, on the basis of the calculations, a different active site residue compared to previous proposals is suggested to act as the general acid in the reaction. The mechanism put forward here is consistent with the available mutagenesis experiments and the calculated energy barrier is in agreement with measured rate constants. The detailed mechanistic understanding developed here might be extended to other members of the family of PAD-type enzymes. It could also be useful to rationalize the recently developed alternative promiscuous reactivities of these enzymes.
authors.affiliation: Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University, Sweden.
authors.forename: Xiang
authors.initials: X
authors.lastname: Sheng
authors.affiliation: Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University, Sweden.
authors.forename: Maria E S
authors.initials: ME
authors.lastname: Lind
authors.affiliation: Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University, Sweden.
authors.forename: Fahmi
authors.initials: F
authors.lastname: Himo
mesh_terms: D019943:Amino Acid Substitution; D001412:Bacillus subtilis / Q000201:enzymology*; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D055162:Biocatalysis; D002262:Carboxy-Lyases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D020134:Catalytic Domain; D003373:Coumaric Acids / Q000737:chemistry / Q000378:metabolism*; D004735:Energy Transfer; D018698:Glutamic Acid / Q000737:chemistry; D006860:Hydrogen Bonding; D008958:Models, Molecular; D008968:Molecular Conformation; D050505:Mutant Proteins / Q000737:chemistry / Q000378:metabolism; D011422:Propionates; D011487:Protein Conformation; D011789:Quantum Theory
chemical_list: D001426:Bacterial Proteins; D003373:Coumaric Acids; D050505:Mutant Proteins; D011422:Propionates; D018698:Glutamic Acid; D002262:Carboxy-Lyases; C417714:phenolic acid decarboxylase; C495469:p-coumaric acid
keywords: biocatalysis; decarboxylation; density functional theory; phenolic acid decarboxylase; transition state