Mechanistic insights into the catalytic reaction of ferulic acid decarboxylase from Aspergillus niger: a QM/MM study

Abstract

Ubiquinone plays a pivotal role in the aerobic cellular respiratory electron transport chain, whereas ferulic acid decarboxylase (FDC) is involved in the biosynthesis of ubiquinone precursor. Recently, the complete crystal structure of FDC (based on the co-expression of the A. niger fdc1 gene in E. coli with the associated ubix gene from E. coli) at high resolution was reported. Herein, the detailed catalytic non-oxidative decarboxylation mechanism of FDC has been investigated by a combined quantum mechanics/molecular mechanics (QM/MM) approach. Calculation results indicate that, after the 1,3-dipolar cycloaddition of the substrate and cofactor, the carboxylic group can readily split off from the adduct, and the overall energy barrier of the whole catalytic reaction is 23.5 kcal mol⁻¹. According to the energy barrier analysis, the protonation step is rate-limiting. The conserved protonated Glu282 is suggested to be the proton donor through a “water bridge”. Besides, two cases, that is, the generated CO₂ escapes from the active site or remains in the active site, were considered. It was found that the prolonged leaving of CO₂ can facilitate the protonation of the intermediate. In particular, our calculations shed light on the detailed function of both cofactors prFMN^iminium and prFMN^ketamine in the decarboxylation step. The cofactor prFMN^iminium is the catalytically relevant species compared with prFMN^ketamine.