Mechanistic insights into the role of Glu103-mediated hydrogen bond shift in quercetin catalysis by Pirin homologs

Abstract

YhhW and hPirin, as Pirin homologs, catalyze the conversion of quercetin to 2-protocatechuoyl-phloroglucinol carboxylic acid and CO. Compared to hPirin, YhhW exhibits lower catalytic efficiency in quercetin oxygenolysis and lacks C-terminal α-helix and Metal-Glu103 coordination. In this work, combined QM/MM calculations and MD simulations are utilized to investigate the detailed mechanisms of quercetin oxygenolysis by YhhW and hpirin. MD simulations reveal that the C-terminal helix in hPirin is crucial for stabilizing Metal-Glu103 coordination. QM/MM calculations further reveal that this coordination not only stabilizes the intermediate but also facilitates hydrogen bond shifts between Glu103 and the carbonyl group of quercetin, optimizing charge distribution and promoting the final ring formation. In contrast, the distal positioning of Glu103 in YhhW disrupts efficient hydrogen bond switching, leading to diminished activity. This work provides deeper insights into quercetin oxygenolysis mechanisms by Pirin homologs and sheds light on the role of hydrogen bond in enzymatic reactions.