Insights into the decarboxylative hydroxylation of salicylate catalyzed by the Flavin-dependent monooxygenase salicylate hydroxylase

Salicylate hydroxylase (SALH) is a Flavin-dependent monooxygenase responsible for the transformation of salicylate to catechol. In this article, on the basis of the crystal structure obtained from Pseudomonas putida S-1, we performed combined quantum mechanical/molecular mechanical (QM/MM) calculations to investigate the reaction mechanism of SALH. Since the formation of C4a-hydroperoxyflavin has been theoretically proven to be a barrierless process, our calculations started from the C4a-hydroperoxyflavin intermediate. The whole enzymatic reaction contains two parts: the hydroxylation and decarboxylation. Our calculation results indicate that the deprotonated substrate is the active form, whereas the neutral form of salicylate corresponds to very a high energy barrier (39.8 kcal/mol) for the hydroxylation process, which is in line with the experimental result that the optimum pH is 7.6. The calculated results with the deprotonated substrate indicate that the hydroxylation and decarboxylation occur in a stepwise manner and the decarboxylation process is calculated to be the rate-limiting step with an energy barrier of 14.5 kal/mol. Calculations using different functionals (B3LYP, BP, BVWN, PBE, M06 and TPSSH) suggest that the catalytic reaction is highly exothermic, which is consistent with its similar enzyme (PHBH).