Mechanism of the Dinuclear Iron Enzyme p‐Aminobenzoate N‐oxygenase from Density Functional Calculations

• Published in: ChemCatChem 2019-01, Vol.11 (1), p.601-613
• Main Authors: Wei, Wen‐Jie, Siegbahn, Per E. M., Liao, Rong‐Zhen
• Format: Article
• Language: English
• Subjects: Binding; Cleavage; Density; density functional calculations; dinuclear iron enzyme; Electrons; enzyme catalysis; Enzymes; Mathematical models; Oxidation; reaction mechanism; Reaction mechanisms; Substrates; Water chemistry
• ISSN: 1867-3880; 1867-3899; 1867-3899
• DOI: 10.1002/cctc.201801072

AurF is a diiron enzyme that utilizes two dioxygen molecules as the oxidant to catalyze the oxidation of p‐aminobenzoate to p‐nitrobenzoate. Density functional calculations were performed to elucidate the reaction mechanism of this enzyme. Two different models were considered, with the oxygenated intermediate being a diferric peroxo species or a diferric hydroperoxo species. The calculations strongly favor the model with a diferric peroxo species and support the mechanism proposed by Bollinger and co‐workers. The reaction starts with the binding of a dioxygen molecule to the diferrous center to generate a diferric peroxide complex. This is followed by the cleavage of the O−O bond, concertedly with the formation of the first N−O bond, which has a barrier of only 9.2 kcal/mol. Subsequently, the first‐shell ligand Glu227 s a proton from the substrate. After the delivery of two electrons from the external reductant and two protons from solution, a water molecule and the experimentally suggested intermediate p‐hydroxylaminobenzoate are produced and the diferrous center is regenerated. The oxidation of the p‐hydroxylaminobenzoate intermediate requires the binding of a second dioxygen molecule to the diferrous center to generate the diferric peroxide complex. Similarly to the oxidation of p‐aminobenzoate, the O−O bond cleavage and the formation of the second N−O bond take place in a concerted step. The p‐nitrobenzoate product is formed after the release of two protons and two electrons from the substrate. The model with a hydroperoxo species gave a much high barrier of 28.7 kcal/mol for the substrate oxidation due to the large energy penalty for the generation of the active hydroperoxo species. Iron up or iron down: Density functional calculations were used to investigate the reaction mechanism of AurF. Two different oxidants were considered, the calculations suggested that the active oxygenated intermediate is the peroxo species.