Abstract
AlkB repair enzymes are important nonheme iron enzymes that catalyse the demethylation of alkylated DNA bases in humans, which is a vital reaction in the body that heals externally damaged DNA bases. Its mechanism is currently controversial and in order to resolve the catalytic mechanism of these enzymes, a quantum mechanics/molecular mechanics (QM/MM) study was performed on the demethylation of the N1-methyladenine fragment by AlkB repair enzymes. Firstly, the initial modelling identified the oxygen binding site of the enzyme. Secondly, the oxygen activation mechanism was investigated and a novel pathway was found, whereby the catalytically active iron(IV)–oxo intermediate in the catalytic cycle undergoes an initial isomerisation assisted by an Arg residue in the substrate binding pocket, which then brings the oxo group in close contact with the methyl group of the alkylated DNA base. This enables a subsequent rate-determining hydrogen-atom abstraction on competitive σ-and π-pathways on a quintet spin-state surface. These findings give evidence of different locations of the oxygen and substrate binding channels in the enzyme and the origin of the separation of the oxygen-bound intermediates in the catalytic cycle from substrate. Our studies are compared with small model complexes and the effect of protein and environment on the kinetics and mechanism is explained.
Highlights
Nonheme iron dioxygenases catalyse a range of important reactions in Nature including the biosynthesis of antibiotics in microbes and the metabolism of, for instance, cysteine in mammals.[1,2]
Nonheme iron dioxygenases have been linked to oxygen sensing and collagen cross-linking processes in the body, and as such they have vital functions for the biosystem,[3] but there are many unanswered questions related to their activity and the catalytic transformation of substrates and detailed computational studies can shed light on this and predict a mechanism
The iron(IV)–oxo species is formed in a catalytic cycle from an iron(III)–superoxo complex in a reaction with aKG (Scheme 1), and in the crystal structure displayed in Figure 1 there seems to be a dioxygen binding site trans to His131
Summary
Nonheme iron dioxygenases catalyse a range of important reactions in Nature including the biosynthesis of antibiotics in microbes and the metabolism of, for instance, cysteine in mammals.[1,2] In addition, nonheme iron dioxygenases have been linked to oxygen sensing and collagen cross-linking processes in the body, and as such they have vital functions for the biosystem,[3] but there are many unanswered questions related to their activity and the catalytic transformation of substrates and detailed computational studies can shed light on this and predict a mechanism. To test the relative reactivity of an iron(III)–superoxo versus an iron(IV)–oxo complex with N1-methyladenine, we set up a DFT model complex based on the QM region displayed in Figure 4 and calculated the hydrogen-atom abstraction of both complexes.
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