title: Quantum mechanics/molecular mechanics study on the oxygen binding and substrate hydroxylation step in AlkB repair enzymes.
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 N(1) -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.
authors: Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN (UK).
authors: Matthew G
authors: MG
authors: Quesne
authors: Reza
authors: R
authors: Latifi
authors: Luis E
authors: LE
authors: Gonzalez-Ovalle
authors: Devesh
authors: D
authors: Kumar
authors: Sam P
authors: SP
authors: de Visser
mesh_terms: D000225:Adenine / Q000031:analogs & derivatives / Q000737:chemistry; D001665:Binding Sites; D002384:Catalysis; D056831:Coordination Complexes / Q000737:chemistry; D019175:DNA Methylation; D045643:DNA Repair Enzymes / Q000737:chemistry*; D006900:Hydroxylation; D007501:Iron / Q000737:chemistry; D007536:Isomerism; D056004:Molecular Dynamics Simulation; D010100:Oxygen / Q000737:chemistry*; D011485:Protein Binding; D011789:Quantum Theory
chemical_list: D056831:Coordination Complexes; C008407:1-methyladenine; D007501:Iron; D045643:DNA Repair Enzymes; D000225:Adenine; D010100:Oxygen
keywords: DNA base repair; DNA damage; density functional calculations; hydroxylation; nonheme iron enzymes