title: Ab initio QM/MM calculations show an intersystem crossing in the hydrogen abstraction step in dealkylation catalyzed by AlkB.
abstract: AlkB is a bacterial enzyme that catalyzes the dealkylation of alkylated DNA bases. The rate-limiting step is known to be the abstraction of an H atom from the alkyl group on the damaged base by a Fe(IV)-oxo species in the active site. We have used hybrid ab initio quantum mechanical/molecular mechanical methods to study this step in AlkB. Instead of forming an Fe(III)-oxyl radical from Fe(IV)-oxo near the C-H activation transition state, the reactant is found to be an Fe(III)-oxyl with an intermediate-spin Fe (S = 3/2) ferromagnetically coupled to the oxyl radical, which we explore in detail using molecular orbital and quantum topological analyses. The minimum energy pathway remains on the quintet surface, but there is a transition between (IS)Fe(III)-oxyl and the state with a high-spin Fe (S = 5/2) antiferromagnetically coupled to the oxyl radical. These findings provide clarity for the evolution of the well-known π and σ channels on the quintet surface in the enzyme environment. Additionally, an energy decomposition analysis reveals nine catalytically important residues for the C-H activation step, some of which are conserved in two human homologues. These conserved residues are proposed as targets for experimental mutagenesis studies.
authors: Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
authors: Dong
authors: D
authors: Fang
authors: Richard L
authors: RL
authors: Lord
authors: G Andrés
authors: GA
authors: Cisneros
mesh_terms: D055162:Biocatalysis; D004247:DNA / Q000378:metabolism; D003640:Dealkylation; D004926:Escherichia coli / Q000201:enzymology; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000378:metabolism*; D005290:Ferric Compounds / Q000737:chemistry; D006859:Hydrogen / Q000737:chemistry*; D007501:Iron / Q000737:chemistry; D006899:Mixed Function Oxygenases / Q000737:chemistry / Q000378:metabolism*; D008958:Models, Molecular; D010084:Oxidation-Reduction; D011789:Quantum Theory
chemical_list: D029968:Escherichia coli Proteins; D005290:Ferric Compounds; D006859:Hydrogen; D004247:DNA; D007501:Iron; D006899:Mixed Function Oxygenases; C466427:AlkB protein, E coli