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Abstract Arginine methylation is an important mechanism of epigenetic regulation. Some Fe(II) and 2‐oxoglutarate dependent Jumonji‐C (JmjC) Nϵ‐methyl lysine histone demethylases also have N‐methyl arginine demethylase activity. We report combined molecular dynamic (MD) and Quantum Mechanical/Molecular Mechanical (QM/MM) studies on the mechanism of N‐methyl arginine demethylation by human KDM4E and compare the results with those reported for N‐methyl lysine demethylation by KDM4A. At the KDM4E active site, Glu191, Asn291, and Ser197 form a conserved scaffold that restricts substrate dynamics; substrate binding is also mediated by an out of active site hydrogen‐bond between the substrate Ser1 and Tyr178. The calculations imply that in either C−H or N−H potential bond cleaving pathways for hydrogen atom transfer (HAT) during N‐methyl arginine demethylation, electron transfer occurs via a σ‐channel; the transition state for the N−H pathway is ∼10 kcal/mol higher than for the C−H pathway due to the higher bond dissociation energy of the N−H bond. The results of applying external electric fields (EEFs) reveal EEFs with positive field strengths parallel to the Fe=O bond have a significant barrier‐lowering effect on the C−H pathway, by contrast, such EEFs inhibit the N−H activation rate. The overall results imply that KDM4 catalyzed N‐methyl arginine demethylation and N‐methyl lysine demethylation occur via similar C−H abstraction and rebound mechanisms leading to methyl group hydroxylation, though there are differences in the interactions leading to productive binding of intermediates. 

Abstract This study investigates dioxygen binding and 2‐oxoglutarate (2OG) coordination by two model non‐heme Fe^II/2OG enzymes: a class 7 histone demethylase (PHF8) that catalyzes the hydroxylation of its H3K9me2 histone substrate leading to demethylation reactivity and the ethylene‐forming enzyme (EFE), which catalyzes two competing reactions of ethylene generation and substratel‐Arg hydroxylation. Although both enzymes initially bind 2OG by using anoff‐line2OG coordination mode, in PHF8, the substrate oxidation requires a transition to anin‐linemode, whereas EFE is catalytically productive for ethylene production from 2OG in theoff‐linemode. We used classical molecular dynamics (MD), quantum mechanics/molecular mechanics (QM/MM) MD and QM/MM metadynamics (QM/MM‐MetD) simulations to reveal that it is the dioxygen binding process and, ultimately, the protein environment that control the formation of thein‐lineFe^III‐OO⋅⁻intermediate in PHF8 and theoff‐lineFe^III‐OO⋅⁻intermediate in EFE.