Search for: All records

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. 

The study explores the second branchpoint of the EFE catalytic mechanism, which determines the product distribution of ethylene and 3-hydroxypropionate formation using QM/MM simulations on WT and A198L variants of EFE. 

A forward-looking perspective on optimizing enzyme design through synergizing electric fields, coordination spheres, and dynamics. 

Ethylene formation by the ethylene-forming enzyme (EFE) and 1-aminocyclopropane-1-carboxylate oxidase (ACCO). 

The non-heme Fe( ii ) and 2-oxoglutarate (2OG) dependent ethylene-forming enzyme (EFE) catalyzes both ethylene generation and l -Arg hydroxylation. Despite experimental and computational progress in understanding the mechanism of EFE, no EFE variant has been optimized for ethylene production while simultaneously reducing the l -Arg hydroxylation activity. In this study, we show that the two l -Arg binding conformations, associated with different reactivity preferences in EFE, lead to differences in the intrinsic electric field (IntEF) of EFE. Importantly, we suggest that applying an external electric field (ExtEF) along the Fe–O bond in the EFE·Fe( iii )·OO − ˙·2OG· l -Arg complex can switch the EFE reactivity between l -Arg hydroxylation and ethylene generation. Furthermore, we explored how applying an ExtEF alters the geometry, electronic structure of the key reaction intermediates, and the individual energy contributions of second coordination sphere (SCS) residues through combined quantum mechanics/molecular mechanics (QM/MM) calculations. Experimentally generated variant forms of EFE with alanine substituted for SCS residues responsible for stabilizing the key intermediates in the two reactions of EFE led to changes in enzyme activity, thus demonstrating the key role of these residues. Overall, the results of applying an ExtEF indicate that making the IntEF of EFE less negative and stabilizing the off-line binding of 2OG is predicted to increase ethylene generation while reducing l -Arg hydroxylation.