Mechanistic insights into dioxygen activation, oxygen atom exchange and substrate epoxidation by AsqJ dioxygenase from quantum mechanical/molecular mechanical calculations

Abstract

Herein, we use in-protein quantum mechanical/molecular mechanical (QM/MM) calculations to elucidate the mechanism of dioxygen activation, oxygen atom exchange and substrate epoxidation processes by AsqJ, an Fe/α-ketoglutarate-dependent dioxygenase (α-KGD) using a 2-His-1-Asp facial triad. Our results demonstrated that the whole reaction proceeds through a quintet surface. The dioxygen activation by AsqJ leads to a quintet penta-coordinated Fe-oxo species, which has a square pyramidal geometry with the oxo group trans to His134. This penta-coordinated Fe-oxo species is not the reactive one in the substrate epoxidation reaction since its oxo group is pointing away from the target C[double bond, length as m-dash]C bond. Instead, it can undergo the oxo group isomerization followed by water binding or the water binding followed by oxygen atom exchange to form the reactive hexa-coordinated Fe-oxo species with the oxo group trans to His211. The calculated parameters of Mössbauer spectra for this hexa-coordinated Fe-oxo intermediate are in excellent agreement with the experimental values, suggesting that it is most likely the experimentally trapped species. The calculated energetics indicated that the rate-limiting step is the substrate C[double bond, length as m-dash]C bond activation. This work improves our understanding of the dioxygen activation by α-KGD and provides important structural information about the reactive Fe-oxo species.

Mechanistic Insights into a Stibene Cleavage Oxygenase NOV1 from Quantum Mechanical/Molecular Mechanical Calculations

“…We found that the dioxygen molecule prefers to bind to the iron in a side‐on mode as suggested from the experiment . Most theoretical studies on the nonheme iron enzymes predicted a high spin septet ground state for the Fe−O 2 complex . Here too, the septet state with the side‐on conformation ( 7 1 side‐on in Figure A) was found to be the most stable one, and then was set as the reference point of 0 kcal mol −1 .…”

“…[6] Most theoretical studies on the nonheme iron enzymes predicted a high spin septet ground state for the FeÀ O 2 complex. [21][22][23][24][25][26][27][28][29][30][31][32][33][34][35][36][37][38][39] Here too, the septet state with the side-on conformation ( 7 1 side-on in Figure 1A) was found to be the most stable one, and then was set as the reference point of 0 kcal mol À 1 . To better understand the electronic structure, analysis of the spin natural orbitals (SNOs) were also performed for the FeÀ O 2 complexes.…”

“…It has been extensively showed by theoretical studies that in many mononuclear non-heme enzymes the quintet FeÀ O 2 is the reactive species. [15,29,30,33,35,[38][39][40][41][42][43][44][45][46][47][48] As such, we took 5 1 side-on as the catalytically relevant state for the oxidative cleavage of resveratrol. The subsequent QM/MM calculations were carried out on the quintet surface.…”

On how the binding cavity of AsqJ dioxygenase controls the desaturation reaction regioselectivity: a QM/MM study

“…Such a complex is the most likely species to initiate the oxidation of the primary substrate, as the previous Mössbauer and QM/MM study on AsqJ has revealed [10]. ⁠…”

“…The process was investigated by QM/MM calculations and the proposed mechanism involves the formation of a bond between C10 and the oxo ligand of the oxoferryl species that yields a C3-centered radical [10]. Comparison of these results with the ones reported here for desaturation shows that both AsqJ-catalysed reactions are initiated at the C10 position.…”