Mechanistic insights into a non-heme 2-oxoglutarate-dependent ethylene-forming enzyme: selectivity of ethylene-formation <i>versus</i><scp>l</scp>-Arg hydroxylation

Xue, Junqin; Lu, Jiarui; Lai, Wenzhen

doi:10.1039/c9cp00794f

Cited by 49 publications

(119 citation statements)

References 77 publications

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“…The Fe-O distance has elongated to 1.796 Å and the axial Fe-N bond to 2.204 Å. These changes mimic previous calculations on analogous reaction mechanisms well [26][27][28][29][30][31][32][33][34][35][36]. The transition state has a modest imaginary frequency of i619 cm −1 , which is well lower than typical hydrogen atom abstraction transition states that usually have values well over i1000 cm −1 [72][73].…”

Section: Substrate Desaturation Via Pathways 1 Andsupporting

confidence: 76%

“…For cysteine dioxygenase a combination of UV-Vis absorption and electron paramagnetic resonance studies implicated a short-lived oxygen-bound intermediate, which was tentatively identified as either the iron(III)-superoxo species or the bicyclic ring structure [24]. Many computational studies investigated the structure and properties of the iron(IV)-oxo species of nonheme iron dioxygenases in detail using either density functional theory model complexes or quantum mechanics/molecular mechanics methods [25][26][27][28][29][30][31][32][33][34][35][36]. These studies identified the iron(IV)-oxo as a quintet spin ground state showed it to be an efficient oxidant of substrate hydroxylation reactions.…”

Section: Introductionmentioning

confidence: 99%

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Density Functional Theory Study into the Reaction Mechanism of Isonitrile Biosynthesis by the Nonheme Iron Enzyme ScoE

2021

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The nonheme iron enzyme ScoE catalyzes the biosynthesis of an isonitrile substituent in a peptide chain. To understand details of the reaction mechanism we created a large active site cluster model of 212 atoms that contains substrate, the active oxidant and the first- and second-coordination sphere of the protein and solvent. Several possible reaction mechanisms were tested and it is shown that isonitrile can only be formed through two consecutive catalytic cycles that both use one molecule of dioxygen and α-ketoglutarate. In both cycles the active species is an iron(IV)-oxo species that in the first reaction cycle reacts through two consecutive hydrogen atom abstraction steps: first from the N–H group and thereafter from the C–H group to desaturate the NH-CH2 bond. The alternative ordering of hydrogen atom abstraction steps was also tested but found to be higher in energy. Moreover, the electronic configurations along that pathway implicate an initial hydride transfer followed by proton transfer. We highlight an active site Lys residue that is shown to donate charge in the transition states and influences the relative barrier heights and bifurcation pathways. A second catalytic cycle of the reaction of iron(IV)-oxo with desaturated substrate starts with hydrogen atom abstraction followed by decarboxylation to give isonitrile directly. The catalytic cycle is completed with a proton transfer to iron(II)-hydroxo to generate the iron(II)-water resting state. The work is compared with experimental observation and previous computational studies on this system and put in a larger perspective of nonheme iron chemistry.

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Section: Substrate Desaturation Via Pathways 1 Andsupporting

confidence: 76%

Section: Introductionmentioning

confidence: 99%

Density Functional Theory Study into the Reaction Mechanism of Isonitrile Biosynthesis by the Nonheme Iron Enzyme ScoE

2021

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“…Optimized geometries of the triplet and quintet spin reactant complexes ( 3,5 Re) are shown in Figure 2. Similarly to previous computational studies on analogous iron(IV)-oxo complexes of nonheme iron enzymes [68][69][70][71][72][73][74][75][76][77][78][79][80][81][82][83][84] and experimental EPR and Mössbauer measurements of related nonheme iron dioxygenases, 30,31,[85][86][87] the quintet spin state is the ground state. Because of this molecular orbital occupation, the Fe-O distance is short in 5 Re, i.e.…”

Section: Methodsmentioning

confidence: 80%

Selective Hydrogen Atom Abstraction from Dihydroflavonol by a Nonheme Iron Center Is the Key Step in the Enzymatic Flavonol Synthesis and Avoids Byproducts

2019

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The plant nonheme iron dioxygenase flavonol synthase performs a regioselective desaturation reaction as part of the biosynthesis of the signaling molecule flavonol that triggers the growing of leaves and flowers. These compounds also have health benefits for humans. Desaturation of aliphatic compounds generally proceeds through two consecutive hydrogen atom abstraction steps from two adjacent carbon atoms and in nature often is performed by a high-valent iron(IV)-oxo species. We show that the order of the hydrogen atom abstraction steps; however, are opposite of those expected from the C-H bond strengths in the substrate and determines the product distributions. As such flavonol synthase follows a negative catalysis mechanism. Using density functional theory methods on large active site model complexes we investigated pathways for desaturation and hydroxylation by an iron(IV)-oxo active site model. Against thermochemical predictions, we find that the oxidant abstracts the hydrogen atom from the strong C 2 -H bond rather than the weaker C 3 -H bond of the substrate first. We analyzed the origin of this unexpected selective hydrogen atom abstraction pathway and find that the alternative C 3 -H hydrogen atom abstraction would be followed by a low-energy and competitive substrate hydroxylation mechanism hence, should give considerable amount of by-products. Our computational modelling studies shows that substrate positioning in flavonol synthase is essential as it guides the reactivity to a chemo-and regioselective substrate desaturation from the C 2 -H group leading to desaturation products efficiently.

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“…A recent computational study on EFE focused on the possible reaction pathways for the conversion of αKG into ethylene and three molecules of CO 2 and the alterative reaction mechanism for arginine hydroxylation . Thus, EFE binds a free arginine amino acid as a substrate into the binding pocket and with the help of dioxygen reacts αKG to ethylene, although a small amount of hydroxylated arginine is also observed .…”

Section: Second‐coordination Sphere Effects In Nonheme Iron Enzymesmentioning

confidence: 99%

“…Thus, EFE binds a free arginine amino acid as a substrate into the binding pocket and with the help of dioxygen reacts αKG to ethylene, although a small amount of hydroxylated arginine is also observed . Lai et al . used QM/MM on a full enzyme model of EFE and studied the full reaction mechanism for the two reaction pathways and established mechanisms leading to arginine hydroxylation and ethylene formation, and the key steps for the initial reaction steps are summarized in Scheme .…”

Section: Second‐coordination Sphere Effects In Nonheme Iron Enzymesmentioning

confidence: 99%

Second‐Coordination Sphere Effects on Selectivity and Specificity of Heme and Nonheme Iron Enzymes

Visser

2020

Chemistry A European J

117

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Mononuclear iron‐containing enzymes are highly versatile oxidants that often react stereospecifically and/or regioselectively with substrates. Combined experimental and computational studies on heme monooxygenases, nonheme iron dioxygenases and halogenases have revealed the intricate details of the second‐coordination sphere, which determine this specificity and selectivity. These second‐coordination sphere effects originate from the positioning of the substrate and oxidant, which involve the binding of the co‐factors and substrate into the active site of the protein. In addition, some enzymes affect the selectivity and reactivity through charge‐stabilization from nearby bound cations/anions, an induced electric field or through the positioning of salt bridges and hydrogen‐bonding interactions to first‐coordination sphere iron ligands and/or the substrate. Examples of all of these second‐coordination sphere effects in iron‐containing enzymes and how these influence structure and reactivity are given.

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Mechanistic insights into a non-heme 2-oxoglutarate-dependent ethylene-forming enzyme: selectivity of ethylene-formation versusl-Arg hydroxylation

Cited by 49 publications

References 77 publications

Density Functional Theory Study into the Reaction Mechanism of Isonitrile Biosynthesis by the Nonheme Iron Enzyme ScoE

Density Functional Theory Study into the Reaction Mechanism of Isonitrile Biosynthesis by the Nonheme Iron Enzyme ScoE

Selective Hydrogen Atom Abstraction from Dihydroflavonol by a Nonheme Iron Center Is the Key Step in the Enzymatic Flavonol Synthesis and Avoids Byproducts

Second‐Coordination Sphere Effects on Selectivity and Specificity of Heme and Nonheme Iron Enzymes

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