Can an external electric field switch between ethylene formation and <scp>l</scp>-arginine hydroxylation in the ethylene forming enzyme?

Chaturvedi, Shobhit S.; Rifayee, Simahudeen Bathir Jaber Sathik; Ramanan, Rajeev; Rankin, Joel A.; Hu, Jinglu; Hausinger, Robert P.; Christov, Christo I.

doi:10.1039/d3cp01899g

Cited by 6 publications

(5 citation statements)

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“…Another computational study on a non-heme 2OG dependent ethylene forming enzyme showed that the enzyme utilizes different intrinsic electric elds in the two L-Arg binding conformations, which are associated with distinct reactivity preferences. 71 Importantly, the study also demonstrated that changes in the electric eld of the enzyme could switch between the substrate L-Arg hydroxylation and ethylene forming reactivity of the enzyme. Finally, a study on the Fe(II)/2OG-dependent Ten-Eleven-Translocation-2 (TET2) enzyme demonstrated that clinical mutations related to cancers can inuence the electric eld along the reaction coordinate of the hydrogen atom transfer (HAT) reaction leading to a higher activation barrier and some mutations can even alter the orbital mechanism for the rate-limiting HAT reaction.…”

Section: Optimization Of Enzyme Electric Eldsmentioning

confidence: 83%

From random to rational: improving enzyme design through electric fields, second coordination sphere interactions, and conformational dynamics

Chaturvedi,

Bím,

Christov

et al. 2023

Chem. Sci.

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Section: Optimization Of Enzyme Electric Eldsmentioning

confidence: 83%

From random to rational: improving enzyme design through electric fields, second coordination sphere interactions, and conformational dynamics

Chaturvedi,

Bím,

Christov

et al. 2023

Chem. Sci.

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“…Electronically, the lowest-energy hydrogen atom abstraction barriers in the quintet spin state result from electron transfer from the substrate into the virtual σ* z 2 orbital along the Fe–O bond and give a radical intermediate with configuration π* xy 1 3d xz 1 π* yz 1 σ* x 2 – y 2 1 σ* z 2 1 π Sub 1 : designated the σ-pathway. − Note that in this notation after hydrogen atom abstraction, the π xz /π* xz pair of orbitals split back into atomic orbitals and form a lone pair on iron in 3d xz , while the 2p z on oxygen forms the σ OH orbital. As a consequence, 5 TS1 HA4,I,σ , 5 IM1 HA4,I , 5 TS1 HA5,I,σ , and 5 IM1 HA5,I have a negative spin density on the substrate and a large positive spin density on the iron atom.…”

Section: Resultsmentioning

confidence: 99%

How Does the Nonheme Iron Enzyme NapI React through l-Arginine Desaturation Rather Than Hydroxylation? A Quantum Mechanics/Molecular Mechanics Study

Ali,

Warwicker,

de Visser

2023

ACS Catal.

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The naphthyridinomycin biosynthesis enzyme NapI selectively performs the desaturation of a free L-arginine amino acid at the C 4 −C 5 bond as part of its antibiotic biosynthesis reaction. This is an unusual reaction triggered by a nonheme iron dioxygenase as most L-Arg activating nonheme iron enzymes cause substrate hydroxylation at an aliphatic C−H bond; hence, this reaction has great potential in biotechnology for the efficient synthesis of drug and fragrance molecules. However, desaturation reactions in chemical catalysis are challenging reactions to perform as they often require toxic heavy metals and solvents. Its enzymatic biosynthesis would provide an environmentally benign alternative. To find the biotechnological application of NapI, we performed a computational study on the enzyme. However, the catalytic mechanism of L-Arg desaturation by NapI is controversial and several possible mechanisms have been suggested via either radical or charge-transfer pathways. We set up an enzymatic structure from the deposited crystal structure coordinates of substrate-bound NapI and inserted co-substrate (α-ketoglutarate) and solvated the structure in a water environment. Thereafter, we set up a series of quantum mechanics/molecular mechanics calculations and validated the results against experimental data. Subsequently, we investigated the mechanisms leading to C 5 -and C 4 -hydroxylation and C 4 −C 5 -desaturation of L-Arg via radical and charge-transfer pathways. The calculations give a rate-determining hydrogen atom abstraction step that is lowest for the C 5 −H position and gives a radical intermediate, although the hydrogen atom abstraction from the C 4 −H group is less than ΔG = 2 kcal mol −1 higher in energy. The calculations show that isotopic substitution of key C−H bonds with C−D changes the product distributions dramatically. The C 5 radical intermediate gives bifurcation pathways with a small second hydrogen atom abstraction from the C 4 −H group and a much higher OH rebound barrier. We also located a charge-transfer intermediate of an iron(II)-hydroxo species with a cationic substrate, but its kinetics and thermodynamics with respect to the radical intermediate make it an unviable mechanism. A comparison with alternative hydroxylating enzymes identifies key differences in substrate orientation and positioning and their second coordination sphere interactions with protein that induces a different dipole and electric field direction. Our work shows that the desaturation of L-Arg is governed by the substrate-binding orientation and the polarity and hydrogen bonding interactions in the substrate-binding pocket that guides the reaction to desaturation products by locking the iron(III)-hydroxo group in position. Our understanding has given valuable insight into enzymatic reactivity and may help to design and engineer enzymes better for highly selective reaction processes in biotechnology.

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“…To investigate the effect of external perturbations on lysine C–H bond strengths, we recalculated the C 3 –H, C 4 –H, and C 5 –H BDEs in the presence of an applied electric field along either the molecular x -, y -, or z -axis of the substrate. Previous calculations with electric field effects applied showed these perturbations to affect electronic properties and charge distributions and even lead to selectivity changes. ,− The definitions of the x -, y -, and z -axes in the substrate are shown in Figure with the y -axis along the carbon chain and the x - and z -axes along the C–H bonds. Figure b shows the BDE patterns as a function of the applied electric field along the x - and z -axes, which are both perpendicular to the carbon chain of the substrate.…”

Section: Discussionmentioning

confidence: 99%

An Active Site Tyr Residue Guides the Regioselectivity of Lysine Hydroxylation by Nonheme Iron Lysine-4-hydroxylase Enzymes through Proton-Coupled Electron Transfer

Cao,

Hay,

de Visser

2024

J. Am. Chem. Soc.

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Lysine dioxygenase (KDO) is an important enzyme in human physiology involved in bioprocesses that trigger collagen cross-linking and blood pressure control. There are several KDOs in nature; however, little is known about the factors that govern the regio-and stereoselectivity of these enzymes. To understand how KDOs can selectively hydroxylate their substrate, we did a comprehensive computational study into the mechanisms and features of 4-lysine dioxygenase. In particular, we selected a snapshot from the MD simulation on KDO5 and created large QM cluster models (A, B, and C) containing 297, 312, and 407 atoms, respectively. The largest model predicts regioselectivity that matches experimental observation with rate-determining hydrogen atom abstraction from the C 4 −H position, followed by fast OH rebound to form 4-hydroxylysine products. The calculations show that in model C, the dipole moment is positioned along the C 4 −H bond of the substrate and, therefore, the electrostatic and electric field perturbations of the protein assist the enzyme in creating C 4 −H hydroxylation selectivity. Furthermore, an active site Tyr 233 residue is identified that reacts through proton-coupled electron transfer akin to the axial Trp residue in cytochrome c peroxidase. Thus, upon formation of the iron(IV)-oxo species in the catalytic cycle, the Tyr 233 phenol loses a proton to the nearby Asp 179 residue, while at the same time, an electron is transferred to the iron to create an iron(III)-oxo active species. This charged tyrosyl residue directs the dipole moment along the C 4 −H bond of the substrate and guides the selectivity to the C 4 -hydroxylation of the substrate.

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Can an external electric field switch between ethylene formation and l-arginine hydroxylation in the ethylene forming enzyme?

Abstract: 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...

Cited by 6 publications

References 77 publications

From random to rational: improving enzyme design through electric fields, second coordination sphere interactions, and conformational dynamics

From random to rational: improving enzyme design through electric fields, second coordination sphere interactions, and conformational dynamics

How Does the Nonheme Iron Enzyme NapI React through l-Arginine Desaturation Rather Than Hydroxylation? A Quantum Mechanics/Molecular Mechanics Study

An Active Site Tyr Residue Guides the Regioselectivity of Lysine Hydroxylation by Nonheme Iron Lysine-4-hydroxylase Enzymes through Proton-Coupled Electron Transfer

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