NRVS Studies of the Peroxide Shunt Intermediate in a Rieske Dioxygenase and Its Relation to the Native FeII O2 Reaction

Applying Nuclear Forward Scattering as In Situ and Operando Tool for the Characterization of FeN4 Moieties in the Hydrogen Evolution Reaction

Nuclear forward scattering (NFS) is a synchrotron-based technique relying on the recoil-free nuclear resonance effect similar to Mössbauer spectroscopy. In this work, we introduce NFS for in situ and operando measurements during electrocatalytic reactions. The technique enables faster data acquisition and better discrimination of certain iron sites in comparison to Mössbauer spectroscopy. It is directly accessible at various synchrotrons to a broad community of researchers and is applicable to multiple metal isotopes. We demonstrate the power of this technique with the hydrogen evolution mechanism of an immobilized iron porphyrin supported on carbon. Such catalysts are often considered as model systems for iron-nitrogen-carbon (FeNC) catalysts. Using in situ and operando NFS in combination with theoretical predictions of spectroscopic data enables the identification of the intermediate that is formed prior to the rate-determining step. The conclusions on the reaction mechanism can be used for future optimization of immobilized molecular catalysts and metal-nitrogen-carbon (MNC) catalysts.

Semi-rational design of nitroarene dioxygenase for catalytic ability toward 2,4-dichloronitrobenzene

Rieske non-heme dioxygenase family enzymes play an important role in the aerobic biodegradation of nitroaromatic pollutants, but no active dioxygenases are available in nature for initial reactions in the degradation of many refractory pollutants like 2,4-dichloronitrobenzene (24DCNB). Here, we report the engineering of hotspots in 2,3-dichloronitrobenzene dioxygenase from Diaphorobacter sp. strain JS3051, achieved through molecular dynamic simulation analysis and site-directed mutagenesis, with the aim of enhancing its catalytic activity toward 24DCNB. The computationally predicted activity scores were largely consistent with the detected activities in wet experiments. Among them, the two most beneficial mutations (E204M and M248I) were obtained, and the combined mutant reached up to a 62-fold increase in activity toward 24DCNB, generating a single product, 3,5-dichlorocatechol, which is a naturally occurring compound. In silico analysis confirmed that residue 204 affected the substrate preference for meta-substituted nitroarenes, while residue 248 may influence substrate preference by interaction with residue 295. Overall, this study provides a framework for manipulating nitroarene dioxygenases using computational methods to address various nitroarene contamination problems.IMPORTANCEAs a result of human activities, various nitroaromatic pollutants continue to enter the biosphere with poor degradability, and dioxygenation is an important kickoff step to remove toxic nitro-groups and convert them into degradable products. The biodegradation of many nitroarenes has been reported over the decades; however, many others still lack corresponding enzymes to initiate their degradation. Although rieske non-heme dioxygenase family enzymes play extraordinarily important roles in the aerobic biodegradation of various nitroaromatic pollutants, prediction of their substrate specificity is difficult. This work greatly improved the catalytic activity of dioxygenase against 2,4-dichloronitrobenzene by computer-aided semi-rational design, paving a new way for the evolution strategy of nitroarene dioxygenase. This study highlights the potential for using enzyme structure-function information with computational pre-screening methods to rapidly tailor the catalytic functions of enzymes toward poorly biodegradable contaminants.

Mononuclear Non-Heme Manganese-Catalyzed Enantioselective cis-Dihydroxylation of Alkenes Modeling Rieske Dioxygenases

The practical catalytic enantioselective cis-dihydroxylation of olefins that utilize earth-abundant first-row transition metal catalysts under environmentally friendly conditions is an important yet challenging task. Inspired by the cis-dihydroxylation reactions catalyzed by Rieske dioxygenases and non-heme iron models, we report the biologically inspired cis-dihydroxylation catalysis that employs an inexpensive and readily available mononuclear non-heme manganese complex bearing a tetradentate nitrogen-donor ligand and aqueous hydrogen peroxide (H2O2) and potassium peroxymonosulfate (KHSO5) as terminal oxidants. A wide range of olefins are efficiently oxidized to enantioenriched cis-diols in practically useful yields with excellent cis-dihydroxylation selectivity and enantioselectivity (up to 99% ee). Mechanistic studies, such as isotopically 18O-labeled water experiments, and density functional theory (DFT) calculations support that a manganese(V)-oxo-hydroxo (HO-MnV═O) species, which is formed via the water-assisted heterolytic O-O bond cleavage of putative manganese(III)-hydroperoxide and manganese(III)-peroxysulfate precursors, is the active oxidant that effects the cis-dihydroxylation of olefins; this is reminiscent of the frequently postulated iron(V)-oxo-hydroxo (HO-FeV═O) species in the catalytic arene and alkene cis-dihydroxylation reactions by Rieske dioxygenases and synthetic non-heme iron models. Further, DFT calculations for the mechanism of the HO-MnV═O-mediated enantioselective cis-dihydroxylation of olefins reveal that the first oxo attack step controls the enantioselectivity, which exhibits a high preference for cis-dihydroxylation over epoxidation. In this study, we are able to replicate both the catalytic function and the key chemical principles of Rieske dioxygenases in mononuclear non-heme manganese-catalyzed enantioselective cis-dihydroxylation of olefins.

Custom tuning of Rieske oxygenase reactivity

Rieske oxygenases use a Rieske-type [2Fe-2S] cluster and a mononuclear iron center to initiate a range of chemical transformations. However, few details exist regarding how this catalytic scaffold can be predictively tuned to catalyze divergent reactions. Therefore, in this work, using a combination of structural analyses, as well as substrate and rational protein-based engineering campaigns, we elucidate the architectural trends that govern catalytic outcome in the Rieske monooxygenase TsaM. We identify structural features that permit a substrate to be functionalized by TsaM and pinpoint active-site residues that can be targeted to manipulate reactivity. Exploiting these findings allowed for custom tuning of TsaM reactivity: substrates are identified that support divergent TsaM-catalyzed reactions and variants are created that exclusively catalyze dioxygenation or sequential monooxygenation chemistry. Importantly, we further leverage these trends to tune the reactivity of additional monooxygenase and dioxygenase enzymes, and thereby provide strategies to custom tune Rieske oxygenase reaction outcomes.

Rieske Oxygenases and Other Ferredoxin-Dependent Enzymes: Electron Transfer Principles and Catalytic Capabilities

Enzymes that depend on sophisticated electron transfer via ferredoxins (Fds) exhibit outstanding catalytic capabilities, but despite decades of research, many of them are still not well understood or exploited for synthetic applications. This review aims to provide a general overview of the most important Fd-dependent enzymes and the electron transfer processes involved. While several examples are discussed, we focus in particular on the family of Rieske non-heme iron-dependent oxygenases (ROs). In addition to illustrating their electron transfer principles and catalytic potential, the current state of knowledge on structure-function relationships and the mode of interaction between the redox partner proteins is reviewed. Moreover, we highlight several key catalyzed transformations, but also take a deeper dive into their engineerability for biocatalytic applications. The overall findings from these case studies highlight the catalytic capabilities of these biocatalysts and could stimulate future interest in developing additional Fd-dependent enzyme classes for synthetic applications.

Seeing the cis-Dihydroxylating Intermediate: A Mononuclear Nonheme Iron-Peroxo Complex in cis-Dihydroxylation Reactions Modeling Rieske Dioxygenases

The nature of reactive intermediates and the mechanism of the cis-dihydroxylation of arenes and olefins by Rieske dioxygenases and synthetic nonheme iron catalysts have been the topic of intense research over the past several decades. In this study, we report that a spectroscopically well characterized mononuclear nonheme iron(III)-peroxo complex reacts with olefins and naphthalene derivatives, yielding iron(III) cycloadducts that are isolated and characterized structurally and spectroscopically. Kinetics and product analysis reveal that the nonheme iron(III)-peroxo complex is a nucleophile that reacts with olefins and naphthalenes to yield cis-diol products. The present study reports the first example of the cis-dihydroxylation of substrates by a nonheme iron(III)-peroxo complex that yields cis-diol products.

Room-Temperature Conversion of Methane to Methanediol by [FeO2]. J Phys Chem Lett 2023;14:1633-1640. [PMID: 36752636 DOI: 10.1021/acs.jpclett.2c03786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

Inspired by the activities of P-450 enzyme and Rieske oxygenases in nature, in which the high-valent Fe-oxo complexes play a key role for oxidation of alkanes, the oxidation process of methane by the high-valent iron oxide cation [FeO₂]⁺ has been explored by using Fourier transform-ion cyclotron resonance (FT-ICR) mass spectrometry complemented by high-level quantum chemical calculations. In contrast to the previously reported [FeO]⁺/CH₄ and [Fe(O)OH]⁺/CH₄ systems, which afford [FeOH]⁺ as the main product, the generation of Fe⁺ dominates the reaction of [FeO₂]⁺ with CH₄. Theoretical calculations suggest a novel "oxygen rebound" pathway for the liberation of methanediol. In particular, the inevitable valence increase of Fe prior to C-H activation is similar to the cytochrome P-450 mediated processes. To our best knowledge, this study provides the first example of methane activation by the high-valent Fe(V)-oxo species in the gas phase, which may thus bridge the gas-phase model and the condensed-phase biosystems.

Contrasting Mechanisms of Aromatic and Aryl-Methyl Substituent Hydroxylation by the Rieske Monooxygenase Salicylate 5-Hydroxylase

The hydroxylase component (S5HH) of salicylate-5-hydroxylase catalyzes C5 ring hydroxylation of salicylate but switches to methyl hydroxylation when a C5 methyl substituent is present. The use of 18O2 reveals that both aromatic and aryl-methyl hydroxylations result from monooxygenase chemistry. The functional unit of S5HH comprises a nonheme Fe(II) site located 12 Å across a subunit boundary from a one-electron reduced Rieske-type iron-sulfur cluster. Past studies determined that substrates bind near the Fe(II), followed by O2 binding to the iron to initiate catalysis. Stopped-flow-single-turnover reactions (STOs) demonstrated that the Rieske cluster transfers an electron to the iron site during catalysis. It is shown here that fluorine ring substituents decrease the rate constant for Rieske electron transfer, implying a prior reaction of an Fe(III)-superoxo intermediate with a substrate. We propose that the iron becomes fully oxidized in the resulting Fe(III)-peroxo-substrate-radical intermediate, allowing Rieske electron transfer to occur. STO using 5-CD3-salicylate-d8 occurs with an inverse kinetic isotope effect (KIE). In contrast, STO of a 1:1 mixture of unlabeled and 5-CD3-salicylate-d8 yields a normal product isotope effect. It is proposed that aromatic and aryl-methyl hydroxylation reactions both begin with the Fe(III)-superoxo reaction with a ring carbon, yielding the inverse KIE due to sp2 → sp3 carbon hybridization. After Rieske electron transfer, the resulting Fe(III)-peroxo-salicylate intermediate can continue to aromatic hydroxylation, whereas the equivalent aryl-methyl intermediate formation must be reversible to allow the substrate exchange necessary to yield a normal product isotope effect. The resulting Fe(III)-(hydro)peroxo intermediate may be reactive or evolve through a high-valent iron intermediate to complete the aryl-methyl hydroxylation.

Elucidating the Role of O2 Uncoupling in the Oxidative Biodegradation of Organic Contaminants by Rieske Non-heme Iron Dioxygenases

Oxygenations of aromatic soil and water contaminants with molecular O₂ catalyzed by Rieske dioxygenases are frequent initial steps of biodegradation in natural and engineered environments. Many of these non-heme ferrous iron enzymes are known to be involved in contaminant metabolism, but the understanding of enzyme–substrate interactions that lead to successful biodegradation is still elusive. Here, we studied the mechanisms of O₂ activation and substrate hydroxylation of two nitroarene dioxygenases to evaluate enzyme- and substrate-specific factors that determine the efficiency of oxygenated product formation. Experiments in enzyme assays of 2-nitrotoluene dioxygenase (2NTDO) and nitrobenzene dioxygenase (NBDO) with methyl-, fluoro-, chloro-, and hydroxy-substituted nitroaromatic substrates reveal that typically 20–100% of the enzyme’s activity involves unproductive paths of O₂ activation with generation of reactive oxygen species through so-called O₂ uncoupling. The ¹⁸O and ¹³C kinetic isotope effects of O₂ activation and nitroaromatic substrate hydroxylation, respectively, suggest that O₂ uncoupling occurs after generation of Fe^III-(hydro)peroxo species in the catalytic cycle. While 2NTDO hydroxylates ortho-substituted nitroaromatic substrates more efficiently, NBDO favors meta-substituted, presumably due to distinct active site residues of the two enzymes. Our data implies, however, that the O₂ uncoupling and hydroxylation activity cannot be assessed from simple structure–reactivity relationships. By quantifying O₂ uncoupling by Rieske dioxygenases, our work provides a mechanistic link between contaminant biodegradation, the generation of reactive oxygen species, and possible adaptation strategies of microorganisms to the exposure of new contaminants.

Substrate-Specific Coupling of O2 Activation to Hydroxylations of Aromatic Compounds by Rieske Non-heme Iron Dioxygenases

Rieske dioxygenases catalyze the initial steps in the hydroxylation of aromatic compounds and are critical for the metabolism of xenobiotic substances. Because substrates do not bind to the mononuclear non-heme Fe^II center, elementary steps leading to O₂ activation and substrate hydroxylation are difficult to delineate, thus making it challenging to rationalize divergent observations on enzyme mechanisms, reactivity, and substrate specificity. Here, we show for nitrobenzene dioxygenase, a Rieske dioxygenase capable of transforming nitroarenes to nitrite and substituted catechols, that unproductive O₂ activation with the release of the unreacted substrate and reactive oxygen species represents an important path in the catalytic cycle. Through correlation of O₂ uncoupling for a series of substituted nitroaromatic compounds with ¹⁸O and ¹³C kinetic isotope effects of dissolved O₂ and aromatic substrates, respectively, we show that O₂ uncoupling occurs after the rate-limiting formation of Fe^III-(hydro)peroxo species from which substrates are hydroxylated. Substituent effects on the extent of O₂ uncoupling suggest that the positioning of the substrate in the active site rather than the susceptibility of the substrate for attack by electrophilic oxygen species is responsible for unproductive O₂ uncoupling. The proposed catalytic cycle provides a mechanistic basis for assessing the very different efficiencies of substrate hydroxylation vs unproductive O₂ activation and generation of reactive oxygen species in reactions catalyzed by Rieske dioxygenases.

The Apparently Unreactive Substrate Facilitates the Electron Transfer for Dioxygen Activation in Rieske Dioxygenases

Rieske dioxygenases belong to the non‐heme iron family of oxygenases and catalyze important cis‐dihydroxylation as well as O‐/N‐dealkylation and oxidative cyclization reactions for a wide range of substrates. The lack of substrate coordination at the non‐heme ferrous iron center, however, makes it particularly challenging to delineate the role of the substrate for productive O2 activation. Here, we studied the role of the substrate in the key elementary reaction leading to O2 activation from a theoretical perspective by systematically considering (i) the 6‐coordinate to 5‐coordinate conversion of the non‐heme Fe^II upon abstraction of a water ligand, (ii) binding of O2 , and (iii) transfer of an electron from the Rieske cluster. We systematically evaluated the spin‐state‐dependent reaction energies and structural effects at the active site for all combinations of the three elementary processes in the presence and absence of substrate using naphthalene dioxygenase as a prototypical Rieske dioxygenase. We find that reaction energies for the generation of a coordination vacancy at the non‐heme FeII center through thermoneutral H₂O reorientation and exothermic O2 binding prior to Rieske cluster oxidation are largely insensitive to the presence of naphthalene and do not lead to formation of any of the known reactive Fe‐oxygen species. By contrast, the role of the substrate becomes evident after Rieske cluster oxidation and exclusively for the 6‐coordinate non‐heme FeII sites in that the additional electron is found at the substrate instead of at the iron and oxygen atoms. Our results imply an allosteric control of the substrate on Rieske dioxygenase reactivity to happen prior to changes at the non‐heme FeII in agreement with a strategy that avoids unproductive O2 activation.

Mechanisms of O2 Activation by Mononuclear Non-Heme Iron Enzymes

Two major subclasses of mononuclear non-heme ferrous enzymes use two electron-donating organic cofactors (α-ketoglutarate or pterin) to activate O₂ to form Fe^IV═O intermediates that further react with their substrates through hydrogen atom abstraction or electrophilic aromatic substitution. New spectroscopic methodologies have been developed, enabling the study of the active sites in these enzymes and their oxygen intermediates. Coupled to electronic structure calculations, the results of these spectroscopies provide fundamental insight into mechanism. This Perspective summarizes the results of these studies in elucidating the mechanism of dioxygen activation to form the Fe^IV═O intermediate and the geometric and electronic structure of this intermediate that enables its high reactivity and selectivity in product formation.

C-H Bond Cleavage by Bioinspired Nonheme Metal Complexes

The functionalization of C-H bonds is one of the most challenging transformations in synthetic chemistry. In biology, these processes are well-known and are achieved with a variety of metalloenzymes, many of which contain a single metal center within their active sites. The most well studied are those with Fe centers, and the emerging experimental data show that high-valent iron oxido species are the intermediates responsible for cleaving the C-H bond. This Forum Article describes the state of this field with an emphasis on nonheme Fe enzymes and current experimental results that provide insights into the properties that make these species capable of C-H bond cleavage. These parameters are also briefly considered in regard to manganese oxido complexes and Cu-containing metalloenzymes. Synthetic iron oxido complexes are discussed to highlight their utility as spectroscopic and mechanistic probes and reagents for C-H bond functionalization. Avenues for future research are also examined.

Direct coordination of pterin to FeII enables neurotransmitter biosynthesis in the pterin-dependent hydroxylases

The pterin-dependent nonheme iron enzymes hydroxylate aromatic amino acids to perform the biosynthesis of neurotransmitters to maintain proper brain function. These enzymes activate oxygen using a pterin cofactor and an aromatic amino acid substrate bound to the Fe^II active site to form a highly reactive Fe^IV = O species that initiates substrate oxidation. In this study, using tryptophan hydroxylase, we have kinetically generated a pre-Fe^IV = O intermediate and characterized its structure as a Fe^II-peroxy-pterin species using absorption, Mössbauer, resonance Raman, and nuclear resonance vibrational spectroscopies. From parallel characterization of the pterin cofactor and tryptophan substrate-bound ternary Fe^II active site before the O₂ reaction (including magnetic circular dichroism spectroscopy), these studies both experimentally define the mechanism of Fe^IV = O formation and demonstrate that the carbonyl functional group on the pterin is directly coordinated to the Fe^II site in both the ternary complex and the peroxo intermediate. Reaction coordinate calculations predict a 14 kcal/mol reduction in the oxygen activation barrier due to the direct binding of the pterin carbonyl to the Fe^II site, as this interaction provides an orbital pathway for efficient electron transfer from the pterin cofactor to the iron center. This direct coordination of the pterin cofactor enables the biological function of the pterin-dependent hydroxylases and demonstrates a unified mechanism for oxygen activation by the cofactor-dependent nonheme iron enzymes.

Structural and Biochemical Analysis Reveals a Distinct Catalytic Site of Salicylate 5-Monooxygenase NagGH from Rieske Dioxygenases

Rieske nonheme iron oxygenases (ROs) catalyze the oxidation of a wide variety of substrates and play important roles in aromatic compound degradation and polycyclic aromatic hydrocarbon degradation. Those Rieske dioxygenases that usually act on hydrophobic substrates have been extensively studied and structurally characterized. Here, we report the crystal structure of a novel Rieske monooxygenase, NagGH, the oxygenase component of a salicylate 5-monooxygenase from Ralstonia sp. strain U2 that catalyzes the hydroxylation of a hydrophilic substrate salicylate (2-hydroxybenzoate), forming gentisate (2, 5-dihydroxybenzoate). The large subunit NagG and small subunit NagH share the same fold as that for their counterparts of Rieske dioxygenases and assemble the same α₃β₃ hexamer, despite that they share low (or no identity for NagH) sequence identities with these dioxygenase counterparts. A potential substrate-binding pocket was observed in the vicinity of the nonheme iron site. It featured a positively charged residue Arg323 that was surrounded by hydrophobic residues. The shift of nonheme iron atom caused by residue Leu228 disrupted the usual substrate pocket observed in other ROs. Residue Asn218 at the usual substrate pocket observed in other ROs was likewise involved in substrate binding and oxidation, yet residues Gln316 and Ser367, away from the usual substrate pocket of other ROs, were shown to play a more important role in substrate oxidation than Asn218. The unique binding pocket and unusual substrate-protein hydrophilic interaction provide new insights into Rieske monooxygenases.IMPORTANCE Rieske oxygenases are involved in the degradation of various aromatic compounds. These dioxygenases usually carry out hydroxylation of hydrophobic aromatic compounds and supply substrates with hydroxyl groups for extradiol/intradiol dioxygenases to cleave rings, and have been extensively studied. Salicylate 5-hydroxylase NagGH is a novel Rieske monooxygenase with high similarity to Rieske dioxygenases, and also shares reductase and ferredoxin similarity with a Rieske dioxygenase naphthalene 1,2-dioxygenase (NagAcAd) in Ralstonia sp. strain U2. The structure of NagGH, the oxygenase component of salicylate 5-monooxygenase, gives a representative of those monooxygenases and will help us understand the mechanism of their substrate binding and product regio-selectivity.

Bio-inspired Nonheme Iron Oxidation Catalysis: Involvement of Oxoiron(V) Oxidants in Cleaving Strong C-H Bonds

Nonheme iron enzymes generate powerful and versatile oxidants that perform a wide range of oxidation reactions, including the functionalization of inert C-H bonds, which is a major challenge for chemists. The oxidative abilities of these enzymes have inspired bioinorganic chemists to design synthetic models to mimic their ability to perform some of the most difficult oxidation reactions and study the mechanisms of such transformations. Iron-oxygen intermediates like iron(III)-hydroperoxo and high-valent iron-oxo species have been trapped and identified in investigations of these bio-inspired catalytic systems, with the latter proposed to be the active oxidant for most of these systems. In this Review, we highlight the recent spectroscopic and mechanistic advances that have shed light on the various pathways that can be accessed by bio-inspired nonheme iron systems to form the high-valent iron-oxo intermediates.

Spectroscopic Characterisation of the Naphthalene Dioxygenase from Rhodococcus sp. Strain NCIMB12038

Polycyclic aromatic hydrocarbons (PAHs), such as naphthalene, are potential health risks due to their carcinogenic and mutagenic effects. Bacteria from the genus Rhodococcus are able to metabolise a wide variety of pollutants such as alkanes, aromatic compounds and halogenated hydrocarbons. A naphthalene dioxygenase from Rhodococcus sp. strain NCIMB12038 has been characterised for the first time, using electron paramagnetic resonance (EPR) spectroscopy and UV-Vis spectrophotometry. In the native state, the EPR spectrum of naphthalene 1,2-dioxygenase (NDO) is formed of the mononuclear high spin Fe(III) state contribution and the oxidised Rieske cluster is not visible as EPR-silent. In the presence of the reducing agent dithionite a signal derived from the reduction of the [2Fe-2S] unit is visible. The oxidation of the reduced NDO in the presence of O2-saturated naphthalene increased the intensity of the mononuclear contribution. A study of the "peroxide shunt", an alternative mechanism for the oxidation of substrate in the presence of H2O2, showed catalysis via the oxidation of mononuclear centre while the Rieske-type cluster is not involved in the process. Therefore, the ability of these enzymes to degrade recalcitrant aromatic compounds makes them suitable for bioremediative applications and synthetic purposes.

Insights from 125Te and 57Fe nuclear resonance vibrational spectroscopy: a [4Fe-4Te] cluster from two points of view

Can sulfur-to-tellurium exchange serve as a method to understand iron–sulfur clusters of enzymatic systems?

Iron–sulfur clusters are common building blocks for electron transport and active sites of metalloproteins. Their comprehensive investigation is crucial for understanding these enzymes, which play important roles in modern biomimetic catalysis and biotechnology applications. We address this issue by utilizing (Et₄N)₃[Fe₄Te₄(SPh)₄], a tellurium modified version of a conventional reduced [4Fe–4S]⁺ cluster, and performed both ⁵⁷Fe- and ¹²⁵Te-NRVS to reveal its characteristic vibrational features. Our analysis exposed major differences in the resulting ⁵⁷Fe spectrum profile as compared to that of the respective [4Fe–4S] cluster, and between the ⁵⁷Fe and ¹²⁵Te profiles. DFT calculations are applied to rationalize structural, electronic, vibrational, and redox-dependent properties of the [4Fe–4Te]⁺ core. We herein highlight the potential of sulfur/tellurium exchange as a method to isolate the iron-only motion in enzymatic systems.

Geometric and Electronic Structural Contributions to Fe/O2 Reactivity

While two classes of non-heme iron enzymes use ferric centers to activate singlet organic substrates for the spin forbidden reaction with ³O₂, most classes use high spin ferrous sites to activate dioxygen. These Fe^II active sites do not exhibit intense absorption bands and have an integer spin ground state thus are mostly EPR inactive. We have developed new spectroscopic methodologies that provide geometric and electronic structural insight into the ferrous centers and their interactions with cosubstrates for dioxygen activation and into the nature of the intermediates generated in these reactions. First, we present our variable-temperature variable-field magnetic circular dichroism (VTVH MCD) methodology to experimentally define the geometric and electronic structure of the high spin ferrous active site. Then, we focus on using Nuclear Resonance Vibrational Spectroscopy (NRVS, performed at SPring-8) to define geometric structure and VTVH MCD to define the electronic structure of the Fe^III-OOH and Fe^IV=O intermediates generated in O₂ activation and the spin state dependence of their frontier molecular orbitals (FMOs) in controlling reactivity. Experimentally validated reaction coordinates are derived for the anticancer drug bleomycin in its cleavage of DNA and for an alpha- ketoglutarate dependent dioxygenase in its selective halogenation over the thermodynamically favored hydroxylation of substrate.

Salicylate 5-Hydroxylase: Intermediates in Aromatic Hydroxylation by a Rieske Monooxygenase

Rieske oxygenases (ROs) catalyze a large range of oxidative chemistry. We have shown that cis-dihydrodiol-forming Rieske dioxygenases first react with their aromatic substrates via an active site nonheme Fe(III)-superoxide; electron transfer from the Rieske cluster then completes the product-forming reaction. Alternatively, two-electron-reduced Fe(III)-peroxo or hydroxo-Fe(V)-oxo activated oxygen intermediates are possible and may be utilized by other ROs to expand the catalytic range. Here, the reaction of a Rieske monooxygenase, salicylate 5-hydroxylase, that does not form a cis-dihydrodiol is examined. Single-turnover kinetic studies show fast binding of salicylate and O₂. Transfer of the Rieske electron required to form the gentisate product occurs through bonds over ∼12 Å and must also be very fast. However, the observed rate constant for this reaction is much slower than expected and sensitive to substrate type. This suggests that initial reaction with salicylate occurs using the same Fe(III)-superoxo-level intermediate as Rieske dioxygenases and that this reaction limits the observed rate of electron transfer. A transient intermediate (λ_max = 700 nm) with an electron paramagnetic resonance (EPR) at g = 4.3 is observed after the product is formed in the active site. The use of ¹⁷O₂ (I = ⁵/₂) results in hyperfine broadening of the g = 4.3 signal, showing that gentisate binds to the mononuclear iron via its C5-OH in the intermediate. The chromophore and EPR signal allow study of product release in the catalytic cycle. Comparison of the kinetics of single- and multiple-turnover reactions shows that re-reduction of the metal centers accelerates product release ∼300-fold, providing insight into the regulatory mechanism of ROs.

Soluble Methane Monooxygenase

Aerobic life is possible because the molecular structure of oxygen (O₂) makes direct reaction with most organic materials at ambient temperatures an exceptionally slow process. Of course, these reactions are inherently very favorable, and they occur rapidly with the release of a great deal of energy at high temperature. Nature has been able to tap this sequestered reservoir of energy with great spatial and temporal selectivity at ambient temperatures through the evolution of oxidase and oxygenase enzymes. One mechanism used by these enzymes for O₂ activation has been studied in detail for the soluble form of the enzyme methane monooxygenase. These studies have revealed the step-by-step process of O₂ activation and insertion into the ultimately stable C-H bond of methane. Additionally, an elegant regulatory mechanism has been defined that enlists size selection and quantum tunneling to allow methane oxidation to occur specifically in the presence of more easily oxidized substrates.

Nuclear Resonance Vibrational Spectroscopy Definition of O2 Intermediates in an Extradiol Dioxygenase: Correlation to Crystallography and Reactivity

The extradiol dioxygenases are a large subclass of mononuclear nonheme Fe enzymes that catalyze the oxidative cleavage of catechols distal to their OH groups. These enzymes are important in bioremediation, and there has been significant interest in understanding how they activate O₂. The extradiol dioxygenase homoprotocatechuate 2,3-dioxygenase (HPCD) provides an opportunity to study this process, as two O₂ intermediates have been trapped and crystallographically defined using the slow substrate 4-nitrocatechol (4NC): a side-on Fe-O₂-4NC species and a Fe-O₂-4NC peroxy bridged species. Also with 4NC, two solution intermediates have been trapped in the H200N variant, where H200 provides a second-sphere hydrogen bond in the wild-type enzyme. While the electronic structure of these solution intermediates has been defined previously as Fe^III-superoxo-catecholate and Fe^III-peroxy-semiquinone, their geometric structures are unknown. Nuclear resonance vibrational spectroscopy (NRVS) is an important tool for structural definition of nonheme Fe-O₂ intermediates, as all normal modes with Fe displacement have intensity in the NRVS spectrum. In this study, NRVS is used to define the geometric structure of the H200N-4NC solution intermediates in HPCD as an end-on Fe^III-superoxo-catecholate and an end-on Fe^III-hydroperoxo-semiquinone. Parallel calculations are performed to define the electronic structures and protonation states of the crystallographically defined wild-type HPCD-4NC intermediates, where the side-on intermediate is found to be a Fe^III-hydroperoxo-semiquinone. The assignment of this crystallographic intermediate is validated by correlation to the NRVS data through computational removal of H200. While the side-on hydroperoxo semiquinone intermediate is computationally found to be nonreactive in peroxide bridge formation, it is isoenergetic with a superoxo catecholate species that is competent in performing this reaction. This study provides insight into the relative reactivities of Fe^III-superoxo and Fe^III-hydroperoxo intermediates in nonheme Fe enzymes and into the role H200 plays in facilitating extradiol catalysis.