1
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Wu P, Zhu W, Chen Y, Wang Z, Kumar A, Wang B, Nam W. cis-Dihydroxylation by Synthetic Iron(III)-Peroxo Intermediates and Rieske Dioxygenases: Experimental and Theoretical Approaches Reveal the Key O-O Bond Activation Step. J Am Chem Soc 2024. [PMID: 39436369 DOI: 10.1021/jacs.4c09354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2024]
Abstract
Dioxygen (O2) activation by iron-containing enzymes and biomimetic compounds generates iron-oxygen intermediates, such as iron-superoxo, -peroxo, -hydroperoxo, and -oxo, that mediate oxidative reactions in biological and abiological systems. Among the iron-oxygen intermediates, iron(III)-peroxo species are less frequently implicated as active intermediates in oxidation reactions. In this study, we present the combined experimental and theoretical investigations on cis-dihydroxylation reactions mediated by synthetic mononuclear nonheme iron-peroxo intermediates, demonstrating the importance of supporting ligands and metal centers in activating the peroxo ligand toward the O-O bond homolysis for the cis-dihydroxylation reactions. We found a significant ring size effect of the TMC ligand in [FeIII(O2)(n-TMC)]+ (TMC = tetramethylated tetraazacycloalkane; n = 12, 13, and 14) on the cis-dihydroxylation reactivity order: [FeIII(O2)(12-TMC)]+ > [FeIII(O2)(13-TMC)]+ > [FeIII(O2)(14-TMC)]+. Additionally, we found that only [FeIII(O2)(n-TMC)]+, but not other metal-peroxo complexes such as [MIII(O2)(n-TMC)]+ (M = Mn, Co, and Ni), is reactive for the cis-dihydroxylation of olefins. Using density functional theory (DFT) calculations, we revealed that electron transfer from the Fe dxz orbital to the peroxo σ*(O-O) orbital facilitates the O-O bond homolysis, with the O-O bond cleavage barrier well correlated with the energy gap between the frontier molecular orbitals of dxz and σ*(O-O). Further computational studies showed that the reactivity of the synthetic [FeIII(O2)(12-TMC)]+ complex is comparable to that of Rieske dioxygenases in cis-dihydroxylation, providing compelling evidence of the potential involvement of Fe(III)-peroxo species in Rieske dioxygenases. Thus, the present results significantly advance our understanding of the cis-dihydroxylation mechanisms by Rieske dioxygenases and synthetic nonheme iron-peroxo models.
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Affiliation(s)
- Peng Wu
- State Key Laboratory of High-Efficiency Utilization of Coal and Green Chemical Engineering, School of Chemistry and Chemical Engineering, Ningxia University, Yinchuan 750021, P. R. China
| | - Wenjuan Zhu
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Yanru Chen
- Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Zikuan Wang
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an der Ruhr D-45470, Germany
| | - Akhilesh Kumar
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Binju Wang
- Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Wonwoo Nam
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
- College of Chemistry and Chemical Engineering, Henan Key Laboratory of Function-Oriented Porous Materials, Luoyang Normal University, Luoyang 471934, P. R. China
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2
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Bopp C, Bernet NM, Meyer F, Khan R, Robinson SL, Kohler HPE, Buller R, Hofstetter TB. Elucidating the Role of O 2 Uncoupling for the Adaptation of Bacterial Biodegradation Reactions Catalyzed by Rieske Oxygenases. ACS ENVIRONMENTAL AU 2024; 4:204-218. [PMID: 39035869 PMCID: PMC11258757 DOI: 10.1021/acsenvironau.4c00016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/26/2024] [Accepted: 04/26/2024] [Indexed: 07/23/2024]
Abstract
Oxygenation of aromatic and aliphatic hydrocarbons by Rieske oxygenases is the initial step of various biodegradation pathways for environmental organic contaminants. Microorganisms carrying Rieske oxygenases are able to quickly adapt their substrate spectra to alternative carbon and energy sources that are structurally related to the original target substrate, yet the molecular events responsible for this rapid adaptation are not well understood. Here, we evaluated the hypothesis that reactive oxygen species (ROS) generated by unproductive activation of O2, the so-called O2 uncoupling, in the presence of the alternative substrate exert a selective pressure on the bacterium for increasing the oxygenation efficiency of Rieske oxygenases. To that end, we studied wild-type 2-nitrotoluene dioxygenase from Acidovorax sp. strain JS42 and five enzyme variants that have evolved from adaptive laboratory evolution experiments with 3- and 4-nitrotoluene as alternative growth substrates. The enzyme variants showed a substantially increased oxygenation efficiency toward the new target substrates concomitant with a reduction of ROS production, while mechanisms and kinetics of enzymatic O2 activation remained unchanged. Structural analyses and docking studies suggest that amino acid substitutions in enzyme variants occurred at residues lining both substrate and O2 transport tunnels, enabling tighter binding of the target substrates in the active site. Increased oxygenation efficiencies measured in vitro for the various enzyme (variant)-substrate combinations correlated linearly with in vivo changes in growth rates for evolved Acidovorax strains expressing the variants. Our data suggest that the selective pressure from oxidative stress toward more efficient oxygenation by Rieske oxygenases was most notable when O2 uncoupling exceeded 60%.
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Affiliation(s)
- Charlotte
E. Bopp
- Eawag,
Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute
of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
| | - Nora M. Bernet
- Eawag,
Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute
of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
| | - Fabian Meyer
- Competence
Center for Biocatalysis, Institute of Chemistry and Biotechnology, Zürich University of Applied Sciences, 8820 Wädenswil, Switzerland
| | - Riyaz Khan
- Eawag,
Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Serina L. Robinson
- Eawag,
Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Hans-Peter E. Kohler
- Eawag,
Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Rebecca Buller
- Competence
Center for Biocatalysis, Institute of Chemistry and Biotechnology, Zürich University of Applied Sciences, 8820 Wädenswil, Switzerland
| | - Thomas B. Hofstetter
- Eawag,
Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute
of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
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3
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Solomon EI, Gipson RR. Spectroscopic definition of ferrous active sites in non-heme iron enzymes. Methods Enzymol 2024; 703:29-49. [PMID: 39261000 PMCID: PMC11391101 DOI: 10.1016/bs.mie.2024.05.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2024]
Abstract
Non-heme iron enzymes play key roles in antibiotic, neurotransmitter, and natural product biosynthesis, DNA repair, hypoxia regulation, and disease states. These enzymes had been refractory to traditional bioinorganic spectroscopic methods. Thus, we developed variable-temperature variable-field magnetic circular dichroism (VTVH MCD) spectroscopy to experimentally define the excited and ground ligand field states of non-heme ferrous enzymes (Solomon et al., 1995). This method provides detailed geometric and electronic structure insight and thus enables a molecular level understanding of catalytic mechanisms. Application of this method across the five classes of non-heme ferrous enzymes has defined that a general mechanistic strategy is utilized where O2 activation is controlled to occur only in the presence of all cosubstrates.
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Affiliation(s)
- Edward I Solomon
- Department of Chemistry, Stanford University, Stanford, CA, United States; Stanford Synchrotron Radiation Lightsource, SLAC National Acceleration Laboratory, Stanford University, Menlo Park, CA, United States.
| | - Robert R Gipson
- Department of Chemistry, Stanford University, Stanford, CA, United States
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4
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Xu J, Li T, Huang WE, Zhou NY. Semi-rational design of nitroarene dioxygenase for catalytic ability toward 2,4-dichloronitrobenzene. Appl Environ Microbiol 2024; 90:e0143623. [PMID: 38709097 PMCID: PMC11218619 DOI: 10.1128/aem.01436-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 04/05/2024] [Indexed: 05/07/2024] Open
Abstract
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.
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Affiliation(s)
- Jia Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Tao Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Wei E. Huang
- Department of Engineering Science, University of Oxford, Oxford, United Kingdom
| | - Ning-Yi Zhou
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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5
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Rogers MS, Lipscomb JD. Approaches to determination of the mechanism of the Rieske monooxygenase salicylate 5-hydroxylase. Methods Enzymol 2024; 704:259-290. [PMID: 39300650 DOI: 10.1016/bs.mie.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2024]
Abstract
Rieske oxygenases catalyze an exceptionally broad range of discrete types of reactions despite the utilization of a highly conserved quaternary structure and metal cofactor complement. Oxygen activation within this family occurs at a mononuclear FeII site, which is located approximately 12 Å from a one-electron reduced Rieske-type iron-sulfur cluster. Electron transfer from the Rieske cluster to the mononuclear iron site occurs during O2 activation and product formation. A key question is whether all Rieske oxygenase reactions involve the same type of activated oxygen species. This question has been explored using the Rieske oxygenase salicylate 5-hydroxylase, which catalyzes both aromatic hydroxylation of salicylate and aromatic methyl hydroxylation when a methyl substituent is placed in the normal position of aromatic ring hydroxylation. We show here that the combined application of kinetic, biophysical, computational, and isotope effect methods reveals a uniform mechanism for initial O2 activation and substrate attack for both types of reactivity. However, the mechanism diverges during the later phases of the reactions in response to the electronic nature and geometry of the substrates as well as the lifetime of intermediates. Similar factors may be encountered broadly in the Rieske oxygenase family.
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Affiliation(s)
- Melanie S Rogers
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, United States
| | - John D Lipscomb
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, United States.
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6
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Heppe N, Gallenkamp C, Snitkoff-Sol RZ, Paul SD, Segura-Salas N, Haak H, Moritz DC, Kaiser B, Jaegermann W, Potapkin V, Jafari A, Schünemann V, Leupold O, Elbaz L, Krewald V, Kramm UI. Applying Nuclear Forward Scattering as In Situ and Operando Tool for the Characterization of FeN 4 Moieties in the Hydrogen Evolution Reaction. J Am Chem Soc 2024; 146:12496-12510. [PMID: 38630640 PMCID: PMC11082898 DOI: 10.1021/jacs.4c00436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/24/2024] [Accepted: 03/26/2024] [Indexed: 04/19/2024]
Abstract
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.
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Affiliation(s)
- Nils Heppe
- Catalysts
and Electrocatalysts, Eduard-Zintl-Institute of Inorganic and Physical
Chemistry, Department of Chemistry, Technical
University Darmstadt, Otto-Berndt-Str. 3, 64287 Darmstadt, Germany
| | - Charlotte Gallenkamp
- Catalysts
and Electrocatalysts, Eduard-Zintl-Institute of Inorganic and Physical
Chemistry, Department of Chemistry, Technical
University Darmstadt, Otto-Berndt-Str. 3, 64287 Darmstadt, Germany
- Quantum
Chemistry, Eduard-Zintl-Institute of Inorganic and Physical Chemistry,
Department of Chemistry, Technical University
Darmstadt, Peter-Grünberg-Str.
4, 64287 Darmstadt, Germany
| | - Rifael Z. Snitkoff-Sol
- Bar-Ilan
Center for Nanotechnology and Advanced Materials and the Department
of Chemistry, Bar-Ilan University, Ramat-Gan 529002, Israel
| | - Stephen D. Paul
- Catalysts
and Electrocatalysts, Eduard-Zintl-Institute of Inorganic and Physical
Chemistry, Department of Chemistry, Technical
University Darmstadt, Otto-Berndt-Str. 3, 64287 Darmstadt, Germany
| | - Nicole Segura-Salas
- Catalysts
and Electrocatalysts, Eduard-Zintl-Institute of Inorganic and Physical
Chemistry, Department of Chemistry, Technical
University Darmstadt, Otto-Berndt-Str. 3, 64287 Darmstadt, Germany
| | - Hendrik Haak
- Catalysts
and Electrocatalysts, Eduard-Zintl-Institute of Inorganic and Physical
Chemistry, Department of Chemistry, Technical
University Darmstadt, Otto-Berndt-Str. 3, 64287 Darmstadt, Germany
| | - Dominik C. Moritz
- Surface
Science Division, Institute of Materials Science, Department of Materials
and Earth Sciences, Technical University
Darmstadt, Otto-Berndt-Str.
3, 64287 Darmstadt, Germany
| | - Bernhard Kaiser
- Surface
Science Division, Institute of Materials Science, Department of Materials
and Earth Sciences, Technical University
Darmstadt, Otto-Berndt-Str.
3, 64287 Darmstadt, Germany
| | - Wolfram Jaegermann
- Surface
Science Division, Institute of Materials Science, Department of Materials
and Earth Sciences, Technical University
Darmstadt, Otto-Berndt-Str.
3, 64287 Darmstadt, Germany
| | - Vasily Potapkin
- Catalysts
and Electrocatalysts, Eduard-Zintl-Institute of Inorganic and Physical
Chemistry, Department of Chemistry, Technical
University Darmstadt, Otto-Berndt-Str. 3, 64287 Darmstadt, Germany
| | - Atefeh Jafari
- Deutsches
Elektronen-Synchrotron, Notkestraße 85, 22607 Hamburg, Germany
| | - Volker Schünemann
- Department
of Physics, University of Kaiserslautern-Landau, Erwin-Schrödinger Straße
56, 67663 Kaiserslautern, Germany
| | - Olaf Leupold
- Deutsches
Elektronen-Synchrotron, Notkestraße 85, 22607 Hamburg, Germany
| | - Lior Elbaz
- Bar-Ilan
Center for Nanotechnology and Advanced Materials and the Department
of Chemistry, Bar-Ilan University, Ramat-Gan 529002, Israel
| | - Vera Krewald
- Quantum
Chemistry, Eduard-Zintl-Institute of Inorganic and Physical Chemistry,
Department of Chemistry, Technical University
Darmstadt, Peter-Grünberg-Str.
4, 64287 Darmstadt, Germany
| | - Ulrike I. Kramm
- Catalysts
and Electrocatalysts, Eduard-Zintl-Institute of Inorganic and Physical
Chemistry, Department of Chemistry, Technical
University Darmstadt, Otto-Berndt-Str. 3, 64287 Darmstadt, Germany
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7
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Chen J, Zhang J, Sun Y, Xu Y, Yang Y, Lee YM, Ji W, Wang B, Nam W, Wang B. Mononuclear Non-Heme Manganese-Catalyzed Enantioselective cis-Dihydroxylation of Alkenes Modeling Rieske Dioxygenases. J Am Chem Soc 2023; 145:27626-27638. [PMID: 38064642 DOI: 10.1021/jacs.3c09508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
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.
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Affiliation(s)
- Jie Chen
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Jinyan Zhang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Ying Sun
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Yuankai Xu
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Yinan Yang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Yong-Min Lee
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Wenhua Ji
- Key Laboratory for Applied Technology of Sophisticated Analytical Instruments of Shandong Province, Shandong Analysis and Test Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Wonwoo Nam
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Bin Wang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
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8
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Tian J, Liu J, Knapp M, Donnan PH, Boggs DG, Bridwell-Rabb J. Custom tuning of Rieske oxygenase reactivity. Nat Commun 2023; 14:5858. [PMID: 37730711 PMCID: PMC10511449 DOI: 10.1038/s41467-023-41428-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 08/27/2023] [Indexed: 09/22/2023] Open
Abstract
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.
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Affiliation(s)
- Jiayi Tian
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jianxin Liu
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Madison Knapp
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Patrick H Donnan
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - David G Boggs
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
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9
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Runda ME, de Kok NAW, Schmidt S. Rieske Oxygenases and Other Ferredoxin-Dependent Enzymes: Electron Transfer Principles and Catalytic Capabilities. Chembiochem 2023; 24:e202300078. [PMID: 36964978 DOI: 10.1002/cbic.202300078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/24/2023] [Accepted: 03/24/2023] [Indexed: 03/27/2023]
Abstract
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.
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Affiliation(s)
- Michael E Runda
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Niels A W de Kok
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Sandy Schmidt
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
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10
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Zhu W, Kumar A, Xiong J, Abernathy MJ, Li XX, Seo MS, Lee YM, Sarangi R, Guo Y, Nam W. Seeing the cis-Dihydroxylating Intermediate: A Mononuclear Nonheme Iron-Peroxo Complex in cis-Dihydroxylation Reactions Modeling Rieske Dioxygenases. J Am Chem Soc 2023; 145:4389-4393. [PMID: 36795537 PMCID: PMC10544271 DOI: 10.1021/jacs.2c13551] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
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.
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Affiliation(s)
- Wenjuan Zhu
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Akhilesh Kumar
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Jin Xiong
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Macon J Abernathy
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford, California 94025, United States
| | - Xiao-Xi Li
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
- Institute of Molecular Sciences and Engineering, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao 266237, China
| | - Mi Sook Seo
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Yong-Min Lee
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Ritimukta Sarangi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford, California 94025, United States
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Wonwoo Nam
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
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11
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Guo M, Zhou S, Sun X. Room-Temperature Conversion of Methane to Methanediol by [FeO 2] . 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] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
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.
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Affiliation(s)
- Mengdi Guo
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
| | - Shaodong Zhou
- College of Chemical and Biological Engineering, Zhejiang Provincial Key Laboratory of Advanced Chemical Engineering Manufacture Technology, Zhejiang University, Hangzhou 310027, China
- Institute of Zhejiang University─Quzhou, Zheda Road No. 99, Quzhou 324000, China
| | - Xiaoyan Sun
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
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12
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Rogers MS, Gordon AM, Rappe TM, Goodpaster JD, Lipscomb JD. Contrasting Mechanisms of Aromatic and Aryl-Methyl Substituent Hydroxylation by the Rieske Monooxygenase Salicylate 5-Hydroxylase. Biochemistry 2023; 62:507-523. [PMID: 36583545 PMCID: PMC9854337 DOI: 10.1021/acs.biochem.2c00610] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
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.
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Affiliation(s)
- Melanie S. Rogers
- Department of Biochemistry, Molecular Biology, and Biophysics and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Adrian M. Gordon
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Todd M. Rappe
- Minnesota NMR Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Jason D. Goodpaster
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - John D. Lipscomb
- Department of Biochemistry, Molecular Biology, and Biophysics and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
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13
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Maldonado-Domínguez M, Srnec M. H-Atom Abstraction Reactivity through the Lens of Asynchronicity and Frustration with Their Counteracting Effects on Barriers. Inorg Chem 2022; 61:18811-18822. [DOI: 10.1021/acs.inorgchem.2c03269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Mauricio Maldonado-Domínguez
- J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences, Dolejškova 3, Prague 8 18223, Czech Republic
| | - Martin Srnec
- J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences, Dolejškova 3, Prague 8 18223, Czech Republic
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14
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Bopp CE, Bernet NM, Kohler HPE, Hofstetter TB. Elucidating the Role of O 2 Uncoupling in the Oxidative Biodegradation of Organic Contaminants by Rieske Non-heme Iron Dioxygenases. ACS ENVIRONMENTAL AU 2022; 2:428-440. [PMID: 36164353 PMCID: PMC9502038 DOI: 10.1021/acsenvironau.2c00023] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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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 FeIII-(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.
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Affiliation(s)
- Charlotte E. Bopp
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
| | - Nora M. Bernet
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Hans-Peter E. Kohler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Thomas B. Hofstetter
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
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15
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Recent progress in oxidation chemistry of high-valent ruthenium-oxo and osmium-oxo complexes and related species. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2022.214536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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16
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Treu P, Sarma BB, Grunwaldt JD, Saraçi E. Oxidative cleavage of vicinal diols catalyzed by monomeric Fe‐sites inside MFI zeolite. ChemCatChem 2022. [DOI: 10.1002/cctc.202200993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Philipp Treu
- Karlsruhe Institute of Technology: Karlsruher Institut fur Technologie Institute of Catalysis Research and Technology GERMANY
| | - Bidyut Bikash Sarma
- Karlsruhe Institute of Technology: Karlsruher Institut fur Technologie Institute of Catalysis Research and Technology GERMANY
| | - Jan-Dierk Grunwaldt
- Karlsruhe Institute of Technology: Karlsruher Institut fur Technologie Institute for Chemical Technology and Polymer Chemistry GERMANY
| | - Erisa Saraçi
- Karlsruhe Institute of Technology Institute for Catalysis Science and Technology Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen GERMANY
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17
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Pati SG, Bopp CE, Kohler HPE, Hofstetter TB. Substrate-Specific Coupling of O 2 Activation to Hydroxylations of Aromatic Compounds by Rieske Non-heme Iron Dioxygenases. ACS Catal 2022; 12:6444-6456. [PMID: 35692249 PMCID: PMC9171724 DOI: 10.1021/acscatal.2c00383] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/09/2022] [Indexed: 02/07/2023]
Abstract
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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
FeII 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 FeIII-(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.
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Affiliation(s)
- Sarah G. Pati
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
| | - Charlotte E. Bopp
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
| | - Hans-Peter E. Kohler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Thomas B. Hofstetter
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
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18
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Csizi K, Eckert L, Brunken C, Hofstetter TB, Reiher M. The Apparently Unreactive Substrate Facilitates the Electron Transfer for Dioxygen Activation in Rieske Dioxygenases. Chemistry 2022; 28:e202103937. [PMID: 35072969 PMCID: PMC9306888 DOI: 10.1002/chem.202103937] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Indexed: 12/29/2022]
Abstract
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 O 2 activation. Here, we studied the role of the substrate in the key elementary reaction leading to O 2 activation from a theoretical perspective by systematically considering (i) the 6-coordinate to 5-coordinate conversion of the non-heme FeII upon abstraction of a water ligand, (ii) binding of O 2 , 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 H2 O reorientation and exothermic O 2 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 O 2 activation.
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Affiliation(s)
- Katja‐Sophia Csizi
- EawagSwiss Federal Institute of Aquatic Science and TechnologyÜberlandstrasse 1338600DübendorfSwitzerland
- ETH ZürichLaboratory for Physical ChemistryVladimir-Prelog-Weg 28093ZürichSwitzerland
| | - Lina Eckert
- ETH ZürichLaboratory for Physical ChemistryVladimir-Prelog-Weg 28093ZürichSwitzerland
| | - Christoph Brunken
- EawagSwiss Federal Institute of Aquatic Science and TechnologyÜberlandstrasse 1338600DübendorfSwitzerland
- ETH ZürichLaboratory for Physical ChemistryVladimir-Prelog-Weg 28093ZürichSwitzerland
| | - Thomas B. Hofstetter
- EawagSwiss Federal Institute of Aquatic Science and TechnologyÜberlandstrasse 1338600DübendorfSwitzerland
| | - Markus Reiher
- ETH ZürichLaboratory for Physical ChemistryVladimir-Prelog-Weg 28093ZürichSwitzerland
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19
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Solomon EI, DeWeese DE, Babicz JT. Mechanisms of O 2 Activation by Mononuclear Non-Heme Iron Enzymes. Biochemistry 2021; 60:3497-3506. [PMID: 34266238 PMCID: PMC8768060 DOI: 10.1021/acs.biochem.1c00370] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Two major subclasses of mononuclear non-heme ferrous enzymes use two electron-donating organic cofactors (α-ketoglutarate or pterin) to activate O2 to form FeIV═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 FeIV═O intermediate and the geometric and electronic structure of this intermediate that enables its high reactivity and selectivity in product formation.
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Affiliation(s)
- Edward I. Solomon
- Department of Chemistry, Stanford University, 333 Campus Dr. Stanford, CA, 94305, United States,SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, 94025, United States
| | - Dory E. DeWeese
- Department of Chemistry, Stanford University, 333 Campus Dr. Stanford, CA, 94305, United States
| | - Jeffrey T. Babicz
- Department of Chemistry, Stanford University, 333 Campus Dr. Stanford, CA, 94305, United States
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20
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Lee JL, Ross DL, Barman SK, Ziller JW, Borovik AS. C-H Bond Cleavage by Bioinspired Nonheme Metal Complexes. Inorg Chem 2021; 60:13759-13783. [PMID: 34491738 DOI: 10.1021/acs.inorgchem.1c01754] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
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.
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Affiliation(s)
- Justin L Lee
- Department of Chemistry, University of California-Irvine, 1102 Natural Sciences II, Irvine, California 92697, United States
| | - Dolores L Ross
- Department of Chemistry, University of California-Irvine, 1102 Natural Sciences II, Irvine, California 92697, United States
| | - Suman K Barman
- Department of Chemistry, University of California-Irvine, 1102 Natural Sciences II, Irvine, California 92697, United States
| | - Joseph W Ziller
- Department of Chemistry, University of California-Irvine, 1102 Natural Sciences II, Irvine, California 92697, United States
| | - A S Borovik
- Department of Chemistry, University of California-Irvine, 1102 Natural Sciences II, Irvine, California 92697, United States
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21
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Direct coordination of pterin to Fe II enables neurotransmitter biosynthesis in the pterin-dependent hydroxylases. Proc Natl Acad Sci U S A 2021; 118:2022379118. [PMID: 33876764 PMCID: PMC8053929 DOI: 10.1073/pnas.2022379118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
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 FeII active site to form a highly reactive FeIV = O species that initiates substrate oxidation. In this study, using tryptophan hydroxylase, we have kinetically generated a pre-FeIV = O intermediate and characterized its structure as a FeII-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 FeII active site before the O2 reaction (including magnetic circular dichroism spectroscopy), these studies both experimentally define the mechanism of FeIV = O formation and demonstrate that the carbonyl functional group on the pterin is directly coordinated to the FeII 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 FeII 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.
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22
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Structural and Biochemical Analysis Reveals a Distinct Catalytic Site of Salicylate 5-Monooxygenase NagGH from Rieske Dioxygenases. Appl Environ Microbiol 2021; 87:AEM.01629-20. [PMID: 33452034 DOI: 10.1128/aem.01629-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 12/22/2020] [Indexed: 11/20/2022] Open
Abstract
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.
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23
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Kal S, Xu S, Que L. Bio-inspired Nonheme Iron Oxidation Catalysis: Involvement of Oxoiron(V) Oxidants in Cleaving Strong C-H Bonds. Angew Chem Int Ed Engl 2020; 59:7332-7349. [PMID: 31373120 DOI: 10.1002/anie.201906551] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Indexed: 11/11/2022]
Abstract
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.
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Affiliation(s)
- Subhasree Kal
- Department of Chemistry, University of Minnesota, Twin Cities, 207 Pleasant Street SE, Minneapolis, MN, 55455, USA
| | - Shuangning Xu
- Department of Chemistry, University of Minnesota, Twin Cities, 207 Pleasant Street SE, Minneapolis, MN, 55455, USA
| | - Lawrence Que
- Department of Chemistry, University of Minnesota, Twin Cities, 207 Pleasant Street SE, Minneapolis, MN, 55455, USA
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24
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Kal S, Xu S, Que L. Bioinspirierte Nicht‐Häm‐Eisenoxidationskatalyse: Beteiligung von Oxoeisen(V)‐Oxidantien an der Spaltung starker C‐H‐Bindungen. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201906551] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Subhasree Kal
- Department of Chemistry University of Minnesota, Twin Cities 207 Pleasant Street SE Minneapolis MN 55455 USA
| | - Shuangning Xu
- Department of Chemistry University of Minnesota, Twin Cities 207 Pleasant Street SE Minneapolis MN 55455 USA
| | - Lawrence Que
- Department of Chemistry University of Minnesota, Twin Cities 207 Pleasant Street SE Minneapolis MN 55455 USA
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25
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Rogers MS, Lipscomb JD. Salicylate 5-Hydroxylase: Intermediates in Aromatic Hydroxylation by a Rieske Monooxygenase. Biochemistry 2019; 58:5305-5319. [PMID: 31066545 PMCID: PMC6856394 DOI: 10.1021/acs.biochem.9b00292] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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 (λmax = 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.
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Affiliation(s)
- Melanie S. Rogers
- Department of Biochemistry, Molecular Biology, and Biophysics and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - John D. Lipscomb
- Department of Biochemistry, Molecular Biology, and Biophysics and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
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Baratto MC, Lipscomb DA, Larkin MJ, Basosi R, Allen CCR, Pogni R. Spectroscopic Characterisation of the Naphthalene Dioxygenase from Rhodococcus sp. Strain NCIMB12038. Int J Mol Sci 2019; 20:E3402. [PMID: 31373299 PMCID: PMC6678576 DOI: 10.3390/ijms20143402] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/01/2019] [Accepted: 07/09/2019] [Indexed: 12/27/2022] Open
Abstract
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.
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Affiliation(s)
- Maria Camilla Baratto
- Department of Biotechnology, Chemistry and Pharmacy, Via A. Moro 2, 53100 Siena, Italy.
- Consorzio per lo Sviluppo dei Sistemi a Grande Interfase (CSGI), via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.
| | - David A Lipscomb
- School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast BT9 5DL, UK
| | - Michael J Larkin
- School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast BT9 5DL, UK
| | - Riccardo Basosi
- Department of Biotechnology, Chemistry and Pharmacy, Via A. Moro 2, 53100 Siena, Italy
- Consorzio per lo Sviluppo dei Sistemi a Grande Interfase (CSGI), via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Christopher C R Allen
- School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast BT9 5DL, UK.
| | - Rebecca Pogni
- Department of Biotechnology, Chemistry and Pharmacy, Via A. Moro 2, 53100 Siena, Italy
- Consorzio per lo Sviluppo dei Sistemi a Grande Interfase (CSGI), via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
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Wittkamp F, Mishra N, Wang H, Wille HC, Steinbrügge R, Kaupp M, Cramer SP, Apfel UP, Pelmenschikov V. Insights from 125Te and 57Fe nuclear resonance vibrational spectroscopy: a [4Fe-4Te] cluster from two points of view. Chem Sci 2019; 10:7535-7541. [PMID: 31588304 PMCID: PMC6761874 DOI: 10.1039/c9sc02025j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 06/22/2019] [Indexed: 11/21/2022] Open
Abstract
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.
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Affiliation(s)
- Florian Wittkamp
- Department of Chemistry and Biochemistry , Inorganic Chemistry I , Ruhr-Universität Bochum , Universitätsstraße 150 , 44801 Bochum , Germany .
| | - Nakul Mishra
- Department of Chemistry , University of California , Davis, One Shields Avenue , Davis , California 95616 , USA .
| | - Hongxin Wang
- Department of Chemistry , University of California , Davis, One Shields Avenue , Davis , California 95616 , USA .
| | - Hans-Christian Wille
- Deutsches Elektronen-Synchrotron DESY , Notkestraße 85 , 22607 Hamburg , Germany
| | - René Steinbrügge
- Deutsches Elektronen-Synchrotron DESY , Notkestraße 85 , 22607 Hamburg , Germany
| | - Martin Kaupp
- Institute of Chemistry , Theoretical Chemistry/Quantum Chemistry , Technical University of Berlin , Sekr. C7, Straße des 17. Juni 135 , 10623 Berlin , Germany .
| | - Stephen P Cramer
- Department of Chemistry , University of California , Davis, One Shields Avenue , Davis , California 95616 , USA .
| | - Ulf-Peter Apfel
- Department of Chemistry and Biochemistry , Inorganic Chemistry I , Ruhr-Universität Bochum , Universitätsstraße 150 , 44801 Bochum , Germany . .,Fraunhofer UMSICHT , Osterfelder Straße 3 , 46047 Oberhausen , Germany
| | - Vladimir Pelmenschikov
- Institute of Chemistry , Theoretical Chemistry/Quantum Chemistry , Technical University of Berlin , Sekr. C7, Straße des 17. Juni 135 , 10623 Berlin , Germany .
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Solomon EI, Iyer SR. Geometric and Electronic Structural Contributions to Fe/O 2 Reactivity. ACTA ACUST UNITED AC 2019; 73:3-14. [PMID: 32391114 DOI: 10.4019/bjscc.73.3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
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 FeII 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 FeIII-OOH and FeIV=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.
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Lyakin OY, Bryliakov KP, Talsi EP. Non-heme oxoiron(V) intermediates in chemo-, regio- and stereoselective oxidation of organic substrates. Coord Chem Rev 2019. [DOI: 10.1016/j.ccr.2019.01.010] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Abstract
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.
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Affiliation(s)
- Rahul Banerjee
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA; , ,
| | - Jason C Jones
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA; , ,
| | - John D Lipscomb
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA; , ,
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31
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Sutherlin KD, Wasada-Tsutsui Y, Mbughuni MM, Rogers MS, Park K, Liu LV, Kwak Y, Srnec M, Böttger LH, Frenette M, Yoda Y, Kobayashi Y, Kurokuzu M, Saito M, Seto M, Hu M, Zhao J, Alp EE, Lipscomb JD, Solomon EI. Nuclear Resonance Vibrational Spectroscopy Definition of O 2 Intermediates in an Extradiol Dioxygenase: Correlation to Crystallography and Reactivity. J Am Chem Soc 2018; 140:16495-16513. [PMID: 30418018 DOI: 10.1021/jacs.8b06517] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
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 FeIII-superoxo-catecholate and FeIII-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 FeIII-superoxo-catecholate and an end-on FeIII-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 FeIII-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 FeIII-superoxo and FeIII-hydroperoxo intermediates in nonheme Fe enzymes and into the role H200 plays in facilitating extradiol catalysis.
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Affiliation(s)
- Kyle D Sutherlin
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Yuko Wasada-Tsutsui
- Department of Life Science and Applied Chemistry, Graduate School of Engineering , Nagoya Institute of Technology , Gokiso-cho, Showa-ku, Nagoya 466-8555 , Japan
| | - Michael M Mbughuni
- Department of Biochemistry, Molecular Biology, & Biophysics , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Melanie S Rogers
- Department of Biochemistry, Molecular Biology, & Biophysics , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Kiyoung Park
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Lei V Liu
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Yeonju Kwak
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Martin Srnec
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Lars H Böttger
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Mathieu Frenette
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Yoshitaka Yoda
- Japan Synchrotron Radiation Research Institute , Hyogo 679-5198 , Japan
| | | | - Masayuki Kurokuzu
- Research Reactor Institute, Kyoto University , Osaka 590-0494 , Japan
| | - Makina Saito
- Research Reactor Institute, Kyoto University , Osaka 590-0494 , Japan
| | - Makoto Seto
- Research Reactor Institute, Kyoto University , Osaka 590-0494 , Japan
| | - Michael Hu
- Advanced Photon Source , Argonne National Laboratory , Lemont , Illinois 60439 , United States
| | - Jiyong Zhao
- Advanced Photon Source , Argonne National Laboratory , Lemont , Illinois 60439 , United States
| | - E Ercan Alp
- Advanced Photon Source , Argonne National Laboratory , Lemont , Illinois 60439 , United States
| | - John D Lipscomb
- Department of Biochemistry, Molecular Biology, & Biophysics , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Edward I Solomon
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States.,SLAC National Accelerator Laboratory , Menlo Park , California 94025 , United States
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