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Babicz JT, Rogers MS, DeWeese DE, Sutherlin KD, Banerjee R, Böttger LH, Yoda Y, Nagasawa N, Saito M, Kitao S, Kurokuzu M, Kobayashi Y, Tamasaku K, Seto M, Lipscomb JD, Solomon EI. Nuclear Resonance Vibrational Spectroscopy Definition of Peroxy Intermediates in Catechol Dioxygenases: Factors that Determine Extra- versus Intradiol Cleavage. J Am Chem Soc 2023; 145:15230-15250. [PMID: 37414058 PMCID: PMC10804917 DOI: 10.1021/jacs.3c02242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
The extradiol dioxygenases (EDOs) and intradiol dioxygenases (IDOs) are nonheme iron enzymes that catalyze the oxidative aromatic ring cleavage of catechol substrates, playing an essential role in the carbon cycle. The EDOs and IDOs utilize very different FeII and FeIII active sites to catalyze the regiospecificity in their catechol ring cleavage products. The factors governing this difference in cleavage have remained undefined. The EDO homoprotocatechuate 2,3-dioxygenase (HPCD) and IDO protocatechuate 3,4-dioxygenase (PCD) provide an opportunity to understand this selectivity, as key O2 intermediates have been trapped for both enzymes. Nuclear resonance vibrational spectroscopy (in conjunction with density functional theory calculations) is used to define the geometric and electronic structures of these intermediates as FeII-alkylhydroperoxo (HPCD) and FeIII-alkylperoxo (PCD) species. Critically, in both intermediates, the initial peroxo bond orientation is directed toward extradiol product formation. Reaction coordinate calculations were thus performed to evaluate both the extra- and intradiol O-O cleavage for the simple organic alkylhydroperoxo and for the FeII and FeIII metal catalyzed reactions. These results show the FeII-alkylhydroperoxo (EDO) intermediate undergoes facile extradiol O-O bond homolysis due to its extra e-, while for the FeIII-alkylperoxo (IDO) intermediate the extradiol cleavage involves a large barrier and would yield the incorrect extradiol product. This prompted our evaluation of a viable mechanism to rearrange the FeIII-alkylperoxo IDO intermediate for intradiol cleavage, revealing a key role in the rebinding of the displaced Tyr447 ligand in this rearrangement, driven by the proton delivery necessary for O-O bond cleavage.
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Affiliation(s)
- Jeffrey T. Babicz
- Department of Chemistry, Stanford University, 380 Roth Way, Stanford, California 94305, United States
| | - Melanie S. Rogers
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55391, United States
| | - Dory E. DeWeese
- Department of Chemistry, Stanford University, 380 Roth Way, Stanford, California 94305, United States
| | - Kyle D. Sutherlin
- Department of Chemistry, Stanford University, 380 Roth Way, Stanford, California 94305, United States
| | - Rahul Banerjee
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55391, United States
| | - Lars H. Böttger
- Department of Chemistry, Stanford University, 380 Roth Way, Stanford, California 94305, United States
| | - Yoshitaka Yoda
- Japan Synchrotron Radiation Research Institute, Hyogo 679-5198, Japan
| | - Nobumoto Nagasawa
- Japan Synchrotron Radiation Research Institute, Hyogo 679-5198, Japan
| | - Makina Saito
- Department of Physics, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Shinji Kitao
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka 590-0494, Japan
| | - Masayuki Kurokuzu
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka 590-0494, Japan
| | - Yasuhiro Kobayashi
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka 590-0494, Japan
| | - Kenji Tamasaku
- RIKEN SPring-8 Center, RIKEN, Sayo, Hyogo 679-5148, Japan
| | - Makoto Seto
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka 590-0494, Japan
| | - John D. Lipscomb
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55391, United States
| | - Edward I. Solomon
- Department of Chemistry, Stanford University, 380 Roth Way, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
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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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Jacobs AB, Banerjee R, Deweese DE, Braun A, Babicz JT, Gee LB, Sutherlin KD, Böttger LH, Yoda Y, Saito M, Kitao S, Kobayashi Y, Seto M, Tamasaku K, Lipscomb JD, Park K, Solomon EI. Nuclear Resonance Vibrational Spectroscopic Definition of the Fe(IV) 2 Intermediate Q in Methane Monooxygenase and Its Reactivity. J Am Chem Soc 2021; 143:16007-16029. [PMID: 34570980 PMCID: PMC8631202 DOI: 10.1021/jacs.1c05436] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Methanotrophic bacteria utilize the nonheme diiron enzyme soluble methane monooxygenase (sMMO) to convert methane to methanol in the first step of their metabolic cycle under copper-limiting conditions. The structure of the sMMO Fe(IV)2 intermediate Q responsible for activating the inert C-H bond of methane (BDE = 104 kcal/mol) remains controversial, with recent studies suggesting both "open" and "closed" core geometries for its active site. In this study, we employ nuclear resonance vibrational spectroscopy (NRVS) to probe the geometric and electronic structure of intermediate Q at cryogenic temperatures. These data demonstrate that Q decays rapidly during the NRVS experiment. Combining data from several years of measurements, we derive the NRVS vibrational features of intermediate Q as well as its cryoreduced decay product. A library of 90 open and closed core models of intermediate Q is generated using density functional theory to analyze the NRVS data of Q and its cryoreduced product as well as prior spectroscopic data on Q. Our analysis reveals that a subset of closed core models reproduce these newly acquired NRVS data as well as prior data. The reaction coordinate with methane is also evaluated using both closed and open core models of Q. These studies show that the potent reactivity of Q toward methane resides in the "spectator oxo" of its Fe(IV)2O2 core, in contrast to nonheme mononuclear Fe(IV)═O enzyme intermediates that H atoms abstract from weaker C-H bonds.
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Affiliation(s)
- Ariel B. Jacobs
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, California, 94305, United States
| | - Rahul Banerjee
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55391 U.S.A
| | - Dory E. Deweese
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, California, 94305, United States
| | - Augustin Braun
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, California, 94305, United States
| | - Jeffrey T. Babicz
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, California, 94305, United States
| | - Leland B. Gee
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, California, 94305, United States
| | - Kyle D. Sutherlin
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, California, 94305, United States
| | - Lars H. Böttger
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, California, 94305, United States
| | - Yoshitaka Yoda
- Japan Synchrotron Radiation Research Institute, Hyogo 679-5198, Japan
| | - Makina Saito
- Department of Physics, Graduate School of Science, Tohoku University, Sendai, Miyagi 980-8578 Japan
| | - Shinji Kitao
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka, 590-0494
| | - Yasuhiro Kobayashi
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka, 590-0494
| | - Makoto Seto
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka, 590-0494
| | - Kenji Tamasaku
- RIKEN SPring-8 Center, RIKEN, Sayo, Hyogo, 679-5148, Japan
| | - John D. Lipscomb
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55391 U.S.A
| | - Kiyoung Park
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Edward I. Solomon
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, California, 94305, United States,Stanford Synchrotron Radiation Light Source, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California, 94025, United States
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Chen G, Gee LB, Xu W, Zhu Y, Lezama-Pacheco JS, Huang Z, Li Z, Babicz JT, Choudhury S, Chang TH, Reed E, Solomon EI, Bao Z. Valence-Dependent Electrical Conductivity in a 3D Tetrahydroxyquinone-Based Metal-Organic Framework. J Am Chem Soc 2020; 142:21243-21248. [PMID: 33315385 DOI: 10.1021/jacs.0c09379] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Electrically conductive metal-organic frameworks (cMOFs) have become a topic of intense interest in recent years because of their great potential in electrochemical energy storage, electrocatalysis, and sensing applications. Most of the cMOFs reported hitherto are 2D structures, and 3D cMOFs remain rare. Herein we report FeTHQ, a 3D cMOF synthesized from tetrahydroxy-1,4-quinone (THQ) and iron(II) sulfate salt. FeTHQ exhibited a conductivity of 3.3 ± 0.55 mS cm-1 at 300 K, which is high for 3D cMOFs. The conductivity of FeTHQ is valence-dependent. A higher conductivity was measured with the as-prepared FeTHQ than with the air-oxidized and sodium naphthalenide-reduced samples.
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Affiliation(s)
- Gan Chen
- Department of Materials Science and Engineering, Stanford University, Stanford, California 94305, United States
| | - Leland B Gee
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Wenqian Xu
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Yanbing Zhu
- Department of Applied Physics, Stanford University, Stanford, California 94305, United States
| | - Juan S Lezama-Pacheco
- Department of Earth System Science, Stanford University, Stanford, California 94305, United States
| | - Zhehao Huang
- Berzelii Centre EXSELENT on Porous Materials, Department of Materials and Environmental Chemistry, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Zongqi Li
- Department of Materials Science and Engineering, Stanford University, Stanford, California 94305, United States
| | - Jeffrey T Babicz
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Snehashis Choudhury
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Ting-Hsiang Chang
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Evan Reed
- Department of Materials Science and Engineering, Stanford University, Stanford, California 94305, United States
| | - Edward I Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305, United States.,Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Zhenan Bao
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
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Goudarzi S, Babicz JT, Kabil O, Banerjee R, Solomon EI. Spectroscopic and Electronic Structure Study of ETHE1: Elucidating the Factors Influencing Sulfur Oxidation and Oxygenation in Mononuclear Nonheme Iron Enzymes. J Am Chem Soc 2018; 140:14887-14902. [PMID: 30362717 DOI: 10.1021/jacs.8b09022] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
ETHE1 is a member of a growing subclass of nonheme Fe enzymes that catalyzes transformations of sulfur-containing substrates without a cofactor. ETHE1 dioxygenates glutathione persulfide (GSSH) to glutathione (GSH) and sulfite in a reaction which is similar to that of cysteine dioxygenase (CDO), but with monodentate (vs bidentate) substrate coordination and a 2-His/1-Asp (vs 3-His) ligand set. In this study, we demonstrate that GSS- binds directly to the iron active site, causing coordination unsaturation to prime the site for O2 activation. Nitrosyl complexes without and with GSSH were generated and spectroscopically characterized as unreactive analogues for the invoked ferric superoxide intermediate. New spectral features from persulfide binding to the FeIII include the appearance of a low-energy FeIII ligand field transition, an energy shift of a NO- to FeIII CT transition, and two new GSS- to FeIII CT transitions. Time-dependent density functional theory calculations were used to simulate the experimental spectra to determine the persulfide orientation. Correlation of these spectral features with those of monodentate cysteine binding in isopenicillin N synthase (IPNS) shows that the persulfide is a poorer donor but still results in an equivalent frontier molecular orbital for reactivity. The ETHE1 persulfide dioxygenation reaction coordinate was calculated, and while the initial steps are similar to the reaction coordinate of CDO, an additional hydrolysis step is required in ETHE1 to break the S-S bond. Unlike ETHE1 and CDO, which both oxygenate sulfur, IPNS oxidizes sulfur through an initial H atom abstraction. Thus, factors that determine oxygenase vs oxidase reactivity were evaluated. In general, sulfur oxygenation is thermodynamically favored and has a lower barrier for reactivity. However, in IPNS, second-sphere residues in the active site pocket constrain the substrate, raising the barrier for sulfur oxygenation relative to oxidation via H atom abstraction.
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Affiliation(s)
- Serra Goudarzi
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Jeffrey T Babicz
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Omer Kabil
- Department of Biological Chemistry , University of Michigan Medical School , Ann Arbor , Michigan 48109 , United States
| | - Ruma Banerjee
- Department of Biological Chemistry , University of Michigan Medical School , Ann Arbor , Michigan 48109 , 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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6
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Machczynski MC, Babicz JT. Correlating the structures and activities of the resting oxidized and native intermediate states of a small laccase by paramagnetic NMR. J Inorg Biochem 2016; 159:62-9. [PMID: 26918900 DOI: 10.1016/j.jinorgbio.2016.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Revised: 01/10/2016] [Accepted: 02/10/2016] [Indexed: 02/01/2023]
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