1
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Ali HS, de Visser SP. QM/MM Study Into the Mechanism of Oxidative C=C Double Bond Cleavage by Lignostilbene-α,β-Dioxygenase. Chemistry 2024; 30:e202304172. [PMID: 38373118 DOI: 10.1002/chem.202304172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/29/2024] [Accepted: 02/19/2024] [Indexed: 02/21/2024]
Abstract
The enzymatic biosynthesis of fragrance molecules from lignin fragments is an important reaction in biotechnology for the sustainable production of fine chemicals. In this work we investigated the biosynthesis of vanillin from lignostilbene by a nonheme iron dioxygenase using QM/MM and tested several suggested proposals via either an epoxide or dioxetane intermediate. Binding of dioxygen to the active site of the protein results in the formation of an iron(II)-superoxo species with lignostilbene cation radical. The dioxygenase mechanism starts with electrophilic attack of the terminal oxygen atom of the superoxo group on the central C=C bond of lignostilbene, and the second-coordination sphere effects in the substrate binding pocket guide the reaction towards dioxetane formation. The computed mechanism is rationalized with thermochemical cycles and valence bond schemes that explain the electron transfer processes during the reaction mechanism. Particularly, the polarity of the protein and the local electric field and dipole moments enable a facile electron transfer and an exergonic dioxetane formation pathway.
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Affiliation(s)
- Hafiz Saqib Ali
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Sam P de Visser
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
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2
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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] [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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3
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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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4
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Fu Y, Wang B, Cao Z. Biodegradation of 2,5-Dihydroxypyridine by 2,5-Dihydroxypyridine Dioxygenase and Its Mutants: Insights into O–O Bond Activation and Flexible Reaction Mechanisms from QM/MM Simulations. Inorg Chem 2022; 61:20501-20512. [DOI: 10.1021/acs.inorgchem.2c03229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Yuzhuang Fu
- 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
| | - 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
| | - Zexing Cao
- 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
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5
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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
![]()
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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6
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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: 19] [Impact Index Per Article: 6.3] [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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7
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Goldberg AM, Robinson MK, Starr ES, Marasco RN, Alana AC, Cochrane CS, Klugh KL, Strzeminski DJ, Du M, Colabroy KL, Peterson LW. L-DOPA Dioxygenase Activity on 6-Substituted Dopamine Analogues. Biochemistry 2021; 60:2492-2507. [PMID: 34324302 DOI: 10.1021/acs.biochem.1c00310] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Dioxygenase enzymes are essential protein catalysts for the breakdown of catecholic rings, structural components of plant woody tissue. This powerful chemistry is used in nature to make antibiotics and other bioactive materials or degrade plant material, but we have a limited understanding of the breadth and depth of substrate space for these potent catalysts. Here we report steady-state and pre-steady-state kinetic analysis of dopamine derivatives substituted at the 6-position as substrates of L-DOPA dioxygenase, and an analysis of that activity as a function of the electron-withdrawing nature of the substituent. Steady-state and pre-steady-state kinetic data demonstrate the dopamines are impaired in binding and catalysis with respect to the cosubstrate molecular oxygen, which likely afforded spectroscopic observation of an early reaction intermediate, the semiquinone of dopamine. The reaction pathway of dopamine in the pre-steady state is consistent with a nonproductive mode of binding of oxygen at the active site. Despite these limitations, L-DOPA dioxygenase is capable of binding all of the dopamine derivatives and catalyzing multiple turnovers of ring cleavage for dopamine, 6-bromodopamine, 6-carboxydopamine, and 6-cyanodopamine. 6-Nitrodopamine was a single-turnover substrate. The variety of substrates accepted by the enzyme is consistent with an interplay of factors, including the capacity of the active site to bind large, negatively charged groups at the 6-position and the overall oxidizability of each catecholamine, and is indicative of the utility of extradiol cleavage in semisynthetic and bioremediation applications.
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Affiliation(s)
- Alexander M Goldberg
- Department of Chemistry, Muhlenberg College, 2400 Chew Street, Allentown, Pennsylvania 18104, United States
| | - Miranda K Robinson
- Department of Chemistry, Muhlenberg College, 2400 Chew Street, Allentown, Pennsylvania 18104, United States
| | - Erykah S Starr
- Department of Chemistry, Rhodes College, 2000 North Parkway, Memphis, Tennessee 38112, United States
| | - Ryan N Marasco
- Department of Chemistry, Rhodes College, 2000 North Parkway, Memphis, Tennessee 38112, United States
| | - Alexa C Alana
- Department of Chemistry, Rhodes College, 2000 North Parkway, Memphis, Tennessee 38112, United States
| | - C Skyler Cochrane
- Department of Chemistry, Rhodes College, 2000 North Parkway, Memphis, Tennessee 38112, United States
| | - Kameron L Klugh
- Department of Chemistry, Rhodes College, 2000 North Parkway, Memphis, Tennessee 38112, United States
| | - David J Strzeminski
- Department of Chemistry, Muhlenberg College, 2400 Chew Street, Allentown, Pennsylvania 18104, United States
| | - Muxue Du
- Department of Chemistry, Muhlenberg College, 2400 Chew Street, Allentown, Pennsylvania 18104, United States
| | - Keri L Colabroy
- Department of Chemistry, Muhlenberg College, 2400 Chew Street, Allentown, Pennsylvania 18104, United States
| | - Larryn W Peterson
- Department of Chemistry, Rhodes College, 2000 North Parkway, Memphis, Tennessee 38112, United States
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8
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Wang J, Wang X, Ouyang Q, Liu W, Shan J, Tan H, Li X, Chen G. N-Nitrosation Mechanism Catalyzed by Non-heme Iron-Containing Enzyme SznF Involving Intramolecular Oxidative Rearrangement. Inorg Chem 2021; 60:7719-7731. [PMID: 34004115 DOI: 10.1021/acs.inorgchem.1c00057] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The non-heme iron-dependent enzyme SznF catalyzes a critical N-nitrosation step during the N-nitrosourea pharmacophore biosynthesis in streptozotocin. The intramolecular oxidative rearrangement process is known to proceed at the FeII-containing active site in the cupin domain of SznF, but its mechanism has not been elucidated to date. In this study, based on the density functional theory calculations, a unique mechanism was proposed for the N-nitrosation reaction catalyzed by SznF in which a four-electron oxidation process is accomplished through a series of complicated electron transferring between the iron center and substrate to bypass the high-valent FeIV═O species. In the catalytic reaction pathway, the O2 binds to the iron center and attacks on the substrate to form the peroxo bridge intermediate by obtaining two electrons from the substrate exclusively. Then, instead of cleaving the peroxo bridge, the Cε-Nω bond of the substrate is homolytically cleaved first to form a carbocation intermediate, which polarizes the peroxo bridge and promotes its heterolysis. After O-O bond cleavage, the following reaction steps proceed effortlessly so that the N-nitrosation is accomplished without NO exchange among reaction species.
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Affiliation(s)
- Junkai Wang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Xixi Wang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Qingwen Ouyang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Wei Liu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Jiankai Shan
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Hongwei Tan
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Xichen Li
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Guangju Chen
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
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9
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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: 7] [Impact Index Per Article: 2.3] [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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10
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Zhao R, Guo J, Zhang C, Lu Y, Dagnaw WM, Wang ZX. DFT Mechanistic Insight into the Dioxygenase-like Reactivity of a Co III-peroxo Complex: O–O Bond Cleavage via a [1,3]-Sigmatropic Rearrangement-like Mechanism. Inorg Chem 2020; 59:2051-2061. [DOI: 10.1021/acs.inorgchem.9b03470] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ruihua Zhao
- School of Chemical Sciences, University of Chinese Academy of Sciences, Jia #19, Yuquan Road, Beijing 100039, China
| | - Jiandong Guo
- School of Chemical Sciences, University of Chinese Academy of Sciences, Jia #19, Yuquan Road, Beijing 100039, China
| | - Chaoshen Zhang
- School of Chemical Sciences, University of Chinese Academy of Sciences, Jia #19, Yuquan Road, Beijing 100039, China
| | - Yu Lu
- School of Chemical Sciences, University of Chinese Academy of Sciences, Jia #19, Yuquan Road, Beijing 100039, China
| | - Wasihun Menberu Dagnaw
- School of Chemical Sciences, University of Chinese Academy of Sciences, Jia #19, Yuquan Road, Beijing 100039, China
| | - Zhi-Xiang Wang
- School of Chemical Sciences, University of Chinese Academy of Sciences, Jia #19, Yuquan Road, Beijing 100039, China
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11
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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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12
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Khadka N, Farquhar ER, Hill HE, Shi W, von Lintig J, Kiser PD. Evidence for distinct rate-limiting steps in the cleavage of alkenes by carotenoid cleavage dioxygenases. J Biol Chem 2019; 294:10596-10606. [PMID: 31138651 DOI: 10.1074/jbc.ra119.007535] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 05/24/2019] [Indexed: 11/06/2022] Open
Abstract
Carotenoid cleavage dioxygenases (CCDs) use a nonheme Fe(II) cofactor to split alkene bonds of carotenoid and stilbenoid substrates. The iron centers of CCDs are typically five-coordinate in their resting states, with solvent occupying an exchangeable site. The involvement of this iron-bound solvent in CCD catalysis has not been experimentally addressed, but computational studies suggest two possible roles. 1) Solvent dissociation provides a coordination site for O2, or 2) solvent remains bound to iron but changes its equilibrium position to allow O2 binding and potentially acts as a proton source. To test these predictions, we investigated isotope effects (H2O versus D2O) on two stilbenoid-cleaving CCDs, Novosphingobium aromaticivorans oxygenase 2 (NOV2) and Neurospora crassa carotenoid oxygenase 1 (CAO1), using piceatannol as a substrate. NOV2 exhibited an inverse isotope effect (k H/k D ∼ 0.6) in an air-saturated buffer, suggesting that solvent dissociates from iron during the catalytic cycle. By contrast, CAO1 displayed a normal isotope effect (k H/k D ∼ 1.7), suggesting proton transfer in the rate-limiting step. X-ray absorption spectroscopy on NOV2 and CAO1 indicated that the protonation states of the iron ligands are unchanged within pH 6.5-8.5 and that the Fe(II)-aquo bond is minimally altered by substrate binding. We pinpointed the origin of the differential kinetic behaviors of NOV2 and CAO1 to a single amino acid difference near the solvent-binding site of iron, and X-ray crystallography revealed that the substitution alters binding of diffusible ligands to the iron center. We conclude that solvent-iron dissociation and proton transfer are both associated with the CCD catalytic mechanism.
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Affiliation(s)
- Nimesh Khadka
- From the Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
| | - Erik R Farquhar
- National Synchrotron Light Source-II, Brookhaven National Laboratory, Upton, New York 11973.,Center for Proteomics and Bioinformatics, Center for Synchrotron Biosciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106-4988, and
| | - Hannah E Hill
- From the Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
| | - Wuxian Shi
- National Synchrotron Light Source-II, Brookhaven National Laboratory, Upton, New York 11973.,Center for Proteomics and Bioinformatics, Center for Synchrotron Biosciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106-4988, and
| | - Johannes von Lintig
- From the Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
| | - Philip D Kiser
- From the Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, .,Research Service, Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio 44106
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13
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Gass IA, Lu J, Ojha R, Asadi M, Lupton DW, Geoghegan BL, Moubaraki B, Martin LL, Bond AM, Murray KS. [FeII(L•)2][TCNQF4•−]2: A Redox-Active Double Radical Salt. Aust J Chem 2019. [DOI: 10.1071/ch19175] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The reaction of [FeII(L•)2][BF4]2 with LiTCNQF4 results in the formation of [FeII(L•)2][TCNQF4•−]2·2CH3CN (1) (L• is the neutral aminoxyl radical ligand 4,4-dimethyl-2,2-di(2-pyridyl)oxazolidine-N-oxide; TCNQF4 is 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane). Single-crystal X-ray diffraction; Raman, Fourier-transform infrared (FTIR) and ultraviolet–visible spectroscopies; and electrochemical studies are all consistent with the presence of a low-spin FeII ion, the neutral radical form (L•) of the ligand, and the radical anion TCNQF4•−. 1 is largely diamagnetic and the electrochemistry shows five well-resolved, diffusion-controlled, reversible one-electron processes.
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