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Miyazaki Y, Oohora K, Hayashi T. Focusing on a nickel hydrocorphinoid in a protein matrix: methane generation by methyl-coenzyme M reductase with F430 cofactor and its models. Chem Soc Rev 2022; 51:1629-1639. [PMID: 35148362 DOI: 10.1039/d1cs00840d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Methyl-coenzyme M reductase (MCR) containing a nickel hydrocorphinoid cofactor, F430, is an essential enzyme that catalyzes anaerobic methane generation and oxidation. The active Ni(I) species in MCR converts methyl-coenzyme M (CH3S-CoM) and coenzyme B (HS-CoB) to methane and heterodisulfide (CoM-S-S-CoB). Extensive experimental and theoretical studies focusing on the substrate-binding cavity including the F430 cofactor in MCR have suggested two principally different reaction mechanisms involving an organonickel CH3-Ni(III) species or a transient methyl radical species. In parallel with research on native MCR itself, the functionality of MCR has been investigated in the context of model complexes of F430 and recent protein-based functional models, which include a nickel complex. In the latter case, hemoproteins reconstituted with tetradehydro- and didehydrocorrinoid nickel complexes have been found to represent useful model systems that are responsible for methane generation. These efforts support the proposed mechanism of the enzymatic reaction and provide important insight into replicating the MCR-like methane-generation process. Furthermore, the modeling of MCR described here is expected to lead to understanding of protein-supported nickel porphyrinoid chemistry as well as the creation of MCR-inspired catalysis.
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Affiliation(s)
- Yuta Miyazaki
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita 565-0871, Japan.
| | - Koji Oohora
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita 565-0871, Japan.
| | - Takashi Hayashi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita 565-0871, Japan.
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2
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Oohora K, Hayashi T. Myoglobins engineered with artificial cofactors serve as artificial metalloenzymes and models of natural enzymes. Dalton Trans 2021; 50:1940-1949. [PMID: 33433532 DOI: 10.1039/d0dt03597a] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Metalloenzymes naturally achieve various reactivities by assembling limited types of cofactors with endogenous amino acid residues. Enzymes containing metal porphyrinoid cofactors such as heme, cobalamin and F430 exert precise control over the reactivities of the cofactors with protein matrices. This perspective article focuses on our recent efforts to assemble metal complexes of non-natural porphyrinoids within the protein matrix of myoglobin, an oxygen storage hemoprotein. Engineered myoglobins with suitable metal complexes as artificial cofactors demonstrate unique reactivities toward C-H bond hydroxylation, olefin cyclopropanation, methyl group transfer and methane generation. In these cases, the protein matrix enhances the catalytic activities of the cofactors and allows us to monitor the active intermediates. The present findings indicate that placing artificial cofactors in protein matrices provides a useful strategy for creating artificial metalloenzymes that catalyse otherwise unfavourable reactions and providing enzyme models for elucidating the complicated reaction mechanisms of natural enzymes.
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Affiliation(s)
- Koji Oohora
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, 565-0871, Japan.
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3
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Kisgeropoulos EC, Manesis AC, Shafaat HS. Ligand Field Inversion as a Mechanism to Gate Bioorganometallic Reactivity: Investigating a Biochemical Model of Acetyl CoA Synthase Using Spectroscopy and Computation. J Am Chem Soc 2021; 143:849-867. [PMID: 33415980 DOI: 10.1021/jacs.0c10135] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The biological global carbon cycle is largely regulated through microbial nickel enzymes, including carbon monoxide dehydrogenase (CODH), acetyl coenzyme A synthase (ACS), and methyl coenzyme M reductase (MCR). These systems are suggested to utilize organometallic intermediates during catalysis, though characterization of these species has remained challenging. We have established a mutant of nickel-substituted azurin as a scaffold upon which to develop protein-based models of enzymatic intermediates, including the organometallic states of ACS. In this work, we report the comprehensive investigation of the S = 1/2 Ni-CO and Ni-CH3 states using pulsed EPR spectroscopy and computational techniques. While the Ni-CO state shows conventional metal-ligand interactions and a classical ligand field, the Ni-CH3 hyperfine interactions between the methyl protons and the nickel indicate a closer distance than would be expected for an anionic methyl ligand. Structural analysis instead suggests a near-planar methyl ligand that can be best described as cationic. Consistent with this conclusion, the frontier molecular orbitals of the Ni-CH3 species indicate a ligand-centered LUMO, with a d9 population on the metal center, rather than the d7 population expected for a typical metal-alkyl species generated by oxidative addition. Collectively, these data support the presence of an inverted ligand field configuration for the Ni-CH3 Az species, in which the lowest unoccupied orbital is centered on the ligands rather than the more electropositive metal. These analyses provide the first evidence for an inverted ligand field within a biological system. The functional relevance of the electronic structures of both the Ni-CO and Ni-CH3 species are discussed in the context of native ACS, and an inverted ligand field is proposed as a mechanism by which to gate reactivity both within ACS and in other thiolate-containing metalloenzymes.
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Affiliation(s)
- Effie C Kisgeropoulos
- Department of Chemistry and Biochemistry and Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, United States
| | - Anastasia C Manesis
- Department of Chemistry and Biochemistry and Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, United States
| | - Hannah S Shafaat
- Department of Chemistry and Biochemistry and Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, United States
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4
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Hirscher NA, Arnett CH, Oyala PH, Agapie T. Characterization of Cr-Hydrocarbyl Species via Pulse EPR in the Study of Ethylene Tetramerization Catalysis. Organometallics 2020. [DOI: 10.1021/acs.organomet.0c00521] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nathanael A. Hirscher
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Charles H. Arnett
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Paul H. Oyala
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Theodor Agapie
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
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5
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Miyazaki Y, Oohora K, Hayashi T. Methane Generation and Reductive Debromination of Benzylic Position by Reconstituted Myoglobin Containing Nickel Tetradehydrocorrin as a Model of Methyl-coenzyme M Reductase. Inorg Chem 2020; 59:11995-12004. [PMID: 32794737 DOI: 10.1021/acs.inorgchem.0c00901] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Methyl-coenzyme M reductase (MCR), which contains the nickel hydrocorphinoid cofactor F430, is responsible for biological methane generation under anaerobic conditions via a reaction mechanism which has not been completely elucidated. In this work, myoglobin reconstituted with an artificial cofactor, nickel(I) tetradehydrocorrin (NiI(TDHC)), is used as a protein-based functional model for MCR. The reconstituted protein, rMb(NiI(TDHC)), is found to react with methyl donors such as methyl p-toluenesulfonate and trimethylsulfonium iodide with methane evolution observed in aqueous media containing dithionite. Moreover, rMb(NiI(TDHC)) is found to convert benzyl bromide derivatives to reductively debrominated products without homocoupling products. The reactivity increases in the order of primary > secondary > tertiary benzylic carbons, indicating steric effects on the reaction of the nickel center with the benzylic carbon in the initial step. In addition, Hammett plots using a series of para-substituted benzyl bromides exhibit enhancement of the reactivity with introduction of electron-withdrawing substituents, as shown by the positive slope against polar substituent constants. These results suggest a nucleophilic SN2-type reaction of the Ni(I) species with the benzylic carbon to provide an organonickel species as an intermediate. The reaction in D2O buffer at pD 7.0 causes a complete isotope shift of the product by +1 mass unit, supporting our proposal that protonation of the organonickel intermediate occurs during product formation. Although the turnover numbers are limited due to inactivation of the cofactor by side reactions, the present findings will contribute to elucidating the reaction mechanism of MCR-catalyzed methane generation from activated methyl sources and dehalogenation.
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Affiliation(s)
- Yuta Miyazaki
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita 565-0871, Japan
| | - Koji Oohora
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita 565-0871, Japan
| | - Takashi Hayashi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita 565-0871, Japan
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6
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Nickel(II)‐Mediated Reversible Thiolate/Disulfide Conversion as a Mimic for a Key Step of the Catalytic Cycle of Methyl‐Coenzyme M Reductase. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202001363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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7
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Bhandari A, Mishra S, Maji RC, Kumar A, Olmstead MM, Patra AK. Nickel(II)‐Mediated Reversible Thiolate/Disulfide Conversion as a Mimic for a Key Step of the Catalytic Cycle of Methyl‐Coenzyme M Reductase. Angew Chem Int Ed Engl 2020; 59:9177-9185. [DOI: 10.1002/anie.202001363] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Indexed: 01/22/2023]
Affiliation(s)
- Anirban Bhandari
- Department of Chemistry National Institute of Technology Durgapur Mahatma Gandhi Avenue Durgapur 713 209 (WB) India
| | - Saikat Mishra
- Department of Chemistry National Institute of Technology Durgapur Mahatma Gandhi Avenue Durgapur 713 209 (WB) India
| | - Ram Chandra Maji
- Department of Chemistry National Institute of Technology Durgapur Mahatma Gandhi Avenue Durgapur 713 209 (WB) India
| | - Akhilesh Kumar
- Department of Chemistry Indian Institute of Technology Kanpur Kanpur 208016 India
| | | | - Apurba K. Patra
- Department of Chemistry National Institute of Technology Durgapur Mahatma Gandhi Avenue Durgapur 713 209 (WB) India
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8
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Methane generation via intraprotein C–S bond cleavage in cytochrome b562 reconstituted with nickel didehydrocorrin. J Organomet Chem 2019. [DOI: 10.1016/j.jorganchem.2019.120945] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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9
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Oohora K, Miyazaki Y, Hayashi T. Myoglobin Reconstituted with Ni Tetradehydrocorrin as a Methane‐Generating Model of Methyl‐coenzyme M Reductase. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201907584] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Koji Oohora
- Department of Applied Chemistry Graduate School of Engineering Osaka University 2-1 Yamadaoka Suita 565-0871 Japan
- Frontier Research Base for Global Young Researchers Graduate School of Engineering Osaka University 2-1 Yamadaoka Suita 565-0871 Japan
| | - Yuta Miyazaki
- Department of Applied Chemistry Graduate School of Engineering Osaka University 2-1 Yamadaoka Suita 565-0871 Japan
| | - Takashi Hayashi
- Department of Applied Chemistry Graduate School of Engineering Osaka University 2-1 Yamadaoka Suita 565-0871 Japan
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10
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Oohora K, Miyazaki Y, Hayashi T. Myoglobin Reconstituted with Ni Tetradehydrocorrin as a Methane-Generating Model of Methyl-coenzyme M Reductase. Angew Chem Int Ed Engl 2019; 58:13813-13817. [PMID: 31347228 DOI: 10.1002/anie.201907584] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/20/2019] [Indexed: 11/05/2022]
Abstract
Myoglobin reconstituted with Ni tetradehydrocorrin was investigated as a model of F430-containing methyl-coenzyme M reductase, which catalyzes anaerobic methane generation. The NiII tetradehydrocorrin complex has a NiII /NiI redox potential of -0.34 V vs. SHE and EPR spectroscopy indicates the formation of a NiI species upon reduction by dithionite. This redox potential is approximately 0.31 V more positive than that of F430. The NiI tetradehydrocorrin moiety is bound to the apo-form of myoglobin to yield the reconstituted protein. Methane gas is generated in the reaction of the model with methyl iodide in the presence of the reconstituted protein under reductive conditions, whereas the NiI complex itself does not produce methane gas. This is the first example of a protein-based functional model of F430-containing methyl-coenzyme M reductase.
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Affiliation(s)
- Koji Oohora
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, 565-0871, Japan.,Frontier Research Base for Global Young Researchers, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, 565-0871, Japan
| | - Yuta Miyazaki
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, 565-0871, Japan
| | - Takashi Hayashi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, 565-0871, Japan
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11
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Abstract
The advancements of quantum chemical methods and computer power allow detailed mechanistic investigations of metalloenzymes. In particular, both quantum chemical cluster and combined QM/MM approaches have been used, which have been proven to successfully complement experimental studies. This review starts with a brief introduction of nickel-dependent enzymes and then summarizes theoretical studies on the reaction mechanisms of these enzymes, including NiFe hydrogenase, methyl-coenzyme M reductase, nickel CO dehydrogenase, acetyl CoA synthase, acireductone dioxygenase, quercetin 2,4-dioxygenase, urease, lactate racemase, and superoxide dismutase.
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12
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Thauer RK. Methyl (Alkyl)-Coenzyme M Reductases: Nickel F-430-Containing Enzymes Involved in Anaerobic Methane Formation and in Anaerobic Oxidation of Methane or of Short Chain Alkanes. Biochemistry 2019; 58:5198-5220. [PMID: 30951290 PMCID: PMC6941323 DOI: 10.1021/acs.biochem.9b00164] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Methyl-coenzyme
M reductase (MCR) catalyzes the methane-forming
step in methanogenic archaea. The active enzyme harbors the nickel(I)
hydrocorphin coenzyme F-430 as a prosthetic group and catalyzes the
reversible reduction of methyl-coenzyme M (CH3–S-CoM)
with coenzyme B (HS-CoM) to methane and CoM-S–S-CoB. MCR is
also involved in anaerobic methane oxidation in reverse of methanogenesis
and most probably in the anaerobic oxidation of ethane, propane, and
butane. The challenging question is how the unreactive CH3–S thioether bond in methyl-coenzyme M and the even more unreactive
C–H bond in methane and the other hydrocarbons are anaerobically
cleaved. A key to the answer is the negative redox potential (Eo′) of the Ni(II)F-430/Ni(I)F-430 couple
below −600 mV and the radical nature of Ni(I)F-430. However,
the negative one-electron redox potential is also the Achilles heel
of MCR; it makes the nickel enzyme one of the most O2-sensitive
enzymes known to date. Even under physiological conditions, the Ni(I)
in MCR is oxidized to the Ni(II) or Ni(III) states, e.g., when in
the cells the redox potential (E′) of the
CoM-S–S-CoB/HS-CoM and HS-CoB couple (Eo′ = −140 mV) gets too high. Methanogens therefore
harbor an enzyme system for the reactivation of inactivated MCR in
an ATP-dependent reduction reaction. Purification of active MCR in
the Ni(I) oxidation state is very challenging and has been achieved
in only a few laboratories. This perspective reviews the function,
structure, and properties of MCR, what is known and not known about
the catalytic mechanism, how the inactive enzyme is reactivated, and
what remains to be discovered.
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Affiliation(s)
- Rudolf K Thauer
- Max Planck Institute for Terrestrial Microbiology , Karl-von-Frisch-Strasse 10 , Marburg 35043 , Germany
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13
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Manesis AC, Musselman BW, Keegan BC, Shearer J, Lehnert N, Shafaat HS. A Biochemical Nickel(I) State Supports Nucleophilic Alkyl Addition: A Roadmap for Methyl Reactivity in Acetyl Coenzyme A Synthase. Inorg Chem 2019; 58:8969-8982. [PMID: 30788970 PMCID: PMC6635881 DOI: 10.1021/acs.inorgchem.8b03546] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
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Nickel-containing
enzymes such as methyl coenzyme M reductase (MCR) and carbon monoxide
dehydrogenase/acetyl coenzyme A synthase (CODH/ACS) play a critical
role in global energy conversion reactions, with significant contributions
to carbon-centered processes. These enzymes are implied to cycle through
a series of nickel-based organometallic intermediates during catalysis,
though identification of these intermediates remains challenging.
In this work, we have developed and characterized a nickel-containing
metalloprotein that models the methyl-bound organometallic intermediates
proposed in the native enzymes. Using a nickel(I)-substituted azurin
mutant, we demonstrate that alkyl binding occurs via nucleophilic
addition of methyl iodide as a methyl donor. The paramagnetic NiIII-CH3 species initially generated can be rapidly
reduced to a high-spin NiII-CH3 species in the
presence of exogenous reducing agent, following a reaction sequence
analogous to that proposed for ACS. These two distinct bioorganometallic
species have been characterized by optical, EPR, XAS, and MCD spectroscopy,
and the overall mechanism describing methyl reactivity with nickel
azurin has been quantitatively modeled using global kinetic simulations.
A comparison between the nickel azurin protein system and existing
ACS model compounds is presented. NiIII-CH3 Az
is only the second example of two-electron addition of methyl iodide
to a NiI center to give an isolable species and the first
to be formed in a biologically relevant system. These results highlight
the divergent reactivity of nickel across the two intermediates, with
implications for likely reaction mechanisms and catalytically relevant
states in the native ACS enzyme. A bioorganometallic model
for acetyl coenzyme A synthase has been developed. This model protein
is able to bind a cationic methyl group via direct addition to the
nickel(I) center. The resultant nickel(III)-methyl species has been
characterized via optical and electron paramagnetic resonance spectroscopy,
and the reduced nickel(II)-methyl state has been characterized using
magnetic circular dichroism and X-ray spectroscopy. Implications for
further reactivity with CO are gleaned from electronic structure analysis
of the nickel-methyl species.
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Affiliation(s)
- Anastasia C Manesis
- Department of Chemistry and Biochemistry , The Ohio State University , 100 W. 18th Avenue , Columbus , Ohio 43210 , United States
| | - Bradley W Musselman
- Department of Chemistry , University of Michigan , 930 N. University Avenue , Ann Arbor , Michigan 48109 , United States
| | - Brenna C Keegan
- Department of Chemistry , Trinity University , One Trinity Place , San Antonio , Texas 78212 , United States
| | - Jason Shearer
- Department of Chemistry , Trinity University , One Trinity Place , San Antonio , Texas 78212 , United States
| | - Nicolai Lehnert
- Department of Chemistry , University of Michigan , 930 N. University Avenue , Ann Arbor , Michigan 48109 , United States
| | - Hannah S Shafaat
- Department of Chemistry and Biochemistry , The Ohio State University , 100 W. 18th Avenue , Columbus , Ohio 43210 , United States
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14
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Zhang T, Zhang X, Chung LW. Computational Insights into the Reaction Mechanisms of Nickel-Catalyzed Hydrofunctionalizations and Nickel-Dependent Enzymes. ASIAN J ORG CHEM 2018. [DOI: 10.1002/ajoc.201700645] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Tonghuan Zhang
- Department of Chemistry; South University of Science and Technology of China (SUSTech); Shenzhen 518055 China
- Lab of Computational Chemistry and Drug Design; Key Laboratory of Chemical Genomics; Peking University Shenzhen Graduate School; Shenzhen 518055 China
| | - Xiaoyong Zhang
- Department of Chemistry; South University of Science and Technology of China (SUSTech); Shenzhen 518055 China
| | - Lung Wa Chung
- Department of Chemistry; South University of Science and Technology of China (SUSTech); Shenzhen 518055 China
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15
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Ragsdale SW, Raugei S, Ginovska B, Wongnate T. Biochemistry of Methyl-Coenzyme M Reductase. THE BIOLOGICAL CHEMISTRY OF NICKEL 2017. [DOI: 10.1039/9781788010580-00149] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Methanogens are masters of CO2 reduction. They conserve energy by coupling H2 oxidation to the reduction of CO2 to CH4, the primary constituent of natural gas. They also generate methane by the reduction of acetic acid, methanol, methane thiol, and methylamines. Methanogens produce 109 tons of methane per year and are the major source of the earth’s atmospheric methane. Reverse methanogenesis or anaerobic methane oxidation, which is catalyzed by methanotrophic archaea living in consortia among bacteria that can act as an electron acceptor, is responsible for annual oxidation of 108 tons of methane to CO2. This chapter briefly describes the overall process of methanogenesis and then describes the enzymatic mechanism of the nickel enzyme, methyl-CoM reductase (MCR), the key enzyme in methane synthesis and oxidation. MCR catalyzes the formation of methane and the heterodisulfide (CoBSSCoM) from methyl-coenzyme M (methyl-CoM) and coenzyme B (HSCoB). Uncovering the mechanistic and molecular details of MCR catalysis is critical since methane is an abundant and important fuel and is the second (to CO2) most prevalent greenhouse gas.
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Affiliation(s)
- Stephen W. Ragsdale
- Department of Biological Chemistry, University of Michigan Medical School 1150 W. Medical Center Dr., 5301 MSRB III Ann Arbor MI 48109-0606 USA
| | - Simone Raugei
- Physical Sciences Division, Pacific Northwest National Laboratory, Post Office Box 999 K1-83 Richland WA 99352 USA
| | - Bojana Ginovska
- Physical Sciences Division, Pacific Northwest National Laboratory, Post Office Box 999 K1-83 Richland WA 99352 USA
| | - Thanyaporn Wongnate
- School of Bioresources and Technology and Excellent Center of Waste Utilization and Management (ECoWaste), King Mongkut's University of Technology Thonburi Bangkhunthian, Bangkok 10140 Thailand
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16
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Zimmermann P, Limberg C. Activation of Small Molecules at Nickel(I) Moieties. J Am Chem Soc 2017; 139:4233-4242. [DOI: 10.1021/jacs.6b12434] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Philipp Zimmermann
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489 Berlin, Germany
| | - Christian Limberg
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489 Berlin, Germany
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17
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Wongnate T, Sliwa D, Ginovska B, Smith D, Wolf MW, Lehnert N, Raugei S, Ragsdale SW. The radical mechanism of biological methane synthesis by methyl-coenzyme M reductase. Science 2016; 352:953-8. [PMID: 27199421 DOI: 10.1126/science.aaf0616] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 04/05/2016] [Indexed: 12/16/2022]
Abstract
Methyl-coenzyme M reductase, the rate-limiting enzyme in methanogenesis and anaerobic methane oxidation, is responsible for the biological production of more than 1 billion tons of methane per year. The mechanism of methane synthesis is thought to involve either methyl-nickel(III) or methyl radical/Ni(II)-thiolate intermediates. We employed transient kinetic, spectroscopic, and computational approaches to study the reaction between the active Ni(I) enzyme and substrates. Consistent with the methyl radical-based mechanism, there was no evidence for a methyl-Ni(III) species; furthermore, magnetic circular dichroism spectroscopy identified the Ni(II)-thiolate intermediate. Temperature-dependent transient kinetics also closely matched density functional theory predictions of the methyl radical mechanism. Identifying the key intermediate in methanogenesis provides fundamental insights to develop better catalysts for producing and activating an important fuel and potent greenhouse gas.
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Affiliation(s)
- Thanyaporn Wongnate
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109-0606, USA
| | - Dariusz Sliwa
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109-0606, USA
| | - Bojana Ginovska
- Physical Sciences Division, Pacific Northwest National Laboratory, Post Office Box 999, K1-83, Richland, WA 99352, USA
| | - Dayle Smith
- Physical Sciences Division, Pacific Northwest National Laboratory, Post Office Box 999, K1-83, Richland, WA 99352, USA
| | - Matthew W Wolf
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Nicolai Lehnert
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Simone Raugei
- Physical Sciences Division, Pacific Northwest National Laboratory, Post Office Box 999, K1-83, Richland, WA 99352, USA
| | - Stephen W Ragsdale
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109-0606, USA.
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18
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Corona T, Pfaff FF, Acuña-Parés F, Draksharapu A, Whiteoak CJ, Martin-Diaconescu V, Lloret-Fillol J, Browne WR, Ray K, Company A. Reactivity of a Nickel(II) Bis(amidate) Complex with meta-Chloroperbenzoic Acid: Formation of a Potent Oxidizing Species. Chemistry 2015; 21:15029-38. [PMID: 26311073 DOI: 10.1002/chem.201501841] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Indexed: 12/14/2022]
Abstract
Herein, we report the formation of a highly reactive nickel-oxygen species that has been trapped following reaction of a Ni(II) precursor bearing a macrocyclic bis(amidate) ligand with meta-chloroperbenzoic acid (HmCPBA). This compound is only detectable at temperatures below 250 K and is much more reactive toward organic substrates (i.e., C-H bonds, C=C bonds, and sulfides) than previously reported well-defined nickel-oxygen species. Remarkably, this species is formed by heterolytic O-O bond cleavage of a Ni-HmCPBA precursor, which is concluded from experimental and computational data. On the basis of spectroscopy and DFT calculations, this reactive species is proposed to be a Ni(III) -oxyl compound.
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Affiliation(s)
- Teresa Corona
- Group de Química Bioinorgànica, Supramolecular i Catàlisi (QBIS-CAT), Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, Campus Montilivi, 17071 Girona (Spain), Fax: (+34) 972-41-81-50
| | - Florian F Pfaff
- Humboldt Universität zu Berlin, Department of Chemistry, Brook-Taylor Strasse 2, 12489 Berlin (Germany)
| | - Ferran Acuña-Parés
- Group de Química Bioinorgànica, Supramolecular i Catàlisi (QBIS-CAT), Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, Campus Montilivi, 17071 Girona (Spain), Fax: (+34) 972-41-81-50
| | - Apparao Draksharapu
- Stratingh Institute for Chemistry, Faculty of Mathematics and Natural Sciences, University of Groningen, Nijenborgh 4, 9747 AG Groningen (The Netherlands)
| | - Christopher J Whiteoak
- Group de Química Bioinorgànica, Supramolecular i Catàlisi (QBIS-CAT), Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, Campus Montilivi, 17071 Girona (Spain), Fax: (+34) 972-41-81-50
| | - Vlad Martin-Diaconescu
- Group de Química Bioinorgànica, Supramolecular i Catàlisi (QBIS-CAT), Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, Campus Montilivi, 17071 Girona (Spain), Fax: (+34) 972-41-81-50
| | - Julio Lloret-Fillol
- Group de Química Bioinorgànica, Supramolecular i Catàlisi (QBIS-CAT), Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, Campus Montilivi, 17071 Girona (Spain), Fax: (+34) 972-41-81-50.,Current address: Institute of Chemical Research of Catalonia (ICIQ), Av. Països Catalans 16, 43007 Tarragona (Spain)
| | - Wesley R Browne
- Stratingh Institute for Chemistry, Faculty of Mathematics and Natural Sciences, University of Groningen, Nijenborgh 4, 9747 AG Groningen (The Netherlands)
| | - Kallol Ray
- Humboldt Universität zu Berlin, Department of Chemistry, Brook-Taylor Strasse 2, 12489 Berlin (Germany)
| | - Anna Company
- Group de Química Bioinorgànica, Supramolecular i Catàlisi (QBIS-CAT), Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, Campus Montilivi, 17071 Girona (Spain), Fax: (+34) 972-41-81-50.
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19
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Wongnate T, Ragsdale SW. The reaction mechanism of methyl-coenzyme M reductase: how an enzyme enforces strict binding order. J Biol Chem 2015; 290:9322-34. [PMID: 25691570 DOI: 10.1074/jbc.m115.636761] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Indexed: 01/03/2023] Open
Abstract
Methyl-coenzyme M reductase (MCR) is a nickel tetrahydrocorphinoid (coenzyme F430) containing enzyme involved in the biological synthesis and anaerobic oxidation of methane. MCR catalyzes the conversion of methyl-2-mercaptoethanesulfonate (methyl-SCoM) and N-7-mercaptoheptanoylthreonine phosphate (CoB7SH) to CH4 and the mixed disulfide CoBS-SCoM. In this study, the reaction of MCR from Methanothermobacter marburgensis, with its native substrates was investigated using static binding, chemical quench, and stopped-flow techniques. Rate constants were measured for each step in this strictly ordered ternary complex catalytic mechanism. Surprisingly, in the absence of the other substrate, MCR can bind either substrate; however, only one binary complex (MCR·methyl-SCoM) is productive whereas the other (MCR·CoB7SH) is inhibitory. Moreover, the kinetic data demonstrate that binding of methyl-SCoM to the inhibitory MCR·CoB7SH complex is highly disfavored (Kd = 56 mM). However, binding of CoB7SH to the productive MCR·methyl-SCoM complex to form the active ternary complex (CoB7SH·MCR(Ni(I))·CH3SCoM) is highly favored (Kd = 79 μM). Only then can the chemical reaction occur (kobs = 20 s(-1) at 25 °C), leading to rapid formation and dissociation of CH4 leaving the binary product complex (MCR(Ni(II))·CoB7S(-)·SCoM), which undergoes electron transfer to regenerate Ni(I) and the final product CoBS-SCoM. This first rapid kinetics study of MCR with its natural substrates describes how an enzyme can enforce a strictly ordered ternary complex mechanism and serves as a template for identification of the reaction intermediates.
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Affiliation(s)
- Thanyaporn Wongnate
- From the Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - Stephen W Ragsdale
- From the Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109
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20
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Cloutier JP, Vabre B, Moungang-Soumé B, Zargarian D. Synthesis and Reactivities of New NCN-Type Pincer Complexes of Nickel. Organometallics 2014. [DOI: 10.1021/om5010176] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Boris Vabre
- Département de chimie, Université de Montréal, Montréal, Québec, Canada H3C 3J7
| | | | - Davit Zargarian
- Département de chimie, Université de Montréal, Montréal, Québec, Canada H3C 3J7
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21
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Mougang-Soumé B, Belanger-Gariépy F, Zargarian D. Synthesis, Characterization, and Oxidation of New POCNimine-Type Pincer Complexes of Nickel. Organometallics 2014. [DOI: 10.1021/om500529e] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
| | | | - Davit Zargarian
- Department of Chemistry, Université de Montréal, Montreal, Quebec, Canada
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22
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Zheng B, Tang F, Luo J, Schultz JW, Rath NP, Mirica LM. Organometallic Nickel(III) Complexes Relevant to Cross-Coupling and Carbon–Heteroatom Bond Formation Reactions. J Am Chem Soc 2014; 136:6499-504. [DOI: 10.1021/ja5024749] [Citation(s) in RCA: 146] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Bo Zheng
- Department
of Chemistry, Washington University, One Brookings Drive, St. Louis, Missouri 63130-4899, United States
| | - Fengzhi Tang
- Department
of Chemistry, Washington University, One Brookings Drive, St. Louis, Missouri 63130-4899, United States
| | - Jia Luo
- Department
of Chemistry, Washington University, One Brookings Drive, St. Louis, Missouri 63130-4899, United States
| | - Jason W. Schultz
- Department
of Chemistry, Washington University, One Brookings Drive, St. Louis, Missouri 63130-4899, United States
| | - Nigam P. Rath
- Department
of Chemistry and Biochemistry, University of Missouri-St. Louis, One University Boulevard, St. Louis, Missouri 63121-4400, United States
| | - Liviu M. Mirica
- Department
of Chemistry, Washington University, One Brookings Drive, St. Louis, Missouri 63130-4899, United States
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23
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Blomberg MRA, Borowski T, Himo F, Liao RZ, Siegbahn PEM. Quantum chemical studies of mechanisms for metalloenzymes. Chem Rev 2014; 114:3601-58. [PMID: 24410477 DOI: 10.1021/cr400388t] [Citation(s) in RCA: 436] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Margareta R A Blomberg
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University , SE-106 91 Stockholm, Sweden
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24
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Biochemistry of methyl-coenzyme M reductase: the nickel metalloenzyme that catalyzes the final step in synthesis and the first step in anaerobic oxidation of the greenhouse gas methane. Met Ions Life Sci 2014; 14:125-45. [PMID: 25416393 DOI: 10.1007/978-94-017-9269-1_6] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Methane, the major component of natural gas, has been in use in human civilization since ancient times as a source of fuel and light. Methanogens are responsible for synthesis of most of the methane found on Earth. The enzyme responsible for catalyzing the chemical step of methanogenesis is methyl-coenzyme M reductase (MCR), a nickel enzyme that contains a tetrapyrrole cofactor called coenzyme F430, which can traverse the Ni(I), (II), and (III) oxidation states. MCR and methanogens are also involved in anaerobic methane oxidation. This review describes structural, kinetic, and computational studies aimed at elucidating the mechanism of MCR. Such studies are expected to impact the many ramifications of methane in our society and environment, including energy production and greenhouse gas warming.
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25
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Scheller S, Goenrich M, Thauer RK, Jaun B. Methyl-Coenzyme M Reductase from Methanogenic Archaea: Isotope Effects on the Formation and Anaerobic Oxidation of Methane. J Am Chem Soc 2013; 135:14975-84. [DOI: 10.1021/ja406485z] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Silvan Scheller
- Laboratory
of Organic Chemistry, ETH Zurich, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland
| | - Meike Goenrich
- Max Planck Institute for Terrestrial Microbiology, Karl-Von-Frisch-Strasse 10, 35043 Marburg, Germany
| | - Rudolf K. Thauer
- Max Planck Institute for Terrestrial Microbiology, Karl-Von-Frisch-Strasse 10, 35043 Marburg, Germany
| | - Bernhard Jaun
- Laboratory
of Organic Chemistry, ETH Zurich, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland
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26
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An Y, Cheng C, Pan B, Wang Z. Mechanistic Insight into the Nickel-Catalyzed Intermolecular [3+2+2] Cocyclization of Ethyl Cyclopropylideneacetate with Alkynes: DFT Calculations. European J Org Chem 2012. [DOI: 10.1002/ejoc.201200363] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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27
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Pfaff FF, Heims F, Kundu S, Mebs S, Ray K. Spectroscopic capture and reactivity of S = 1/2 nickel(iii)–oxygen intermediates in the reaction of a NiII-salt with mCPBA. Chem Commun (Camb) 2012; 48:3730-2. [DOI: 10.1039/c2cc30716b] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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28
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Duin EC, Prakash D, Brungess C. Methyl-coenzyme M reductase from Methanothermobacter marburgensis. Methods Enzymol 2011; 494:159-87. [PMID: 21402215 DOI: 10.1016/b978-0-12-385112-3.00009-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
Methyl-coenzyme M reductase catalyzes the reversible synthesis of methane from methyl-coenzyme M in methanogenic and ANME-1 and ANME-2 Archaea. The purification procedure for methyl-coenzyme M reductase from Methanothermobacter marburgensis is described. The procedure is an accumulation of almost 30 years of research on MCR starting with the first purification described by Ellefson and Wolfe (Ellefson, W.L., and Wolfe, R.S. (1981). Component C of the methylreductase system of Methanobacterium. J. Biol. Chem.256, 4259-4262). To provide a context for this procedure, some background information is provided, including a description of whole cell experiments that provided much of our knowledge of the behavior and properties of methyl-coenzyme M reductase.
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Affiliation(s)
- Evert C Duin
- Department of Chemistry and Biochemistry, Auburn University, Alabama, USA
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29
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Cedervall PE, Dey M, Li X, Sarangi R, Hedman B, Ragsdale SW, Wilmot CM. Structural analysis of a Ni-methyl species in methyl-coenzyme M reductase from Methanothermobacter marburgensis. J Am Chem Soc 2011; 133:5626-8. [PMID: 21438550 DOI: 10.1021/ja110492p] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present the 1.2 Å resolution X-ray crystal structure of a Ni-methyl species that is a proposed catalytic intermediate in methyl-coenzyme M reductase (MCR), the enzyme that catalyzes the biological formation of methane. The methyl group is situated 2.1 Å proximal of the Ni atom of the MCR coenzyme F(430). A rearrangement of the substrate channel has been posited to bring together substrate species, but Ni(III)-methyl formation alone does not lead to any observable structural changes in the channel.
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Affiliation(s)
- Peder E Cedervall
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
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30
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Dey M, Li X, Kunz RC, Ragsdale SW. Detection of Organometallic and Radical Intermediates in the Catalytic Mechanism of Methyl-Coenzyme M Reductase Using the Natural Substrate Methyl-Coenzyme M and a Coenzyme B Substrate Analogue. Biochemistry 2010; 49:10902-11. [DOI: 10.1021/bi101562m] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mishtu Dey
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Xianghui Li
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Ryan C. Kunz
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Stephen W. Ragsdale
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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31
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Cedervall PE, Dey M, Pearson AR, Ragsdale SW, Wilmot CM. Structural insight into methyl-coenzyme M reductase chemistry using coenzyme B analogues . Biochemistry 2010; 49:7683-93. [PMID: 20707311 DOI: 10.1021/bi100458d] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Methyl-coenzyme M reductase (MCR) catalyzes the final and rate-limiting step in methane biogenesis: the reduction of methyl-coenzyme M (methyl-SCoM) by coenzyme B (CoBSH) to methane and a heterodisulfide (CoBS-SCoM). Crystallographic studies show that the active site is deeply buried within the enzyme and contains a highly reduced nickel-tetrapyrrole, coenzyme F(430). Methyl-SCoM must enter the active site prior to CoBSH, as species derived from methyl-SCoM are always observed bound to the F(430) nickel in the deepest part of the 30 A long substrate channel that leads from the protein surface to the active site. The seven-carbon mercaptoalkanoyl chain of CoBSH binds within a 16 A predominantly hydrophobic part of the channel close to F(430), with the CoBSH thiolate lying closest to the nickel at a distance of 8.8 A. It has previously been suggested that binding of CoBSH initiates catalysis by inducing a conformational change that moves methyl-SCoM closer to the nickel promoting cleavage of the C-S bond of methyl-SCoM. In order to better understand the structural role of CoBSH early in the MCR mechanism, we have determined crystal structures of MCR in complex with four different CoBSH analogues: pentanoyl, hexanoyl, octanoyl, and nonanoyl derivatives of CoBSH (CoB(5)SH, CoB(6)SH, CoB(8)SH, and CoB(9)SH, respectively). The data presented here reveal that the shorter CoB(5)SH mercaptoalkanoyl chain overlays with that of CoBSH but terminates two units short of the CoBSH thiolate position. In contrast, the mercaptoalkanoyl chain of CoB(6)SH adopts a different conformation, such that its thiolate is coincident with the position of the CoBSH thiolate. This is consistent with the observation that CoB(6)SH is a slow substrate. A labile water in the substrate channel was found to be a sensitive indicator for the presence of CoBSH and HSCoM. The longer CoB(8)SH and CoB(9)SH analogues can be accommodated in the active site through exclusion of this water. These analogues react with Ni(III)-methyl, a proposed MCR catalytic intermediate of methanogenesis. The CoB(8)SH thiolate is 2.6 A closer to the nickel than that of CoBSH, but the additional carbon of CoB(9)SH only decreases the nickel thiolate distance a further 0.3 A. Although the analogues do not induce any structural changes in the substrate channel, the thiolates appear to preferentially bind at two distinct positions in the channel, one being the previously observed CoBSH thiolate position and the other being at a hydrophobic annulus of residues that lines the channel proximal to the nickel.
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Affiliation(s)
- Peder E Cedervall
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
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32
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Li X, Telser J, Kunz RC, Hoffman BM, Gerfen G, Ragsdale SW. Observation of organometallic and radical intermediates formed during the reaction of methyl-coenzyme M reductase with bromoethanesulfonate. Biochemistry 2010; 49:6866-76. [PMID: 20597483 DOI: 10.1021/bi100650m] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Methyl-coenzyme M reductase (MCR) from methanogenic archaea catalyzes the final step of methane formation, in which methyl-coenzyme M (2-methylthioethanesulfonate, methyl-SCoM) is reduced with coenzyme B (N-(7-mercaptoheptanoyl)threonine phosphate, CoBSH) to form methane and the heterodisulfide CoBS-SCoM. The active dimeric form of MCR contains two Ni(I)-F(430) prosthetic groups, one in each monomer. This report describes studies of the reaction of the active Ni(I) state of MCR (MCR(red1)) with BES (2-bromoethanesulfonate) and CoBSH or its analogue, CoB(6)SH (N-(6-mercaptohexanoyl)threonine phosphate), by transient kinetic measurements using EPR and UV-visible spectroscopy and by global fits of the data. This reaction is shown to lead to the formation of three intermediates, the first of which is assigned as an alkyl-Ni(III) species that forms as the active Ni(I)-MCR(red1) state of the enzyme decays. Subsequently, a radical (MCR(BES) radical) is formed that was characterized by multifrequency electron paramagnetic resonance (EPR) studies at X- ( approximately 9 GHz), Q- ( approximately 35 GHz), and D- ( approximately 130 GHz) bands and by electron-nuclear double resonance (ENDOR) spectroscopy. The MCR(BES) radical is characterized by g-values at 2.00340 and 1.99832 and includes a strongly coupled nonexchangeable proton with a hyperfine coupling constant of 50 MHz. Based on transient kinetic measurements, the formation and decay of the radical coincide with a species that exhibits absorption peaks at 426 and 575 nm. Isotopic substitution, multifrequency EPR, and ENDOR spectroscopic experiments rule out the possibility that MCR(BES) is a tyrosyl radical and indicate that if a tyrosyl radical is formed during the reaction, it does not accumulate to detectable levels. The results provide support for a hybrid mechanism of methanogenesis by MCR that includes both alkyl-Ni and radical intermediates.
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Affiliation(s)
- Xianghui Li
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
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33
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Lee CM, Chen CH, Liao FX, Hu CH, Lee GH. Mononuclear NiIII−Alkyl Complexes (Alkyl = Me and Et): Relevance to the Acetyl-CoA Synthase and Methyl-CoM Reductase. J Am Chem Soc 2010; 132:9256-8. [DOI: 10.1021/ja102430d] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chien-Ming Lee
- Department of Applied Science, National Taitung University, Taitung City 95092, Taiwan, School of Applied Chemistry, Chung Shan Medical University, Taichung City 40201, Taiwan, Department of Chemistry, National Changhua University of Education, Changhua 50058, Taiwan, and Instrumentation Center, National Taiwan University, Taipei 10764, Taiwan
| | - Chien-Hong Chen
- Department of Applied Science, National Taitung University, Taitung City 95092, Taiwan, School of Applied Chemistry, Chung Shan Medical University, Taichung City 40201, Taiwan, Department of Chemistry, National Changhua University of Education, Changhua 50058, Taiwan, and Instrumentation Center, National Taiwan University, Taipei 10764, Taiwan
| | - Fu-Xing Liao
- Department of Applied Science, National Taitung University, Taitung City 95092, Taiwan, School of Applied Chemistry, Chung Shan Medical University, Taichung City 40201, Taiwan, Department of Chemistry, National Changhua University of Education, Changhua 50058, Taiwan, and Instrumentation Center, National Taiwan University, Taipei 10764, Taiwan
| | - Ching-Han Hu
- Department of Applied Science, National Taitung University, Taitung City 95092, Taiwan, School of Applied Chemistry, Chung Shan Medical University, Taichung City 40201, Taiwan, Department of Chemistry, National Changhua University of Education, Changhua 50058, Taiwan, and Instrumentation Center, National Taiwan University, Taipei 10764, Taiwan
| | - Gene-Hsiang Lee
- Department of Applied Science, National Taitung University, Taitung City 95092, Taiwan, School of Applied Chemistry, Chung Shan Medical University, Taichung City 40201, Taiwan, Department of Chemistry, National Changhua University of Education, Changhua 50058, Taiwan, and Instrumentation Center, National Taiwan University, Taipei 10764, Taiwan
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34
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Stull JA, Stich TA, Service RJ, Debus RJ, Mandal SK, Armstrong WH, Britt RD. 13C ENDOR reveals that the D1 polypeptide C-terminus is directly bound to Mn in the photosystem II oxygen evolving complex. J Am Chem Soc 2010; 132:446-7. [PMID: 20038096 DOI: 10.1021/ja908688t] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Antiferromagnetically coupled Mn(III)Mn(IV) dimers have been commonly used to study biological systems that exhibit complex exchange interactions. Such is the case for the oxygen evolving complex (OEC) in photosystem II (PSII), where we have studied whether the C-terminal carboxylate of D1-Ala344 is directly bound to the Mn cluster. To probe these protein-derived carboxylate hyperfine interactions, which give direct bonding information, Q-band (34 GHz) Mims ENDOR was performed on a Mn(III)Mn(IV) dimer ([Mn(III)Mn(IV)(mu-O)(2)mu-OAc(TACN)(2)](BPh(4))(2)) (1) that was labeled with (13)C (I = (1)/(2)) at the carboxylate position of the acetate bridge. A(dip) is computed based on atomic coordinates from available X-ray crystal structures to be [-2.4, -0.8, 3.2] MHz. The value for A(iso) was determined based on simulation of the experimental ENDOR data, for complex 1 A(iso) = -1 MHz. Similar studies were then performed on PSII from Synechocystis sp. PCC 6803, in which all alanine-derived C=O groups are labeled with (13)C including the C-terminal alpha-COO(-) group of D1 (Ala344), as well as PSII proteins uniformly labeled with (13)C. Using recent X-ray crystallography data from T. elongatus the values for A(dip) were calculated and simulations of the experimental data led to A(iso) values of 1.2, 1, and 2 MHz, respectively. We infer from complex 1 that an A(iso) significantly larger than 1.2 MHz for a Mn-coordinating carboxylate moiety is unlikely. Therefore, we support the closer arrangement of Ala344 suggested by the Loll and Guskov structures and conclude that the C-terminal carboxylate of D1 polypeptide is directly bound to the Mn cluster.
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Affiliation(s)
- Jamie A Stull
- Department of Chemistry, University of California-Davis, Davis, California 95616, USA
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35
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Ebner S, Jaun B, Goenrich M, Thauer RK, Harmer J. Binding of coenzyme B induces a major conformational change in the active site of methyl-coenzyme M reductase. J Am Chem Soc 2010; 132:567-75. [PMID: 20014831 DOI: 10.1021/ja906367h] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Methyl-coenzyme M reductase (MCR) is the key enzyme in methane formation by methanogenic Archaea. It converts the thioether methyl-coenzyme M and the thiol coenzyme B into methane and the heterodisulfide of coenzyme M and coenzyme B. The catalytic mechanism of MCR and the role of its prosthetic group, the nickel hydrocorphin coenzyme F(430), is still disputed, and no intermediates have been observed so far by fast spectroscopic techniques when the enzyme was incubated with the natural substrates. In the presence of the competitive inhibitor coenzyme M instead of methyl-coenzyme M, addition of coenzyme B to the active Ni(I) state MCR(red1) induces two new species called MCR(red2a) and MCR(red2r) which have been characterized by pulse EPR spectroscopy. Here we show that the two MCR(red2) signals can also be induced by the S-methyl- and the S-trifluoromethyl analogs of coenzyme B. (19)F-ENDOR data for MCR(red2a) and MCR(red2r) induced by S-CF(3)-coenzyme B show that, upon binding of the coenzyme B analog, the end of the 7-thioheptanoyl chain of coenzyme B moves closer to the nickel center of F(430) by more than 2 A as compared to its position in both, the Ni(I) MCR(red1) form and the X-ray structure of the inactive Ni(II) MCR(ox1-silent) form. The finding that the protein is able to undergo a conformational change upon binding of the second substrate helps to explain the dramatic change in the coordination environment induced in the transition from MCR(red1) to MCR(red2) forms and opens the possibility that nickel coordination geometries other than square planar, tetragonal pyramidal, or elongated octahedral might occur in intermediates of the catalytic cycle.
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Affiliation(s)
- Sieglinde Ebner
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
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36
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Van Doorslaer S, Caretti I, Fallis I, Murphy D. The power of electron paramagnetic resonance to study asymmetric homogeneous catalysts based on transition-metal complexes. Coord Chem Rev 2009. [DOI: 10.1016/j.ccr.2008.12.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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37
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Chen SL, Pelmenschikov V, Blomberg MRA, Siegbahn PEM. Is There a Ni-Methyl Intermediate in the Mechanism of Methyl-Coenzyme M Reductase? J Am Chem Soc 2009; 131:9912-3. [DOI: 10.1021/ja904301f] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shi-lu Chen
- Department of Physics, Stockholm University, SE-10691 Stockholm, Sweden, and Scientific Computing and Modelling NV, Theoretical Chemistry, Vrije Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands
| | - Vladimir Pelmenschikov
- Department of Physics, Stockholm University, SE-10691 Stockholm, Sweden, and Scientific Computing and Modelling NV, Theoretical Chemistry, Vrije Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands
| | - Margareta R. A. Blomberg
- Department of Physics, Stockholm University, SE-10691 Stockholm, Sweden, and Scientific Computing and Modelling NV, Theoretical Chemistry, Vrije Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands
| | - Per E. M. Siegbahn
- Department of Physics, Stockholm University, SE-10691 Stockholm, Sweden, and Scientific Computing and Modelling NV, Theoretical Chemistry, Vrije Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands
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38
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Sarangi R, Dey M, Ragsdale SW. Geometric and electronic structures of the Ni(I) and methyl-Ni(III) intermediates of methyl-coenzyme M reductase. Biochemistry 2009; 48:3146-56. [PMID: 19243132 PMCID: PMC2667316 DOI: 10.1021/bi900087w] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
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Methyl-coenzyme M reductase (MCR) catalyzes the terminal step in the formation of biological methane from methyl-coenzyme M (Me-SCoM) and coenzyme B (CoBSH). The active site in MCR contains a Ni−F430 cofactor, which can exist in different oxidation states. The catalytic mechanism of methane formation has remained elusive despite intense spectroscopic and theoretical investigations. On the basis of spectroscopic and crystallographic data, the first step of the mechanism is proposed to involve a nucleophilic attack of the NiI active state (MCRred1) on Me-SCoM to form a NiIII−methyl intermediate, while computational studies indicate that the first step involves the attack of NiI on the sulfur of Me-SCoM, forming a CH3• radical and a NiII−thiolate species. In this study, a combination of Ni K-edge X-ray absorption spectroscopic (XAS) studies and density functional theory (DFT) calculations have been performed on the NiI (MCRred1), NiII (MCRred1−silent), and NiIII−methyl (MCRMe) states of MCR to elucidate the geometric and electronic structures of the different redox states. Ni K-edge EXAFS data are used to reveal a five-coordinate active site with an open upper axial coordination site in MCRred1. Ni K-pre-edge and EXAFS data and time-dependent DFT calculations unambiguously demonstrate the presence of a long Ni−C bond (∼2.04 Å) in the NiIII−methyl state of MCR. The formation and stability of this species support mechanism I, and the Ni−C bond length suggests a homolytic cleavage of the NiIII−methyl bond in the subsequent catalytic step. The XAS data provide insight into the role of the unique F430 cofactor in tuning the stability of the different redox states of MCR.
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Affiliation(s)
- Ritimukta Sarangi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA.
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Kraikivskii PB, Frey M, Bennour HA, Gembus A, Hauptmann R, Svoboda I, Fuess H, Saraev VV, Klein HF. Syntheses and properties of molecular nickel(II) hydride, methyl, and nickel(I) complexes supported by trimethylphosphane and (2-diphenylphosphanyl)thiophenolato and -naphtholato ligands. J Organomet Chem 2009. [DOI: 10.1016/j.jorganchem.2009.01.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Saraev VV, Kraikivskii PB, Svoboda I, Kuzakov AS, Jordan RF. Synthesis, molecular structure, and EPR analysis of the three-coordinate Ni(I) complex [Ni(PPh3)3][BF4]. J Phys Chem A 2009; 112:12449-55. [PMID: 18991433 DOI: 10.1021/jp802462x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The compound [Ni(PPh(3))(3)][BF(4)] x BF(3) x OEt(2) was isolated in crystalline form from the olefin oligomerization catalyst system Ni(PPh(3))(4)/BF(3) x OEt(2) and structurally characterized by X-ray diffraction. The influence of vibronic coupling on the EPR parameters of three-coordinate metal complexes with a 3d(9) electronic configuration was investigated within the framework of ligand field theory. Analytical expressions for g-tensor components and isotropic hyperfine coupling constants with ligand nuclei were obtained using first-order perturbation theory. It has been shown that the account of the vibronic interaction in the excited state predicts the existence of three-axial anisotropy of the g-tensor even at the level of first-order perturbation theory; two axes of the g-tensor located in a plane of three-coordinate structure can rotate about the main z axis when a compound is distorted by motion of ligands. It has been shown that in three points of the potential energy surface minimum, for which linear and quadric constants of the vibronic interactions have an identical signs, the HFS isotropic constant from one ligand is larger than HFS constants from the other two; for different vibronic constant signs the ratio between HFS constants varies on opposite. This theoretical researches are in the quality consent with experimental data for a three-coordinate Ni(I) and Cu(II) flat complexes.
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Affiliation(s)
- V V Saraev
- Irkutsk State University, Str. K. Marksa, 1, Irkutsk, 664003, Russia.
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41
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Ryeng H, Gonzalez E, Ghosh A. DFT at its best: metal- versus ligand-centered reduction in nickel hydroporphyrins. J Phys Chem B 2009; 112:15158-73. [PMID: 18975889 DOI: 10.1021/jp805486b] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DFT calculations, using the PW91, OLYP, and B3LYP functionals, have provided some of the first estimates of the relative energies of the Ni(I) and Ni(II) ligand anion radical states of hydroporphyrin complexes. Although the three functionals chosen sometimes yield discordant results, the results of this study are essentially functional-independent. For isobacteriochlorin derivatives, our calculations predict that the Ni(I) state may be favored by 0.5 eV or more, relative to the ligand anion radical state. For other hydroporphyrins, however, electrochemical studies indicate a much finer balance, which may be tipped one way or the other, depending on the substituents. DFT calculations nicely capture these rather subtle substituent effects. In particular, our results support and extend Bruckner and co-workers' finding (from electrochemical studies) that the most rigid, strongly ruffled nickel chlorins prefer to reduce on the macrocycle, whereas their more flexible congeners undergo metal-centered reduction.
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Affiliation(s)
- Hege Ryeng
- Department of Chemistry, University of Tromsø, 9037 Tromsø, Norway
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Liptak MD, Van Heuvelen KM, Brunold* TC. Computational Studies of Bioorganometallic Enzymes and Cofactors. METAL-CARBON BONDS IN ENZYMES AND COFACTORS 2009. [DOI: 10.1039/9781847559333-00417] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Because of their complex geometric and electronic structures, the active sites and cofactors of bioorganometallic enzymes, which are characterized by their metal–carbon bonds, pose a major challenge for computational chemists. However, recent progress in computer technology and theoretical chemistry, along with insights gained from mechanistic, spectroscopic, and X-ray crystallographic studies, have established an excellent foundation for the successful completion of computational studies aimed at elucidating the electronic structures and catalytic cycles of these species. This chapter briefly reviews the most popular computational approaches employed in theoretical studies of bioorganometallic species and summarizes important information obtained from computational studies of (i) the enzymatic formation and cleavage of the Co–C bond of coenzyme B12; (ii) the catalytic cycle of methyl-coenzyme M reductase and its nickel-containing cofactor F430; (iii) the polynuclear active-site clusters of the bifunctional enzyme carbon monoxide dehydrogenase/acetyl-coenzyme A synthase; and (iv) the magnetic properties of the active-site cluster of Fe-only hydrogenases.
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Affiliation(s)
- Matthew D. Liptak
- Department of Chemistry, University of Wisconsin-Madison Madison WI 53706 USA
| | | | - Thomas C. Brunold*
- Department of Chemistry, University of Wisconsin-Madison Madison WI 53706 USA
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Gonzalez E, Ghosh A. Models of the ox1 state of methylcoenzyme M reductase: where are the electrons? Chemistry 2008; 14:9981-9. [PMID: 18816556 DOI: 10.1002/chem.200800648] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The nature of the nickel center in the ox1 form of methylcoenzyme M reductase (MCR(ox1)), the enzyme that catalyzes the last step of biological methanogenesis, has long been controversial. A recent pulse electron paramagnetic resonance (EPR) study suggested a Ni(III)-thiolate, or equivalently a high-spin Ni(II) thiyl radical, description. The MCR(ox1) hyperfine parameters are best interpreted in terms of a Ni d(x(2)-y(2) ) SOMO, although a pure d(x(2)-y(2) ) SOMO does not explain the fact that about 7 % of the spin-density resides on the sulfur. The key goals of this DFT (PW91) study were to judge whether the Ni(III)-thiolate description is chemically sensible and, if so, to provide a detailed molecular orbital (MO) description of MCR(ox1). An Ni(III)-thiolate description was indeed found to be reasonable and was obtained as the ground state for symmetrized (C(s)) oxaporphyrin-, pyriporphyrin-, and isoporphyrin-based model complexes, as well as for a more realistic, biomimetic model. The model calculations yielded a number of insights, key among which are the following: 1) Although the SOMO topology may be viewed as d(x(2)-y(2) )-like, this MO also has a substantial amount of metal d(z(2) ) character, allowing it to overlap with a thiolate sigma lone pair, which would otherwise be orthogonal. 2) In one case (isoporphyrin), we were able to exploit the symmetry of the molecule to independently optimize the (d(x(2)-y(2) ))(1) and (d(z(2) ))(1) Ni(III) states, which turned out to be very close in energy. 3) The near-degeneracy of these two states provides an elegant explanation for the tendency of these two orbitals to hybridize. Admixture of substantial d(z(2) ) character into the d(x(2)-y(2) )-type SOMO of our most realistic model of MCR(ox1) results in a small but distinct spin population of about 0.04 on the sulfur, apparently nicely confirming the conclusions derived from the pulse EPR study. Other pure functionals also confirm this picture, although the hybrid functional B3LYP yields a spin-density profile that is clearly at odds with the EPR study.
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Affiliation(s)
- Emmanuel Gonzalez
- Department of Chemistry and Center for Theoretical and Experimental Chemistry, University of Tromsø, 9037 Tromsø, Norway
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Dougherty WG, Rangan K, O'Hagan MJ, Yap GPA, Riordan CG. Binuclear complexes containing a methylnickel moiety: relevance to organonickel intermediates in acetyl coenzyme A synthase catalysis. J Am Chem Soc 2008; 130:13510-1. [PMID: 18800791 DOI: 10.1021/ja803795k] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A series of binuclear NiNi complexes supported by a single thiolate bridge and containing a methylnickel moiety have been prepared and fully characterized. The complexes represent structural analogues for the proposed organonickel intermediate in the acetyl coenzyme A synthase catalytic cycle. Variable temperature 31P NMR spectroscopy was used to examine dynamic behavior of the thiolate bridging interaction in two of the derivatives. Kinetic analyses, independent exchange and crossover experiments support an intermolecular exchange mechanism. Carbonylation results in thioester formation via a reductive elimination pathway.
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Affiliation(s)
- William G Dougherty
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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Hinderberger D, Ebner S, Mayr S, Jaun B, Reiher M, Goenrich M, Thauer RK, Harmer J. Coordination and binding geometry of methyl-coenzyme M in the red1m state of methyl-coenzyme M reductase. J Biol Inorg Chem 2008; 13:1275-89. [PMID: 18712421 DOI: 10.1007/s00775-008-0417-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2008] [Accepted: 07/27/2008] [Indexed: 10/21/2022]
Abstract
Methane formation in methanogenic Archaea is catalyzed by methyl-coenzyme M reductase (MCR) and takes place via the reduction of methyl-coenzyme M (CH3-S-CoM) with coenzyme B (HS-CoB) to methane and the heterodisulfide CoM-S-S-CoB. MCR harbors the nickel porphyrinoid coenzyme F430 as a prosthetic group, which has to be in the Ni(I) oxidation state for the enzyme to be active. To date no intermediates in the catalytic cycle of MCRred1 (red for reduced Ni) have been identified. Here, we report a detailed characterization of MCRred1m ("m" for methyl-coenzyme M), which is the complex of MCRred1a ("a" for absence of substrate) with CH3-S-CoM. Using continuous-wave and pulse electron paramagnetic resonance spectroscopy in combination with selective isotope labeling (13C and 2H) of CH3-S-CoM, it is shown that CH3-S-CoM binds in the active site of MCR such that its thioether sulfur is weakly coordinated to the Ni(I) of F430. The complex is stable until the addition of the second substrate, HS-CoB. Results from EPR spectroscopy, along with quantum mechanical calculations, are used to characterize the electronic and geometric structure of this complex, which can be regarded as the first intermediate in the catalytic mechanism.
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Affiliation(s)
- Dariush Hinderberger
- Max-Planck-Institut für Polymerforschung, Ackermannweg 10, 55128, Mainz, Germany.
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Harmer J, Finazzo C, Piskorski R, Ebner S, Duin EC, Goenrich M, Thauer RK, Reiher M, Schweiger A, Hinderberger D, Jaun B. A Nickel Hydride Complex in the Active Site of Methyl-Coenzyme M Reductase: Implications for the Catalytic Cycle. J Am Chem Soc 2008; 130:10907-20. [DOI: 10.1021/ja710949e] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jeffrey Harmer
- Centre for Advanced Electron Spin Resonance, Department of Chemistry, University of Oxford, South Parks Road, OX1 3QR, Oxford, United Kingdom, Laboratory of Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland, Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland, Max Planck Institute for Terrestrial Microbiology, Department of Biochemistry, Karl-von-Frisch Strasse, 35043 Marburg, Germany, and Department of Chemistry and Biochemistry, Auburn University, Alabama 36849-5312
| | - Cinzia Finazzo
- Centre for Advanced Electron Spin Resonance, Department of Chemistry, University of Oxford, South Parks Road, OX1 3QR, Oxford, United Kingdom, Laboratory of Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland, Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland, Max Planck Institute for Terrestrial Microbiology, Department of Biochemistry, Karl-von-Frisch Strasse, 35043 Marburg, Germany, and Department of Chemistry and Biochemistry, Auburn University, Alabama 36849-5312
| | - Rafal Piskorski
- Centre for Advanced Electron Spin Resonance, Department of Chemistry, University of Oxford, South Parks Road, OX1 3QR, Oxford, United Kingdom, Laboratory of Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland, Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland, Max Planck Institute for Terrestrial Microbiology, Department of Biochemistry, Karl-von-Frisch Strasse, 35043 Marburg, Germany, and Department of Chemistry and Biochemistry, Auburn University, Alabama 36849-5312
| | - Sieglinde Ebner
- Centre for Advanced Electron Spin Resonance, Department of Chemistry, University of Oxford, South Parks Road, OX1 3QR, Oxford, United Kingdom, Laboratory of Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland, Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland, Max Planck Institute for Terrestrial Microbiology, Department of Biochemistry, Karl-von-Frisch Strasse, 35043 Marburg, Germany, and Department of Chemistry and Biochemistry, Auburn University, Alabama 36849-5312
| | - Evert C. Duin
- Centre for Advanced Electron Spin Resonance, Department of Chemistry, University of Oxford, South Parks Road, OX1 3QR, Oxford, United Kingdom, Laboratory of Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland, Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland, Max Planck Institute for Terrestrial Microbiology, Department of Biochemistry, Karl-von-Frisch Strasse, 35043 Marburg, Germany, and Department of Chemistry and Biochemistry, Auburn University, Alabama 36849-5312
| | - Meike Goenrich
- Centre for Advanced Electron Spin Resonance, Department of Chemistry, University of Oxford, South Parks Road, OX1 3QR, Oxford, United Kingdom, Laboratory of Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland, Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland, Max Planck Institute for Terrestrial Microbiology, Department of Biochemistry, Karl-von-Frisch Strasse, 35043 Marburg, Germany, and Department of Chemistry and Biochemistry, Auburn University, Alabama 36849-5312
| | - Rudolf K. Thauer
- Centre for Advanced Electron Spin Resonance, Department of Chemistry, University of Oxford, South Parks Road, OX1 3QR, Oxford, United Kingdom, Laboratory of Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland, Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland, Max Planck Institute for Terrestrial Microbiology, Department of Biochemistry, Karl-von-Frisch Strasse, 35043 Marburg, Germany, and Department of Chemistry and Biochemistry, Auburn University, Alabama 36849-5312
| | - Markus Reiher
- Centre for Advanced Electron Spin Resonance, Department of Chemistry, University of Oxford, South Parks Road, OX1 3QR, Oxford, United Kingdom, Laboratory of Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland, Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland, Max Planck Institute for Terrestrial Microbiology, Department of Biochemistry, Karl-von-Frisch Strasse, 35043 Marburg, Germany, and Department of Chemistry and Biochemistry, Auburn University, Alabama 36849-5312
| | - Arthur Schweiger
- Centre for Advanced Electron Spin Resonance, Department of Chemistry, University of Oxford, South Parks Road, OX1 3QR, Oxford, United Kingdom, Laboratory of Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland, Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland, Max Planck Institute for Terrestrial Microbiology, Department of Biochemistry, Karl-von-Frisch Strasse, 35043 Marburg, Germany, and Department of Chemistry and Biochemistry, Auburn University, Alabama 36849-5312
| | - Dariush Hinderberger
- Centre for Advanced Electron Spin Resonance, Department of Chemistry, University of Oxford, South Parks Road, OX1 3QR, Oxford, United Kingdom, Laboratory of Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland, Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland, Max Planck Institute for Terrestrial Microbiology, Department of Biochemistry, Karl-von-Frisch Strasse, 35043 Marburg, Germany, and Department of Chemistry and Biochemistry, Auburn University, Alabama 36849-5312
| | - Bernhard Jaun
- Centre for Advanced Electron Spin Resonance, Department of Chemistry, University of Oxford, South Parks Road, OX1 3QR, Oxford, United Kingdom, Laboratory of Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland, Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland, Max Planck Institute for Terrestrial Microbiology, Department of Biochemistry, Karl-von-Frisch Strasse, 35043 Marburg, Germany, and Department of Chemistry and Biochemistry, Auburn University, Alabama 36849-5312
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Chattopadhyay S, Deb T, Ma H, Petersen JL, Young VG, Jensen MP. Arylthiolate Coordination and Reactivity at Pseudotetrahedral Nickel(II) Centers: Modulation by Noncovalent Interactions. Inorg Chem 2008; 47:3384-92. [PMID: 18345601 DOI: 10.1021/ic702417w] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Swarup Chattopadhyay
- Department of Chemistry and Biochemistry, Ohio University, Athens, Ohio 45701, C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, and X-ray Crystallographic Laboratory, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Tapash Deb
- Department of Chemistry and Biochemistry, Ohio University, Athens, Ohio 45701, C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, and X-ray Crystallographic Laboratory, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Huaibo Ma
- Department of Chemistry and Biochemistry, Ohio University, Athens, Ohio 45701, C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, and X-ray Crystallographic Laboratory, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Jeffrey L. Petersen
- Department of Chemistry and Biochemistry, Ohio University, Athens, Ohio 45701, C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, and X-ray Crystallographic Laboratory, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Victor G. Young
- Department of Chemistry and Biochemistry, Ohio University, Athens, Ohio 45701, C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, and X-ray Crystallographic Laboratory, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Michael P. Jensen
- Department of Chemistry and Biochemistry, Ohio University, Athens, Ohio 45701, C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, and X-ray Crystallographic Laboratory, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
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Duin EC, McKee ML. A new mechanism for methane production from methyl-coenzyme M reductase as derived from density functional calculations. J Phys Chem B 2008; 112:2466-82. [PMID: 18247503 DOI: 10.1021/jp709860c] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We propose a new DFT-based mechanism for methane production using the full F430 cofactor of MCR (methyl-coenzyme M reductase) along with a coordinated O=CH2CH2C(H)NH2C(H)O (surrogate for glutamine) as a model of the active site for conversion of CH3SCoM(-) (CH3SCH2CH2SO3(-)) + HSCoB to methane plus the corresponding heterodisulfide. The cycle begins with the protonation of F430, either on Ni or on the C-ring nitrogen of the tetrapyrrole ring, both of which are nearly equally favorable. The C-ring protonated form is predicted to oxidatively add CH3SCoM(-) to give a 4-coordinate Ni center where the Ni moves out of the plane of the four ring nitrogens. The movement of Ni (and the attached CH3 and SCH2CH2SO3(2-) ligands) toward the SCoB(-) (deprotonated HSCoB) cofactor allows a 2c-3e interaction to form between the two sulfur atoms. The release of the heterodisulfide yields a Ni(III) center with a methyl group attached. The concerted elimination of methane, where the methyl group coordinated to Ni abstracts the proton from the C-ring nitrogen, has a very small calculated activation barrier (5.4 kcal/mol). The NPA charge on Ni for the various reaction steps indicates that the oxidation state changes occur largely on the attached ligands.
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Affiliation(s)
- Evert C Duin
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, USA
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