1
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Zhou Y, Zhou Q, Liu H, Xu W, Wang Z, Qiao S, Ding H, Chen D, Zhu J, Qi Z, Wu X, He Q, Song L. Asymmetric dinitrogen-coordinated nickel single-atomic sites for efficient CO 2 electroreduction. Nat Commun 2023; 14:3776. [PMID: 37355748 DOI: 10.1038/s41467-023-39505-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 06/16/2023] [Indexed: 06/26/2023] Open
Abstract
Developing highly efficient, selective and low-overpotential electrocatalysts for carbon dioxide (CO2) reduction is crucial. This study reports an efficient Ni single-atom catalyst coordinated with pyrrolic nitrogen and pyridinic nitrogen for CO2 reduction to carbon monoxide (CO). In flow cell experiments, the catalyst achieves a CO partial current density of 20.1 mA cmgeo-2 at -0.15 V vs. reversible hydrogen electrode (VRHE). It exhibits a high turnover frequency of over 274,000 site-1 h-1 at -1.0 VRHE and maintains high Faradaic efficiency of CO (FECO) exceeding 90% within -0.15 to -0.9 VRHE. Operando synchrotron-based infrared and X-ray absorption spectra, and theoretical calculations reveal that mono CO-adsorbed Ni single sites formed during electrochemical processes contribute to the balance between key intermediates formation and CO desorption, providing insights into the catalyst's origin of catalytic activity. Overall, this work presents a Ni single-atom catalyst with good selectivity and activity for CO2 reduction while shedding light on its underlying mechanism.
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Affiliation(s)
- Yuzhu Zhou
- National Synchrotron Radiation Laboratory, CAS Center for Excellence in Nanoscience, University of Science and Technology of China, Hefei, 230029, China
| | - Quan Zhou
- National Synchrotron Radiation Laboratory, CAS Center for Excellence in Nanoscience, University of Science and Technology of China, Hefei, 230029, China
| | - Hengjie Liu
- National Synchrotron Radiation Laboratory, CAS Center for Excellence in Nanoscience, University of Science and Technology of China, Hefei, 230029, China
| | - Wenjie Xu
- National Synchrotron Radiation Laboratory, CAS Center for Excellence in Nanoscience, University of Science and Technology of China, Hefei, 230029, China
| | - Zhouxin Wang
- National Synchrotron Radiation Laboratory, CAS Center for Excellence in Nanoscience, University of Science and Technology of China, Hefei, 230029, China
| | - Sicong Qiao
- National Synchrotron Radiation Laboratory, CAS Center for Excellence in Nanoscience, University of Science and Technology of China, Hefei, 230029, China
| | - Honghe Ding
- National Synchrotron Radiation Laboratory, CAS Center for Excellence in Nanoscience, University of Science and Technology of China, Hefei, 230029, China
| | - Dongliang Chen
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China
| | - Junfa Zhu
- National Synchrotron Radiation Laboratory, CAS Center for Excellence in Nanoscience, University of Science and Technology of China, Hefei, 230029, China
| | - Zeming Qi
- National Synchrotron Radiation Laboratory, CAS Center for Excellence in Nanoscience, University of Science and Technology of China, Hefei, 230029, China
| | - Xiaojun Wu
- Hefei National Laboratory for Physical Science at the Microscale, Collaborative Innovation of Center of Chemistry for Energy Materials (iChEM), School of Chemistry and Materials Sciences, University of Science and Technology of China, Hefei, 230026, China
| | - Qun He
- National Synchrotron Radiation Laboratory, CAS Center for Excellence in Nanoscience, University of Science and Technology of China, Hefei, 230029, China.
| | - Li Song
- National Synchrotron Radiation Laboratory, CAS Center for Excellence in Nanoscience, University of Science and Technology of China, Hefei, 230029, China.
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2
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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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3
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Cząstka K, Oughli AA, Rüdiger O, DeBeer S. Enzymatic X-ray absorption spectroelectrochemistry. Faraday Discuss 2022; 234:214-231. [PMID: 35142778 DOI: 10.1039/d1fd00079a] [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
The ability to observe the changes that occur at an enzyme active site during electrocatalysis can provide very valuable information for understanding the mechanism and ultimately aid in catalyst design. Herein, we discuss the development of X-ray absorption spectroscopy (XAS) in combination with electrochemistry for operando studies of enzymatic systems. XAS has had a long history of enabling geometric and electronic structural insights into the catalytic active sites of enzymes, however, XAS combined with electrochemistry (XA-SEC) has been exceedingly rare in bioinorganic applications. Herein, we discuss the challenges and opportunities of applying operando XAS to enzymatic electrocatalysts. The challenges due to the low concentration of the photoabsorber and the instability of the protein in the X-ray beam are discussed. Methods for immobilizing enzymes on the electrodes, while maintaining full redox control are highlighted. A case study of combined XAS and electrochemistry applied to a [NiFe] hydrogenase is presented. By entrapping the [NiFe] hydrogenase in a redox polymer, relatively high protein concentrations can be achieved on the electrode surface, while maintaining redox control. Overall, it is demonstrated that the experiments are feasible, but require precise redox control over the majority of the absorber atoms and careful controls to discriminate between electrochemically-driven changes and beam damage. Opportunities for future applications are discussed.
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Affiliation(s)
- Karolina Cząstka
- Max Planck Institute for Chemical Energy Conversion, Mülheim an der Ruhr, DE, Germany.
| | - Alaa A Oughli
- Technical University Munich, Campus Straubing for Biotechnology and Sustainability, Uferstraße 53, 94315 Straubing, Germany
| | - Olaf Rüdiger
- Max Planck Institute for Chemical Energy Conversion, Mülheim an der Ruhr, DE, Germany.
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion, Mülheim an der Ruhr, DE, Germany.
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4
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Ju L, Lin Q, LiBretto NJ, Wagner CL, Hu CT, Miller JT, Diao T. Reactivity of (bi-Oxazoline)organonickel Complexes and Revision of a Catalytic Mechanism. J Am Chem Soc 2021; 143:14458-14463. [PMID: 34463481 DOI: 10.1021/jacs.1c07139] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Bi-Oxazoline (biOx) has emerged as an effective ligand framework for promoting nickel-catalyzed cross-coupling, cross-electrophile coupling, and photoredox-nickel dual catalytic reactions. This report fills the knowledge gap of the organometallic reactivity of (biOx)Ni complexes, including catalyst reduction, oxidative electrophile activation, radical capture, and reductive elimination. The biOx ligand displays no redox activity in (biOx)Ni(I) complexes, in contrast to other chelating imine and oxazoline ligands. The lack of ligand redox activity results in more negative reduction potentials of (biOx)Ni(II) complexes and accounts for the inability of zinc and manganese to reduce (biOx)Ni(II) species. On the basis of these results, we revise the formerly proposed "sequential reduction" mechanism of a (biOx)Ni-catalyzed cross-electrophile coupling reaction by excluding catalyst reduction steps.
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Affiliation(s)
- Luchuan Ju
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Qiao Lin
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Nicole J LiBretto
- Department of Chemical Engineering, Purdue University, 480 Stadium Mall Drive, West Lafayette, Indiana 47906, United States
| | - Clifton L Wagner
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Chunhua Tony Hu
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Jeffrey T Miller
- Department of Chemical Engineering, Purdue University, 480 Stadium Mall Drive, West Lafayette, Indiana 47906, United States
| | - Tianning Diao
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
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5
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Patwardhan A, Sarangi R, Ginovska B, Raugei S, Ragsdale SW. Nickel-Sulfonate Mode of Substrate Binding for Forward and Reverse Reactions of Methyl-SCoM Reductase Suggest a Radical Mechanism Involving Long-Range Electron Transfer. J Am Chem Soc 2021; 143:5481-5496. [PMID: 33761259 DOI: 10.1021/jacs.1c01086] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Methyl-coenzyme M reductase (MCR) catalyzes both the synthesis and the anaerobic oxidation of methane (AOM). Its catalytic site contains Ni at the core of cofactor F430. The Ni ion, in its low-valent Ni(I) state, lights the fuse leading to homolysis of the C-S bond of methyl-coenzyme M (methyl-SCoM) to generate a methyl radical, which abstracts a hydrogen atom from coenzyme B (HSCoB) to generate methane and the mixed disulfide CoMSSCoB. Direct reversal of this reaction activates methane to initiate anaerobic methane oxidation. On the basis of the crystal structures, which reveal a Ni-thiol interaction between Ni(II)-MCR and inhibitor CoMSH, a Ni(I)-thioether complex with substrate methyl-SCoM has been transposed to canonical MCR mechanisms. Similarly, a Ni(I)-disulfide with CoMSSCoB is proposed for the reverse reaction. However, this Ni(I)-sulfur interaction poses a conundrum for the proposed hydrogen-atom abstraction reaction because the >6 Å distance between the thiol group of SCoB and the thiol of SCoM observed in the structures appears to be too long for such a reaction. The spectroscopic, kinetic, structural, and computational studies described here establish that both methyl-SCoM and CoMSSCoB bind to the active Ni(I) state of MCR through their sulfonate groups, forming a hexacoordinate Ni(I)-N/O complex, not Ni(I)-S. These studies rule out direct Ni(I)-sulfur interactions in both substrate-bound states. As a solution to the mechanistic conundrum, we propose that both the forward and the reverse MCR reactions emanate through long-range electron transfer from the Ni(I)-sulfonate complexes with methyl-SCoM and CoMSSCoB, respectively.
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Affiliation(s)
- Anjali Patwardhan
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48103, United States
| | - Ritimukta Sarangi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Bojana Ginovska
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Simone Raugei
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Stephen W Ragsdale
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48103, United States
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6
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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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7
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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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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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Ryland ES, Zhang K, Vura-Weis J. Sub-100 fs Intersystem Crossing to a Metal-Centered Triplet in Ni(II)OEP Observed with M-Edge XANES. J Phys Chem A 2019; 123:5214-5222. [DOI: 10.1021/acs.jpca.9b03376] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Elizabeth S. Ryland
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Kaili Zhang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Josh Vura-Weis
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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10
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Lukens JT, DiMucci IM, Kurogi T, Mindiola DJ, Lancaster KM. Scrutinizing metal-ligand covalency and redox non-innocence via nitrogen K-edge X-ray absorption spectroscopy. Chem Sci 2019; 10:5044-5055. [PMID: 31183055 PMCID: PMC6530532 DOI: 10.1039/c8sc03350a] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 04/09/2019] [Indexed: 11/21/2022] Open
Abstract
Nitrogen K-edge X-ray absorption spectra (XAS) were obtained for 19 transition metal complexes bearing bipyridine, ethylenediamine, ammine, and nitride ligands. Time-dependent density functional theory (TDDFT) and DFT/restricted open configuration interaction singles (DFT/ROCIS) calculations were found to predict relative N K-edge XAS peak energies with good fidelity to experiment. The average difference (|ΔE|) between experimental and linear corrected calculated energies were found to be 0.55 ± 0.05 eV and 0.46 ± 0.04 eV, respectively, using the B3LYP hybrid density functional and scalar relativistically recontracted ZORA-def2-TZVP(-f) basis set. Deconvolution of these global correlations into individual N-donor ligand classes gave improved agreement between experiment and theory with |ΔE| less than 0.4 eV for all ligand classes in the case of DFT/ROCIS. In addition, calibration method-dependent values for the N 1s → 2p radial dipole integral of 25.4 ± 1.7 and 26.8 ± 1.9 are obtained, affording means to estimate the nitrogen 2p character in unfilled frontier molecular orbitals. For the complexes studied, nitrogen covalency values correlate well to those calculated by hybrid DFT with an R 2 = 0.92 ± 0.01. Additionally, as a test case, a well-characterized PNP ligand framework (PNP = N[2-P(CHMe2)2-4-methylphenyl]2 1-) coordinated to NiII is investigated for its ability to act as a redox non-innocent ligand. Upon oxidation of (PNP)NiCl with [FeCp2](OTf) to its radical cation, [(PNP)NiCl](OTf) (OTf = triflate), a new low-energy feature emerges in the N K-edge XAS spectra. This feature is assigned as N 1s to a PNP-localized acceptor orbital exhibiting 27 ± 2% N 2p aminyl radical character, obtained using the aforementioned nitrogen covalency calibration. Combined, these data showcase a direct spectroscopic means of identifying redox-active N-donor ligands and also estimating nitrogen 2p covalency of frontier molecular orbitals in transition metal complexes.
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Affiliation(s)
- James T Lukens
- Department of Chemistry and Chemical Biology Cornell University , Baker Laboratory , Ithaca , NY 14853 , USA .
| | - Ida M DiMucci
- Department of Chemistry and Chemical Biology Cornell University , Baker Laboratory , Ithaca , NY 14853 , USA .
| | - Takashi Kurogi
- Department of Chemistry , University of Pennsylvania , 231 South 34th Street , Philadelphia , PA 19104 , USA
| | - Daniel J Mindiola
- Department of Chemistry , University of Pennsylvania , 231 South 34th Street , Philadelphia , PA 19104 , USA
| | - Kyle M Lancaster
- Department of Chemistry and Chemical Biology Cornell University , Baker Laboratory , Ithaca , NY 14853 , USA .
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11
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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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12
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Lapointe S, Khaskin E, Fayzullin RR, Khusnutdinova JR. Stable Nickel(I) Complexes with Electron-Rich, Sterically-Hindered, Innocent PNP Pincer Ligands. Organometallics 2019. [DOI: 10.1021/acs.organomet.9b00026] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Sébastien Lapointe
- Okinawa Institute of Science and Technology Graduate University, Coordination Chemistry and Catalysis Unit, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
| | - Eugene Khaskin
- Okinawa Institute of Science and Technology Graduate University, Coordination Chemistry and Catalysis Unit, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
| | - Robert R. Fayzullin
- Arbuzov Institute of Organic and Physical Chemistry, FCR Kazan Scientific Center, Russian Academy of Sciences, 8 Arbuzov Street, Kazan 420088, Russian Federation
| | - Julia R. Khusnutdinova
- Okinawa Institute of Science and Technology Graduate University, Coordination Chemistry and Catalysis Unit, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
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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
![]()
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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Manesis AC, O'Connor MJ, Schneider CR, Shafaat HS. Multielectron Chemistry within a Model Nickel Metalloprotein: Mechanistic Implications for Acetyl-CoA Synthase. J Am Chem Soc 2017; 139:10328-10338. [PMID: 28675928 DOI: 10.1021/jacs.7b03892] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The acetyl coenzyme A synthase (ACS) enzyme plays a central role in the metabolism of anaerobic bacteria and archaea, catalyzing the reversible synthesis of acetyl-CoA from CO and a methyl group through a series of nickel-based organometallic intermediates. Owing to the extreme complexity of the native enzyme systems, the mechanism by which this catalysis occurs remains poorly understood. In this work, we have developed a protein-based model for the NiP center of acetyl coenzyme A synthase using a nickel-substituted azurin protein (NiAz). NiAz is the first model nickel protein system capable of accessing three (NiI/NiII/NiIII) distinct oxidation states within a physiological potential range in aqueous solution, a critical feature for achieving organometallic ACS activity, and binds CO and -CH3 groups with biologically relevant affinity. Characterization of the NiI-CO species through spectroscopic and computational techniques reveals fundamentally similar features between the model NiAz system and the native ACS enzyme, highlighting the potential for related reactivity in this model protein. This work provides insight into the enzymatic process, with implications toward engineering biological catalysts for organometallic processes.
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Affiliation(s)
- Anastasia C Manesis
- The Ohio State University , 100 West 18th Avenue, Newman & Wolfrom Laboratory of Chemistry, Columbus, Ohio 43210, United States
| | - Matthew J O'Connor
- The Ohio State University , 100 West 18th Avenue, Newman & Wolfrom Laboratory of Chemistry, Columbus, Ohio 43210, United States
| | - Camille R Schneider
- The Ohio State University , 100 West 18th Avenue, Newman & Wolfrom Laboratory of Chemistry, Columbus, Ohio 43210, United States
| | - Hannah S Shafaat
- The Ohio State University , 100 West 18th Avenue, Newman & Wolfrom Laboratory of Chemistry, Columbus, Ohio 43210, United States
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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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Rabeah J, Radnik J, Briois V, Maschmeyer D, Stochniol G, Peitz S, Reeker H, La Fontaine C, Brückner A. Tracing Active Sites in Supported Ni Catalysts during Butene Oligomerization by Operando Spectroscopy under Pressure. ACS Catal 2016. [DOI: 10.1021/acscatal.6b02331] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jabor Rabeah
- Leibniz-Institut
für Katalyse e. V., an der Universität Rostock, Albert-Einstein-Straße
29a, D-18059 Rostock, Germany
| | - Jörg Radnik
- Leibniz-Institut
für Katalyse e. V., an der Universität Rostock, Albert-Einstein-Straße
29a, D-18059 Rostock, Germany
| | - Valérie Briois
- SOLEIL
Synchrotron, UR1-CNRS, L’Orme des Merisiers, BP48, Saint-Aubin 91192, Gif-sur Yvette, France
| | | | - Guido Stochniol
- Evonik Performance
Materials GmbH, Paul-Baumann-Str. 1, 45772 Marl, Germany
| | - Stephan Peitz
- Evonik Performance
Materials GmbH, Paul-Baumann-Str. 1, 45772 Marl, Germany
| | - Helene Reeker
- Evonik Performance
Materials GmbH, Paul-Baumann-Str. 1, 45772 Marl, Germany
| | - Camille La Fontaine
- SOLEIL
Synchrotron, UR1-CNRS, L’Orme des Merisiers, BP48, Saint-Aubin 91192, Gif-sur Yvette, France
| | - Angelika Brückner
- Leibniz-Institut
für Katalyse e. V., an der Universität Rostock, Albert-Einstein-Straße
29a, D-18059 Rostock, Germany
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17
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Boer JL, Mulrooney SB, Hausinger RP. Nickel-dependent metalloenzymes. Arch Biochem Biophys 2014; 544:142-52. [PMID: 24036122 PMCID: PMC3946514 DOI: 10.1016/j.abb.2013.09.002] [Citation(s) in RCA: 200] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 08/31/2013] [Accepted: 09/03/2013] [Indexed: 11/29/2022]
Abstract
This review describes the functions, structures, and mechanisms of nine nickel-containing enzymes: glyoxalase I, acireductone dioxygenase, urease, superoxide dismutase, [NiFe]-hydrogenase, carbon monoxide dehydrogenase, acetyl-coenzyme A synthase/decarbonylase, methyl-coenzyme M reductase, and lactate racemase. These enzymes catalyze their various chemistries by using metallocenters of diverse structures, including mononuclear nickel, dinuclear nickel, nickel-iron heterodinuclear sites, more complex nickel-containing clusters, and nickel-tetrapyrroles. Selected other enzymes are active with nickel, but the physiological relevance of this metal specificity is unclear. Additional nickel-containing proteins of undefined function have been identified.
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Affiliation(s)
- Jodi L Boer
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Scott B Mulrooney
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Robert P Hausinger
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA; Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA.
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18
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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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19
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Sarangi R. X-ray absorption near-edge spectroscopy in bioinorganic chemistry: Application to M-O 2 systems. Coord Chem Rev 2012; 257:459-472. [PMID: 23525635 DOI: 10.1016/j.ccr.2012.06.024] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Metal K-edge X-ray absorption spectroscopy (XAS) has been extensively applied to bioinorganic chemistry to obtain geometric structure information on metalloprotein and biomimetic model complex active sites by analyzing the higher energy extended X-ray absorption fine structure (EXAFS) region of the spectrum. In recent years, focus has been on developing methodologies to interpret the lower energy K-pre-edge and rising-edge regions (XANES) and using it for electronic structure determination in complex bioinorganic systems. In this review, the evolution and progress of 3d-transition metal K-pre-edge and rising-edge methodology development is presented with particular focus on applications to bioinorganic systems. Applications to biomimetic transition metal-O2 intermediates (M = Fe, Co, Ni and Cu) are reviewed, which demonstrate the power of the method as an electronic structure determination technique and its impact in understanding the role of supporting ligands in tuning the electronic configuration of transition metal-O2 systems.
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Affiliation(s)
- Ritimukta Sarangi
- Stanford Synchrotron Radiation Lightsource, Stanford National Accelerator Laboratory, MS 69, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
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20
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Chen SL, Blomberg MRA, Siegbahn PEM. How Is Methane Formed and Oxidized Reversibly When Catalyzed by Ni-Containing Methyl-Coenzyme M Reductase? Chemistry 2012; 18:6309-15. [DOI: 10.1002/chem.201200274] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Indexed: 11/07/2022]
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21
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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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22
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Ferry JG. Fundamentals of methanogenic pathways that are key to the biomethanation of complex biomass. Curr Opin Biotechnol 2011; 22:351-7. [PMID: 21555213 DOI: 10.1016/j.copbio.2011.04.011] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Accepted: 04/18/2011] [Indexed: 12/17/2022]
Abstract
The conversion of biomass to CH4 (biomethanation) involves an anaerobic microbial food chain composed of at least three metabolic groups of which the first two decompose the complex biomass primarily to acetate, formate, and H2. The thermodynamics of these conversions are unfavorable requiring a symbiosis with the CH4-producing group (methanogens) that metabolize the decomposition products to favorable concentrations. The methanogens produce CH4 by two major pathways, conversion of the methyl group of acetate and reduction of CO2 coupled to the oxidation of formate or H2. This review covers recent advances in the fundamental understanding of both methanogenic pathways with the view of stimulating research towards improving the rate and reliability of the overall biomethanation process.
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Affiliation(s)
- James G Ferry
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16801, United States.
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23
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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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24
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Scheller S, Goenrich M, Mayr S, Thauer RK, Jaun B. Intermediates in the catalytic cycle of methyl coenzyme M reductase: isotope exchange is consistent with formation of a σ-alkane-nickel complex. Angew Chem Int Ed Engl 2011; 49:8112-5. [PMID: 20857468 DOI: 10.1002/anie.201003214] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Silvan Scheller
- Laboratory of Organic Chemistry, ETH Zurich, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland
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25
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Sarangi R, Cho J, Nam W, Solomon EI. XAS and DFT investigation of mononuclear cobalt(III) peroxo complexes: electronic control of the geometric structure in CoO2 versus NiO2 systems. Inorg Chem 2010; 50:614-20. [PMID: 21142119 DOI: 10.1021/ic101730r] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The geometric and electronic structures of two mononuclear [(L)CoO2](+) complexes, [(12-TMC)CoO2](ClO4) (1) and [(14-TMC)CoO2](ClO4) (2), have been evaluated using Co K-edge X-ray absorption spectroscopy (XAS) and extended X-ray absorption fine structure (EXAFS) and correlated with density functional theory (DFT) calculations to evaluate the differences in the geometric and electronic structures due to changes in the TMC chelate ring size. Co K-edge XAS shows that both 1 and 2 are Co(III) species. Co K-edge EXAFS data show that both 1 and 2 are side-on O2-bound cobalt(III) peroxide complexes. A combination of EXAFS and DFT calculations reveals that while the constrained 12-TMC ring in 1 allows for side-on O2 binding to the Co center with ease, the 14-TMC chelate in 2 has to undergo significant distortion of the ring to overcome steric hindrance posed by the four cis-methyl groups of the chelate to allow side-on O2 binding to the Co center. The Ni analogue of 2, [(14-TMC)NiO2](+), has been shown to form an end-on-bound nickel(II) superoxide species. The electronic and geometric factors that determine the different electronic structures of 2 and [(14-TMC)NiO2](+) are evaluated using DFT calculations. The results show that while the sterics of the cis-14-TMC chelate contribute to the geometry of O2 binding and result in an end-on-bound Ni(II)O2(-) complex in [(14-TMC)NiO2](+), the higher thermodynamic driving force for oxidation of Co(II) overcomes this steric constraint, resulting in stabilization of a side-on-bound Co(III)O2(2-) electronic structure in 2.
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Affiliation(s)
- Ritimukta Sarangi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
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26
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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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27
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Scheller S, Goenrich M, Mayr S, Thauer RK, Jaun B. Zwischenprodukte im Katalysezyklus von Methyl-Coenzym-M- Reduktase: Das Muster des Isotopenaustauschs ist in Einklang mit der Bildung eines σ-Alkan-Nickel-Komplexes. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201003214] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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28
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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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29
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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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30
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31
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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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