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Polêto M, Allen KD, Lemkul JA. Structural Dynamics of the Methyl-Coenzyme M Reductase Active Site Are Influenced by Coenzyme F 430 Modifications. Biochemistry 2024; 63:1783-1794. [PMID: 38914925 PMCID: PMC11256747 DOI: 10.1021/acs.biochem.4c00168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 06/13/2024] [Accepted: 06/17/2024] [Indexed: 06/26/2024]
Abstract
Methyl-coenzyme M reductase (MCR) is a central player in methane biogeochemistry, governing methanogenesis and the anaerobic oxidation of methane (AOM) in methanogens and anaerobic methanotrophs (ANME), respectively. The prosthetic group of MCR is coenzyme F430, a nickel-containing tetrahydrocorphin. Several modified versions of F430 have been discovered, including the 172-methylthio-F430 (mtF430) used by ANME-1 MCR. Here, we employ molecular dynamics (MD) simulations to investigate the active site dynamics of MCR from Methanosarcina acetivorans and ANME-1 when bound to the canonical F430 compared to 172-thioether coenzyme F430 variants and substrates (methyl-coenzyme M and coenzyme B) for methane formation. Our simulations highlight the importance of the Gln to Val substitution in accommodating the 172 methylthio modification in ANME-1 MCR. Modifications at the 172 position disrupt the canonical substrate positioning in M. acetivorans MCR. However, in some replicates, active site reorganization to maintain substrate positioning suggests that the modified F430 variants could be accommodated in a methanogenic MCR. We additionally report the first quantitative estimate of MCR intrinsic electric fields that are pivotal in driving methane formation. Our results suggest that the electric field aligned along the CH3-S-CoM thioether bond facilitates homolytic bond cleavage, coinciding with the proposed catalytic mechanism. Structural perturbations, however, weaken and misalign these electric fields, emphasizing the importance of the active site structure in maintaining their integrity. In conclusion, our results deepen the understanding of MCR active site dynamics, the enzyme's organizational role in intrinsic electric fields for catalysis, and the interplay between active site structure and electrostatics.
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Affiliation(s)
- Marcelo
D. Polêto
- Department of Biochemistry, Virginia Tech, 111 Engel Hall, 340 West Campus Drive, Blacksburg, Virginia 24061, United States
| | - Kylie D. Allen
- Department of Biochemistry, Virginia Tech, 111 Engel Hall, 340 West Campus Drive, Blacksburg, Virginia 24061, United States
| | - Justin A. Lemkul
- Department of Biochemistry, Virginia Tech, 111 Engel Hall, 340 West Campus Drive, Blacksburg, Virginia 24061, United States
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2
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Gendron A, Allen KD. Overview of Diverse Methyl/Alkyl-Coenzyme M Reductases and Considerations for Their Potential Heterologous Expression. Front Microbiol 2022; 13:867342. [PMID: 35547147 PMCID: PMC9081873 DOI: 10.3389/fmicb.2022.867342] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 04/01/2022] [Indexed: 12/02/2022] Open
Abstract
Methyl-coenzyme M reductase (MCR) is an archaeal enzyme that catalyzes the final step of methanogenesis and the first step in the anaerobic oxidation of methane, the energy metabolisms of methanogens and anaerobic methanotrophs (ANME), respectively. Variants of MCR, known as alkyl-coenzyme M reductases, are involved in the anaerobic oxidation of short-chain alkanes including ethane, propane, and butane as well as the catabolism of long-chain alkanes from oil reservoirs. MCR is a dimer of heterotrimers (encoded by mcrABG) and requires the nickel-containing tetrapyrrole prosthetic group known as coenzyme F430. MCR houses a series of unusual post-translational modifications within its active site whose identities vary depending on the organism and whose functions remain unclear. Methanogenic MCRs are encoded in a highly conserved mcrBDCGA gene cluster, which encodes two accessory proteins, McrD and McrC, that are believed to be involved in the assembly and activation of MCR, respectively. The requirement of a unique and complex coenzyme, various unusual post-translational modifications, and many remaining questions surrounding assembly and activation of MCR largely limit in vitro experiments to native enzymes with recombinant methods only recently appearing. Production of MCRs in a heterologous host is an important step toward developing optimized biocatalytic systems for methane production as well as for bioconversion of methane and other alkanes into value-added compounds. This review will first summarize MCR catalysis and structure, followed by a discussion of advances and challenges related to the production of diverse MCRs in a heterologous host.
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Affiliation(s)
| | - Kylie D. Allen
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
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3
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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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4
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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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5
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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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6
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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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7
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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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8
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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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9
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Wang WJ, Wei WJ, Liao RZ. Deciphering the chemoselectivity of nickel-dependent quercetin 2,4-dioxygenase. Phys Chem Chem Phys 2018; 20:15784-15794. [DOI: 10.1039/c8cp02683a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
QM/MM calculations were performed to elucidate the reaction mechanism and chemoselectivity of 2,4-QueD. The protonation state of the first-shell ligand Glu74 plays an important role in dictating the selectivity.
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Affiliation(s)
- Wen-Juan Wang
- Key Laboratory of Material Chemistry for Energy Conversion and Storage
- Ministry of Education
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica
- Hubei Key Laboratory of Materials Chemistry and Service Failure
- School of Chemistry and Chemical Engineering
| | - Wen-Jie Wei
- Key Laboratory of Material Chemistry for Energy Conversion and Storage
- Ministry of Education
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica
- Hubei Key Laboratory of Materials Chemistry and Service Failure
- School of Chemistry and Chemical Engineering
| | - Rong-Zhen Liao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage
- Ministry of Education
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica
- Hubei Key Laboratory of Materials Chemistry and Service Failure
- School of Chemistry and Chemical Engineering
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10
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Yu MJ, Chen SL. From NAD + to Nickel Pincer Complex: A Significant Cofactor Evolution Presented by Lactate Racemase. Chemistry 2017; 23:7545-7557. [PMID: 28374531 DOI: 10.1002/chem.201700405] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Indexed: 02/02/2023]
Abstract
Lactate racemase (LarA), a new nickel enzyme discovered recently, catalyzes the racemization between d- and l-lactates with a novel nickel pincer cofactor (Ni-PTTMN) derived from nicotinic acid. In this study, by using DFT and a 200-atom active-site model, LarA is revealed to employ a modified proton-coupled hydride-transfer mechanism in which a hydride is transferred to a cofactor pyridine carbon from the substrate α-carbon along with proton transfer from the substrate hydroxy group to a histidine, and then moved back from the opposite side. Tyr294 and Lys298 provide significant acceleration effects by orientating substrates and stabilizing the negative charge developing at the substrate hydroxy oxygen. The barrier was determined to be 12.0 kcal mol-1 , which reveals enhanced racemase activity relative to the LarA reaction using NAD+ -like cofactors. Compared with NAD+ , Ni-PTTMN has a stronger hydride-addition reactivity in moderate and high environmental polarity and may fit perfectly the moderately polar active site of LarA.
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Affiliation(s)
- Ming-Jia Yu
- Key Laboratory of Cluster Science of the Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, P.R. China
| | - Shi-Lu Chen
- Key Laboratory of Cluster Science of the Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, P.R. China
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11
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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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12
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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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13
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Szatkowski L, Hall MB. Dehalogenation of chloroalkanes by nickel(i) porphyrin derivatives, a computational study. Dalton Trans 2016; 45:16869-16877. [DOI: 10.1039/c6dt02632j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We constructed theoretical models of the dehalogenation of chloromethane by a nickel(i) isobacteriochlorin anion and compared its reactivity with that of similar Ni(I) complexes with other porphyrin-derived ligands: porphyrin, chlorin, bactreriochlorin, hexahydroporphyrin and octahydroporphyrin.
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Affiliation(s)
- L. Szatkowski
- Department of Chemistry
- Texas A&M University
- College Station
- USA
- Department of Chemistry and Biochemistry
| | - M. B. Hall
- Department of Chemistry
- Texas A&M University
- College Station
- USA
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14
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Mueller TJ, Grisewood MJ, Nazem-Bokaee H, Gopalakrishnan S, Ferry JG, Wood TK, Maranas CD. Methane oxidation by anaerobic archaea for conversion to liquid fuels. ACTA ACUST UNITED AC 2015; 42:391-401. [DOI: 10.1007/s10295-014-1548-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 11/11/2014] [Indexed: 11/24/2022]
Abstract
Abstract
Given the recent increases in natural gas reserves and associated drawbacks of current gas-to-liquids technologies, the development of a bioconversion process to directly convert methane to liquid fuels would generate considerable industrial interest. Several clades of anaerobic methanotrophic archaea (ANME) are capable of performing anaerobic oxidation of methane (AOM). AOM carried out by ANME offers carbon efficiency advantages over aerobic oxidation by conserving the entire carbon flux without losing one out of three carbon atoms to carbon dioxide. This review highlights the recent advances in understanding the key enzymes involved in AOM (i.e., methyl-coenzyme M reductase), the ecological niches of a number of ANME, the putative metabolic pathways for AOM, and the syntrophic consortia that they typically form.
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Affiliation(s)
- Thomas J Mueller
- grid.29857.31 0000000120974281 Department of Chemical Engineering The Pennsylvania State University University Park PA USA
| | - Matthew J Grisewood
- grid.29857.31 0000000120974281 Department of Chemical Engineering The Pennsylvania State University University Park PA USA
| | - Hadi Nazem-Bokaee
- grid.29857.31 0000000120974281 Department of Chemical Engineering The Pennsylvania State University University Park PA USA
| | - Saratram Gopalakrishnan
- grid.29857.31 0000000120974281 Department of Chemical Engineering The Pennsylvania State University University Park PA USA
| | - James G Ferry
- grid.29857.31 0000000120974281 Department of Biochemistry and Molecular Biology The Pennsylvania State University University Park PA USA
| | - Thomas K Wood
- grid.29857.31 0000000120974281 Department of Chemical Engineering The Pennsylvania State University University Park PA USA
- grid.29857.31 0000000120974281 Department of Biochemistry and Molecular Biology The Pennsylvania State University University Park PA USA
| | - Costas D Maranas
- grid.29857.31 0000000120974281 Department of Chemical Engineering The Pennsylvania State University University Park PA USA
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15
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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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16
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Xerri B, Petitjean H, Dupeyrat F, Flament JP, Lorphelin A, Vidaud C, Berthomieu C, Berthomieu D. Mid- and Far-Infrared Marker Bands of the Metal Coordination Sites of the Histidine Side Chains in the Protein Cu,Zn-Superoxide Dismutase. Eur J Inorg Chem 2014. [DOI: 10.1002/ejic.201402263] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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17
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Chen SL, Blomberg MRA, Siegbahn PEM. An investigation of possible competing mechanisms for Ni-containing methyl–coenzyme M reductase. Phys Chem Chem Phys 2014; 16:14029-35. [DOI: 10.1039/c4cp01483a] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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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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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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20
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Callaghan AV. Enzymes involved in the anaerobic oxidation of n-alkanes: from methane to long-chain paraffins. Front Microbiol 2013; 4:89. [PMID: 23717304 PMCID: PMC3653055 DOI: 10.3389/fmicb.2013.00089] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 03/31/2013] [Indexed: 11/13/2022] Open
Abstract
Anaerobic microorganisms play key roles in the biogeochemical cycling of methane and non-methane alkanes. To date, there appear to be at least three proposed mechanisms of anaerobic methane oxidation (AOM). The first pathway is mediated by consortia of archaeal anaerobic methane oxidizers and sulfate-reducing bacteria (SRB) via “reverse methanogenesis” and is catalyzed by a homolog of methyl-coenzyme M reductase. The second pathway is also mediated by anaerobic methane oxidizers and SRB, wherein the archaeal members catalyze both methane oxidation and sulfate reduction and zero-valent sulfur is a key intermediate. The third AOM mechanism is a nitrite-dependent, “intra-aerobic” pathway described for the denitrifying bacterium, ‘Candidatus Methylomirabilis oxyfera.’ It is hypothesized that AOM proceeds via reduction of nitrite to nitric oxide, followed by the conversion of two nitric oxide molecules to dinitrogen and molecular oxygen. The latter can be used to functionalize the methane via a particulate methane monooxygenase. With respect to non-methane alkanes, there also appear to be novel mechanisms of activation. The most well-described pathway is the addition of non-methane alkanes across the double bond of fumarate to form alkyl-substituted succinates via the putative glycyl radical enzyme, alkylsuccinate synthase (also known as methylalkylsuccinate synthase). Other proposed mechanisms include anaerobic hydroxylation via ethylbenzene dehydrogenase-like enzymes and an “intra-aerobic” denitrification pathway similar to that described for ‘Methylomirabilis oxyfera.’
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Affiliation(s)
- Amy V Callaghan
- Department of Microbiology and Plant Biology, University of Oklahoma Norman, OK, USA
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Zhou Y, Dorchak AE, Ragsdale SW. In vivo activation of methyl-coenzyme M reductase by carbon monoxide. Front Microbiol 2013; 4:69. [PMID: 23554601 PMCID: PMC3612591 DOI: 10.3389/fmicb.2013.00069] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 03/11/2013] [Indexed: 12/21/2022] Open
Abstract
Methyl-coenzyme M reductase (MCR) from methanogenic archaea catalyzes the rate-limiting and final step in methane biosynthesis. Using coenzyme B as the two-electron donor, MCR reduces methyl-coenzyme M (CH3-SCoM) to methane and the mixed disulfide, CoBS-SCoM. MCR contains an essential redox-active nickel tetrahydrocorphinoid cofactor, Coenzyme F430, at its active site. The active form of the enzyme (MCRred1) contains Ni(I)-F430. Rapid and efficient conversion of MCR to MCRred1 is important for elucidating the enzymatic mechanism, yet this reduction is difficult because the Ni(I) state is subject to oxidative inactivation. Furthermore, no in vitro methods have yet been described to convert Ni(II) forms into MCRred1. Since 1991, it has been known that MCRred1 from Methanothermobacter marburgensis can be generated in vivo when cells are purged with 100% H2. Here we show that purging cells or cell extracts with CO can also activate MCR. The rate of in vivo activation by CO is about 15 times faster than by H2 (130 and 8 min-1, respectively) and CO leads to twofold higher MCRred1 than H2. Unlike H2-dependent activation, which exhibits a 10-h lag time, there is no lag for CO-dependent activation. Based on cyanide inhibition experiments, carbon monoxide dehydrogenase is required for the CO-dependent activation. Formate, which also is a strong reductant, cannot activate MCR in M. marburgensis in vivo.
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Affiliation(s)
- Yuzhen Zhou
- Department of Biological Chemistry, University of Michigan Medical School, University of Michigan Ann Arbor, MI, USA
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22
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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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Nishigaki JI, Matsumoto T, Tatsumi K. Model Studies of Methyl CoM Reductase: Methane Formation via CH3–S Bond Cleavage of Ni(I) Tetraazacyclic Complexes Having Intramolecular Methyl Sulfide Pendants. Inorg Chem 2012; 51:5173-87. [DOI: 10.1021/ic300017k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jun-ichi Nishigaki
- Research Center for Materials Science, and Department
of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Tsuyoshi Matsumoto
- Research Center for Materials Science, and Department
of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Kazuyuki Tatsumi
- Research Center for Materials Science, and Department
of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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24
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Jensen KP, Ryde U. Comparison of chemical properties of iron, cobalt, and nickel porphyrins, corrins, and hydrocorphins. J PORPHYR PHTHALOCYA 2012. [DOI: 10.1142/s1088424605000691] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Density functional calculations have been used to compare the geometric, electronic, and functional properties of the three important tetrapyrrole systems in biology, heme, coenzyme B 12, and coenzyme F430, formed from iron porphyrin ( Por ), cobalt corrin ( Cor ), and nickel hydrocorphin ( Hcor ). The results show that the flexibility of the ring systems follows the trend Hcor > Cor > Por and that the size of the central cavity follows the trend Cor < Por < Hcor . Therefore, low-spin Co I, Co II, and Co III fit well into the Cor ring, whereas Por seems to be more ideal for the higher spin states of iron, and the cavity in Hcor is tailored for the larger Ni ion, especially in the high-spin Ni II state. This is confirmed by the thermodynamic stabilities of the various combinations of metals and ring systems. Reduction potentials indicate that the +I and +III states are less stable for Ni than for the other metal ions. Moreover, Ni – C bonds are appreciably less stable than Co - C bonds. However, it is still possible that a Ni – CH 3 bond is formed in F 430 by a heterolytic methyl transfer reaction, provided that the donor is appropriate, e.g. if coenzyme M is protonated. This can be facilitated by the adjacent SO 3− group in this coenzyme and by the axial glutamine ligand, which stabilizes the Ni III state. Our results also show that a Ni III– CH 3 complex is readily hydrolysed to form a methane molecule and that the Ni III hydrolysis product can oxidize coenzyme B and M to a heterodisulphide in the reaction mechanism of methyl coenzyme M reductase.
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Affiliation(s)
- Kasper P. Jensen
- Department of Theoretical Chemistry, Chemical Centre, Lund University, P.O. Box 124, S-22100 Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Chemical Centre, Lund University, P.O. Box 124, S-22100 Lund, Sweden
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25
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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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26
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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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27
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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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Abstract
Methane produced in the biosphere is derived from two major pathways. Conversion of the methyl group of acetate to CH(4) in the aceticlastic pathway accounts for at least two-thirds, and reduction of CO(2) with electrons derived from H(2), formate, or CO accounts for approximately one-third. Although both pathways have terminal steps in common, they diverge considerably in the initial steps and energy conservation mechanisms. Steps and enzymes unique to the CO(2) reduction pathway are confined to methanogens and the domain Archaea. On the other hand, steps and enzymes unique to the aceticlastic pathway are widely distributed in the domain Bacteria, the understanding of which has contributed to a broader understanding of prokaryotic biology.
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Affiliation(s)
- James G Ferry
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16801, USA.
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29
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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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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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31
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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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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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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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34
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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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35
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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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36
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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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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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38
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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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39
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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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40
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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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41
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Kunz RC, Dey M, Ragsdale SW. Characterization of the thioether product formed from the thiolytic cleavage of the alkyl-nickel bond in methyl-coenzyme M reductase. Biochemistry 2008; 47:2661-7. [PMID: 18220418 DOI: 10.1021/bi701942w] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Methyl-coenzyme M reductase (MCR) catalyzes the terminal step in methanogenesis by using N-7-mercaptoheptanolyl-threonine phosphate (CoBSH) as the two-electron donor to reduce 2-(methylthiol)ethane sulfonate (methyl-SCoM) to methane, and producing the heterodisulfide, CoBS-SCoM. The active site of MCR includes a noncovalently bound Ni tetrapyrrolic cofactor called coenzyme F430, which is in the Ni(I) state in the active enzyme (MCRred1). Bromopropanesulfonate (BPS) is a potent inhibitor and reversible redox inactivator that reacts with MCRred1 to form an EPR-active state called MCRPS, which is an alkyl-nickel species. When MCRPS is treated with free thiol containing compounds, the enzyme is reconverted to the active MCRred1 state. In this paper, we demonstrate that the reactivation of MCRPS to MCRred1 by thiols involves formation of a thioether product. MCRPS also can be converted to active MCRred1 by treatment with sodium borohydride. Reactivation is highest with the smallest free thiol HS-. Interestingly, MCRPS can also be reductively activated with analogues of CoBSH such as CoB8SH and CoB9SH, but not CoBSH itself. Unambiguous demonstration of the formation of a methylthioether product from thiolysis of an alkyl-Ni species provides support for a methyl-Ni intermediate in the MCR-catalyzed last step in methanogenesis and the first proposed step in anaerobic methane oxidation.
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Affiliation(s)
- Ryan C Kunz
- Department of Biochemistry, University of Nebraska, Lincoln, Nebraska 68588, USA
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42
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Abstract
Methane has long been known to be used as a carbon and energy source by some aerobic alpha- and delta-proteobacteria. In these organisms the metabolism of methane starts with its oxidation with O(2) to methanol, a reaction catalyzed by a monooxygenase and therefore restricted to the aerobic world. Methane has recently been shown to also fuel the growth of anaerobic microorganisms. The oxidation of methane with sulfate and with nitrate have been reported, but the mechanisms of anaerobic methane oxidation still remains elusive. Sulfate-dependent methane oxidation is catalyzed by methanotrophic archaea, which are related to the Methanosarcinales and which grow in close association with sulfate-reducing delta-proteobacteria. There is evidence that anaerobic methane oxidation with sulfate proceeds at least in part via reversed methanogenesis involving the nickel enzyme methyl-coenzyme M reductase for methane activation, which under standard conditions is an endergonic reaction, and thus inherently slow. Methane oxidation coupled to denitrification is mediated by bacteria belonging to a novel phylum and does not involve methyl-coenzyme M reductase. The first step in methane oxidation is most likely the exergonic formation of 2-methylsuccinate from fumarate and methane catalyzed by a glycine-radical enzyme.
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Affiliation(s)
- Rudolf K Thauer
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse, D-35043 Marburg, Germany.
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43
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Dey M, Kunz RC, Lyons DM, Ragsdale SW. Characterization of alkyl-nickel adducts generated by reaction of methyl-coenzyme m reductase with brominated acids. Biochemistry 2007; 46:11969-78. [PMID: 17902704 PMCID: PMC3553217 DOI: 10.1021/bi700925n] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Methyl-coenzyme M reductase (MCR) from methanogenic archaea catalyzes the final step in the biological synthesis of methane. Using coenzyme B (CoBSH) as the two-electron donor, MCR reduces methyl-coenzyme M (methyl-SCoM) to methane and the mixed disulfide, CoB-S-S-CoM. MCR contains coenzyme F430, an essential redox-active nickel tetrahydrocorphin, at its active site. The active form of MCR (MCRred1) contains Ni(I)-F430. When 3-bromopropane sulfonate (BPS) is incubated with MCRred1, an alkyl-Ni(III) species is formed that elicits the MCRPS EPR signal. Here we used EPR and UV-visible spectroscopy and transient kinetics to study the reaction between MCR from Methanothermobacter marburgensis and a series of brominated carboxylic acids, with carbon chain lengths of 4-16. All of these compounds give rise to an alkyl-Ni intermediate with an EPR signal similar to that of the MCRPS species. Reaction of the alkyl-Ni(III) adduct, formed from brominated acids with eight or fewer total carbons, with HSCoM as nucleophile at pH 10.0 results in the formation of a thioether coupled to regeneration of the active MCRred1 state. When reacted with 4-bromobutyrate, MCRred1 forms the alkyl-Ni(III) MCRXA state and then, surprisingly, undergoes "self-reactivation" to regenerate the Ni(I) MCRred1 state and a bromocarboxy ester. The results demonstrate an unexpected reactivity and flexibility of the MCR active site in accommodating a broad range of substrates, which act as molecular rulers for the substrate channel in MCR.
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Affiliation(s)
- Mishtu Dey
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588
| | - Ryan C. Kunz
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588
| | | | - Stephen W. Ragsdale
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588
- CORRESPONDING AUTHOR CONTACT INFORMATION: Phone: 402-472-2943; FAX: 402-472- 4961; AFTER AUG 1, 2007: Phone: (734) 763-6459; FAX: (734) 764-3509;
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44
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Güell M, Siegbahn PEM. Theoretical study of the catalytic mechanism of catechol oxidase. J Biol Inorg Chem 2007; 12:1251-64. [PMID: 17891425 DOI: 10.1007/s00775-007-0293-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2007] [Accepted: 08/16/2007] [Indexed: 10/22/2022]
Abstract
The mechanism for the oxidation of catechol by catechol oxidase has been studied using B3LYP hybrid density functional theory. On the basis of the X-ray structure of the enzyme, the molecular system investigated includes the first-shell protein ligands of the two metal centers as well as the second-shell ligand Cys92. The cycle starts out with the oxidized, open-shell singlet complex with oxidation states Cu(2)(II,II) with a mu-eta(2):eta(2) bridging peroxide, as suggested experimentally, which is obtained from the oxidation of Cu(2)(I,I) by dioxygen. The substrate of each half-reaction is a catechol molecule approaching the dicopper complex: the first half-reaction involves Cu(I) oxidation by peroxide and the second one Cu(II) reduction. The quantitative potential energy profile of the reaction is discussed in connection with experimental data. Since no protons leave or enter the active site during the catalytic cycle, no external base is required. Unlike the previous density functional theory study, the dicopper complex has a charge of +2.
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Affiliation(s)
- Mireia Güell
- Institut de Química Computacional, Universitat de Girona, Campus de Montilivi, Girona, Spain.
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45
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Yang N, Reiher M, Wang M, Harmer J, Duin EC. Formation of a Nickel−Methyl Species in Methyl-Coenzyme M Reductase, an Enzyme Catalyzing Methane Formation. J Am Chem Soc 2007; 129:11028-9. [PMID: 17711279 DOI: 10.1021/ja0734501] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Na Yang
- Department of Chemistry and Biochemistry, Auburn University, Alabama 36849, USA
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46
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Hinderberger D, Piskorski RP, Goenrich M, Thauer RK, Schweiger A, Harmer J, Jaun B. A nickel-alkyl bond in an inactivated state of the enzyme catalyzing methane formation. Angew Chem Int Ed Engl 2007; 45:3602-7. [PMID: 16639771 DOI: 10.1002/anie.200600366] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Dariush Hinderberger
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
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47
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Calle C, Sreekanth A, Fedin M, Forrer J, Garcia-Rubio I, Gromov I, Hinderberger D, Kasumaj B, Léger P, Mancosu B, Mitrikas G, Santangelo M, Stoll S, Schweiger A, Tschaggelar R, Harmer J. Pulse EPR Methods for Studying Chemical and Biological Samples Containing Transition Metals. Helv Chim Acta 2006. [DOI: 10.1002/hlca.200690229] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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48
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Kunz RC, Horng YC, Ragsdale SW. Spectroscopic and kinetic studies of the reaction of bromopropanesulfonate with methyl-coenzyme M reductase. J Biol Chem 2006; 281:34663-76. [PMID: 16966321 DOI: 10.1074/jbc.m606715200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Methyl-coenzyme M reductase (MCR) catalyzes the final step of methanogenesis in which coenzyme B and methyl-coenzyme M are converted to methane and the heterodisulfide, CoMS-SCoB. MCR also appears to initiate anaerobic methane oxidation (reverse methanogenesis). At the active site of MCR is coenzyme F430, a nickel tetrapyrrole. This paper describes the reaction of the active MCR(red1) state with the potent inhibitor, 3-bromopropanesulfonate (BPS; I50 = 50 nM) by UV-visible and EPR spectroscopy and by steady-state and rapid kinetics. BPS was shown to be an alternative substrate of MCR in an ionic reaction that is coenzyme B-independent and leads to debromination of BPS and formation of a distinct state ("MCR(PS)") with an EPR signal that was assigned to a Ni(III)-propylsulfonate species (Hinderberger, D., Piskorski, R. P., Goenrich, M., Thauer, R. K., Schweiger, A., Harmer, J., and Jaun, B. (2006) Angew. Chem. Int. Ed. Engl. 45, 3602-3607). A similar EPR signal was generated by reacting MCR(red1) with several halogenated sulfonate and carboxylate substrates. In rapid chemical quench experiments, the propylsulfonate ligand was identified by NMR spectroscopy and high performance liquid chromatography as propanesulfonic acid after protonolysis of the MCR(PS) complex. Propanesulfonate formation was also observed in steady-state reactions in the presence of Ti(III) citrate. Reaction of the alkylnickel intermediate with thiols regenerates the active MCR(red1) state and eliminates the propylsulfonate group, presumably as the thioether. MCR(PS) is catalytically competent in both the generation of propanesulfonate and reformation of MCR(red1). These results provide evidence for the intermediacy of an alkylnickel species in the final step in anaerobic methane oxidation and in the initial step of methanogenesis.
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Affiliation(s)
- Ryan C Kunz
- Department of Biochemistry, University of Nebraska, Lincoln, Nebraska 68588-0664, USA
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49
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Hinderberger D, Piskorski RP, Goenrich M, Thauer RK, Schweiger A, Harmer J, Jaun B. A Nickel–Alkyl Bond in an Inactivated State of the Enzyme Catalyzing Methane Formation. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200600366] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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50
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Pelmenschikov V, Siegbahn PEM. Nickel Superoxide Dismutase Reaction Mechanism Studied by Hybrid Density Functional Methods. J Am Chem Soc 2006; 128:7466-75. [PMID: 16756300 DOI: 10.1021/ja053665f] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The reaction mechanism for the disproportionation of the toxic superoxide radical to molecular oxygen and hydrogen peroxide by the nickel-dependent superoxide dismutase (NiSOD) has been studied using the B3LYP hybrid DFT method. Based on the recent X-ray structures of the enzyme in the resting oxidized Ni(III) and X-ray-reduced Ni(II) states, the model investigated includes the backbone spacer of six residues (sequence numbers 1-6) as a structural framework. The side chains of residues His1, Cys2, and Cys6, which are essential for nickel binding and catalysis, were modeled explicitly. The catalytic cycle consists of two half-reactions, each initiated by the successive substrate approach to the metal center. The two protons necessary for the dismutation are postulated to be delivered concertedly with the superoxide radical anions. The first (reductive) phase involves Ni(III) reduction to Ni(II), and the second (oxidative) phase involves the metal reoxidation back to its resting state. The Cys2 thiolate sulfur serves as a transient protonation site in the interim between the two half-reactions, allowing for the dioxygen and hydrogen peroxide molecules to be released in the reductive and oxidative phases, respectively. The His1 side chain nitrogen and backbone amides of the active site channel are shown to be less favorable transient proton locations, as compared to the Cys2 sulfur. Comparisons are made to the Cu- and Zn-dependent SOD, studied previously using similar models.
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