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Heryakusuma C, Johnson EF, Purwantini E, Mukhopadhyay B. Nitrite reductase activity in F 420-dependent sulphite reductase (Fsr) from Methanocaldococcus jannaschii. Access Microbiol 2023; 5:000482.v3. [PMID: 37223055 PMCID: PMC10202398 DOI: 10.1099/acmi.0.000482.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 01/25/2023] [Indexed: 05/25/2023] Open
Abstract
Methanocaldococcus jannaschii (Mj), a hyperthermophilic and evolutionarily deeply rooted methanogenic archaeon from a deep-sea hydrothermal vent, produces F420-dependent sulphite reductase (Fsr) in response to exposure to sulphite. This enzyme allows Mj to detoxify sulphite, a potent inhibitor of methyl coenzyme-M reductase (Mcr), by reducing it to sulphide with reduced coenzyme F420 (F420H2) as an electron donor; Mcr is essential for energy production for a methanogen. Fsr allows Mj to utilize sulphite as a sulphur source. Nitrite is another potent inhibitor of Mcr and is toxic to methanogens. It is reduced by most sulphite reductases. In this study, we report that MjFsr reduced nitrite to ammonia with F420H2 with physiologically relevant K m values (nitrite, 8.9 µM; F420H2, 9.7 µM). The enzyme also reduced hydroxylamine with a K m value of 112.4 µM, indicating that it was an intermediate in the reduction of nitrite to ammonia. These results open the possibility that Mj could use nitrite as a nitrogen source if it is provided at a low concentration of the type that occurs in its habitat.
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Affiliation(s)
- Christian Heryakusuma
- Genetics, Bioinformatics, and Computational Biology Ph.D. Program, Virginia Tech, Blacksburg, VA 24061, USA
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
| | - Eric F. Johnson
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
| | - Endang Purwantini
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
| | - Biswarup Mukhopadhyay
- Genetics, Bioinformatics, and Computational Biology Ph.D. Program, Virginia Tech, Blacksburg, VA 24061, USA
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
- Virginia Tech Carilion School of Medicine, Virginia Tech, Blacksburg, VA 24061, USA
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A Reduced F 420-Dependent Nitrite Reductase in an Anaerobic Methanotrophic Archaeon. J Bacteriol 2022; 204:e0007822. [PMID: 35695516 PMCID: PMC9295563 DOI: 10.1128/jb.00078-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Anaerobic methanotrophic archaea (ANME), which oxidize methane in marine sediments through syntrophic associations with sulfate-reducing bacteria, carry homologs of coenzyme F420-dependent sulfite reductase (Fsr) of Methanocaldococcus jannaschii, a hyperthermophilic methanogen from deep-sea hydrothermal vents. M. jannaschii Fsr (MjFsr) and ANME-Fsr belong to two phylogenetically distinct groups, FsrI and FsrII, respectively. MjFsrI reduces sulfite to sulfide with reduced F420 (F420H2), protecting methyl coenzyme M reductase (Mcr), an essential enzyme for methanogens, from sulfite inhibition. However, the function of FsrIIs in ANME, which also rely on Mcr and live in sulfidic environments, is unknown. We have determined the catalytic properties of FsrII from a member of ANME-2c. Since ANME remain to be isolated, we expressed ANME2c-FsrII in a closely related methanogen, Methanosarcina acetivorans. Purified recombinant FsrII contained siroheme, indicating that the methanogen, which lacks a native sulfite reductase, produced this coenzyme. Unexpectedly, FsrII could not reduce sulfite or thiosulfate with F420H2. Instead, it acted as an F420H2-dependent nitrite reductase (FNiR) with physiologically relevant Km values (nitrite, 5 μM; F420H2, 14 μM). From kinetic, thermodynamic, and structural analyses, we hypothesize that in FNiR, F420H2-derived electrons are delivered at the oxyanion reduction site at a redox potential that is suitable for reducing nitrite (E0' [standard potential], +440 mV) but not sulfite (E0', -116 mV). These findings and the known nitrite sensitivity of Mcr suggest that FNiR may protect nondenitrifying ANME from nitrite toxicity. Remarkably, by reorganizing the reductant processing system, Fsr transforms two analogous oxyanions in two distinct archaeal lineages with different physiologies and ecologies. IMPORTANCE Coenzyme F420-dependent sulfite reductase (Fsr) protects methanogenic archaea inhabiting deep-sea hydrothermal vents from the inactivation of methyl coenzyme M reductase (Mcr), one of their essential energy production enzymes. Anaerobic methanotrophic archaea (ANME) that oxidize methane and rely on Mcr, carry Fsr homologs that form a distinct clade. We show that a member of this clade from ANME-2c functions as F420-dependent nitrite reductase (FNiR) and lacks Fsr activity. This specialization arose from a distinct feature of the reductant processing system and not the substrate recognition element. We hypothesize FNiR may protect ANME Mcr from inactivation by nitrite. This is an example of functional specialization within a protein family that is induced by changes in electron transfer modules to fit an ecological need.
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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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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
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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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Affiliation(s)
- Thomas J Lawton
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL 60208, USA.
| | - Amy C Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL 60208, USA.
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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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Duin EC, Wagner T, Shima S, Prakash D, Cronin B, Yáñez-Ruiz DR, Duval S, Rümbeli R, Stemmler RT, Thauer RK, Kindermann M. Mode of action uncovered for the specific reduction of methane emissions from ruminants by the small molecule 3-nitrooxypropanol. Proc Natl Acad Sci U S A 2016; 113:6172-7. [PMID: 27140643 PMCID: PMC4896709 DOI: 10.1073/pnas.1600298113] [Citation(s) in RCA: 151] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Ruminants, such as cows, sheep, and goats, predominantly ferment in their rumen plant material to acetate, propionate, butyrate, CO2, and methane. Whereas the short fatty acids are absorbed and metabolized by the animals, the greenhouse gas methane escapes via eructation and breathing of the animals into the atmosphere. Along with the methane, up to 12% of the gross energy content of the feedstock is lost. Therefore, our recent report has raised interest in 3-nitrooxypropanol (3-NOP), which when added to the feed of ruminants in milligram amounts persistently reduces enteric methane emissions from livestock without apparent negative side effects [Hristov AN, et al. (2015) Proc Natl Acad Sci USA 112(34):10663-10668]. We now show with the aid of in silico, in vitro, and in vivo experiments that 3-NOP specifically targets methyl-coenzyme M reductase (MCR). The nickel enzyme, which is only active when its Ni ion is in the +1 oxidation state, catalyzes the methane-forming step in the rumen fermentation. Molecular docking suggested that 3-NOP preferably binds into the active site of MCR in a pose that places its reducible nitrate group in electron transfer distance to Ni(I). With purified MCR, we found that 3-NOP indeed inactivates MCR at micromolar concentrations by oxidation of its active site Ni(I). Concomitantly, the nitrate ester is reduced to nitrite, which also inactivates MCR at micromolar concentrations by oxidation of Ni(I). Using pure cultures, 3-NOP is demonstrated to inhibit growth of methanogenic archaea at concentrations that do not affect the growth of nonmethanogenic bacteria in the rumen.
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Affiliation(s)
- Evert C Duin
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849
| | - Tristan Wagner
- Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| | - Seigo Shima
- Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| | - Divya Prakash
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849
| | - Bryan Cronin
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849
| | - David R Yáñez-Ruiz
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Cientificas, 18008 Granada, Spain
| | - Stephane Duval
- Research Centre for Animal Nutrition and Health, DSM Nutritional Products France, 68305 Saint Louis, France
| | - Robert Rümbeli
- Research and Development, DSM Nutritional Products, 4002 Basel, Switzerland
| | - René T Stemmler
- Research and Development, DSM Nutritional Products, 4002 Basel, Switzerland
| | - Rudolf Kurt Thauer
- Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany;
| | - Maik Kindermann
- Research and Development, DSM Nutritional Products, 4002 Basel, Switzerland
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9
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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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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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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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12
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Nishigaki JI, Matsumoto T, Tatsumi K. Coordination of Methyl Coenzyme M and Coenzyme M at Divalent and Trivalent Nickel Cyclams: Model Studies of Methyl Coenzyme M Reductase Active Site. Inorg Chem 2012; 51:3690-7. [DOI: 10.1021/ic202686x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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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13
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Electrochemical titrations and reaction time courses monitored in situ by magnetic circular dichroism spectroscopy. Anal Biochem 2011; 419:110-6. [DOI: 10.1016/j.ab.2011.07.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2011] [Revised: 07/24/2011] [Accepted: 07/25/2011] [Indexed: 11/19/2022]
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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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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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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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17
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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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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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19
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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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20
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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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21
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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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22
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Kern DI, Goenrich M, Jaun B, Thauer RK, Harmer J, Hinderberger D. Two sub-states of the red2 state of methyl-coenzyme M reductase revealed by high-field EPR spectroscopy. J Biol Inorg Chem 2007; 12:1097-105. [PMID: 17690920 DOI: 10.1007/s00775-007-0281-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2007] [Accepted: 07/18/2007] [Indexed: 10/23/2022]
Abstract
Methyl-coenzyme M reductase (MCR) catalyzes the formation of methane from methyl-coenzyme M and coenzyme B in methanogenic archaea. The enzyme has two structurally interlinked active sites embedded in an alpha(2)beta(2)gamma(2) subunit structure. Each active site has the nickel porphyrinoid F(430) as a prosthetic group. In the active state, F(430) contains the transition metal in the Ni(I) oxidation state. The active enzyme exhibits an axial Ni(I)-based continuous wave (CW) electron paramagnetic resonance (EPR) signal, called red1a in the absence of substrates or red1c in the presence of coenzyme M. Addition of coenzyme B to the MCR-red1 state can partially and reversibly convert it into the MCR-red2 form, which shows a rhombic Ni(I)-based EPR signal (at X-band microwave frequencies of approximately 9.4 GHz). In this report we present evidence from high-field/high-frequency CW EPR spectroscopy (W-band, microwave frequency of approximately 94 GHz) that the red2 state consists of two substates that could not be resolved by EPR spectroscopy at X-band frequencies. At W-band it becomes apparent that upon addition of coenzyme B to MCR in the red1c state, two red2 EPR signals are induced, not one as was previously believed. The first signal is the well-characterized (ortho)rhombic EPR signal, thus far called red2, while the second previously unidentified signal is axial. We have named the two substates MCR-red2r and MCR-red2a after their rhombic and axial signals, respectively.
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Affiliation(s)
- Denise I Kern
- Laboratorium für Physikalische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10, Zurich, Switzerland
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23
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Staples CR, Lahiri S, Raymond J, Von Herbulis L, Mukhophadhyay B, Blankenship RE. Expression and association of group IV nitrogenase NifD and NifH homologs in the non-nitrogen-fixing archaeon Methanocaldococcus jannaschii. J Bacteriol 2007; 189:7392-8. [PMID: 17660283 PMCID: PMC2168459 DOI: 10.1128/jb.00876-07] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Using genomic analysis, researchers previously identified genes coding for proteins homologous to the structural proteins of nitrogenase (J. Raymond, J. L. Siefert, C. R. Staples, and R. E. Blankenship, Mol. Biol. Evol. 21:541-554, 2004). The expression and association of NifD and NifH nitrogenase homologs (named NflD and NflH for "Nif-like" D and H, respectively) have been detected in a non-nitrogen-fixing hyperthermophilic methanogen, Methanocaldococcus jannaschii. These homologs are expressed constitutively and do not appear to be directly involved with nitrogen metabolism or detoxification of compounds such as cyanide or azide. The NflH and NflD proteins were found to interact with each other, as determined by bacterial two-hybrid studies. Upon immunoisolation, NflD and NflH copurified, along with three other proteins whose functions are as yet uncharacterized. The apparent presence of genes coding for NflH and NflD in all known methanogens, their constitutive expression, and their high sequence similarity to the NifH and NifD proteins or the BchL and BchN/BchB proteins suggest that NflH and NflD participate in an indispensable and fundamental function(s) in methanogens.
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24
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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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25
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Van Doorslaer S, Vinck E. The strength of EPR and ENDOR techniques in revealing structure-function relationships in metalloproteins. Phys Chem Chem Phys 2007; 9:4620-38. [PMID: 17700864 DOI: 10.1039/b701568b] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Recent technological and methodological advances have strongly increased the potential of electron paramagnetic resonance (EPR) and electron nuclear double resonance (ENDOR) techniques to characterize the structure and dynamics of metalloproteins. These developments include the introduction of powerful pulsed EPR/ENDOR methodologies and the development of spectrometers operating at very high microwave frequencies and high magnetic fields. This overview focuses on how valuable information about metalloprotein structure-function relations can be obtained using a combination of EPR and ENDOR techniques. After an overview of the historical development and a limited theoretical description of some of the key EPR and ENDOR techniques, their potential will be highlighted using selected examples of applications to iron-, nickel-, cobalt-, and copper-containing proteins. We will end with an outlook of future developments.
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Affiliation(s)
- Sabine Van Doorslaer
- SIBAC Laboratory, University of Antwerp, Universiteitsplein 1, B-2160, Wilrijk-Antwerp, Belgium.
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26
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Dey M, Kunz R, Van Heuvelen KM, Craft JL, Horng YC, Tang Q, Bocian DF, George SJ, Brunold TC, Ragsdale SW. Spectroscopic and computational studies of reduction of the metal versus the tetrapyrrole ring of coenzyme F430 from methyl-coenzyme M reductase. Biochemistry 2006; 45:11915-33. [PMID: 17002292 PMCID: PMC2526056 DOI: 10.1021/bi0613269] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Methyl-coenzyme M reductase (MCR) catalyzes the final step in methane biosynthesis by methanogenic archaea and contains a redox-active nickel tetrahydrocorphin, coenzyme F430, at its active site. Spectroscopic and computational methods have been used to study a novel form of the coenzyme, called F330, which is obtained by reducing F430 with sodium borohydride (NaBH4). F330 exhibits a prominent absorption peak at 330 nm, which is blue shifted by 100 nm relative to F430. Mass spectrometric studies demonstrate that the tetrapyrrole ring in F330 has undergone reduction, on the basis of the incorporation of protium (or deuterium), upon treatment of F430 with NaBH4 (or NaBD4). One- and two-dimensional NMR studies show that the site of reduction is the exocyclic ketone group of the tetrahydrocorphin. Resonance Raman studies indicate that elimination of this pi-bond increases the overall pi-bond order in the conjugative framework. X-ray absorption, magnetic circular dichroism, and computational results show that F330 contains low-spin Ni(II). Thus, conversion of F430 to F330 reduces the hydrocorphin ring but not the metal. Conversely, reduction of F430 with Ti(III) citrate to generate F380 (corresponding to the active MCR(red1) state) reduces the Ni(II) to Ni(I) but does not reduce the tetrapyrrole ring system, which is consistent with other studies [Piskorski, R., and Jaun, B. (2003) J. Am. Chem. Soc. 125, 13120-13125; Craft, J. L., et al. (2004) J. Biol. Inorg. Chem. 9, 77-89]. The distinct origins of the absorption band shifts associated with the formation of F330 and F380 are discussed within the framework of our computational results. These studies on the nature of the product(s) of reduction of F430 are of interest in the context of the mechanism of methane formation by MCR and in relation to the chemistry of hydroporphinoid systems in general. The spectroscopic and time-dependent DFT calculations add important insight into the electronic structure of the nickel hydrocorphinate in its Ni(II) and Ni(I) valence states.
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Affiliation(s)
- Mishtu Dey
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588
| | - Ryan Kunz
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588
| | | | - Jennifer L. Craft
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Yih-Chern Horng
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588
| | - Qun Tang
- Department of Chemistry, University of California, Riverside 92521
| | - David F. Bocian
- Department of Chemistry, University of California, Riverside 92521
| | - Simon J. George
- Physical Biosciences Division, Lawrence Berkeley National Lab, Berkeley, California 94720
| | - Thomas C. Brunold
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
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27
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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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28
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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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29
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Shima S, Thauer RK. Methyl-coenzyme M reductase and the anaerobic oxidation of methane in methanotrophic Archaea. Curr Opin Microbiol 2005; 8:643-8. [PMID: 16242993 DOI: 10.1016/j.mib.2005.10.002] [Citation(s) in RCA: 133] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2005] [Accepted: 10/06/2005] [Indexed: 11/18/2022]
Abstract
Recent biochemical and metagenomic data indicate that not yet cultured Archaea that are closely related to methanogenic Archaea of the order of Methanosarcinales are involved in the anaerobic oxidation of methane in marine sediments. The DNA from the methanotrophic Archaea has been shown to harbor gene homologues for methyl-coenzyme M reductase, which in methanogenic Archaea catalyses the methane-forming reaction. In microbial mats catalyzing anaerobic oxidation of methane, this nickel enzyme has been shown to be present in concentrations of up to 10% of the total extracted proteins.
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Affiliation(s)
- Seigo Shima
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse, D-35043 Marburg, Germany
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30
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Goenrich M, Duin EC, Mahlert F, Thauer RK. Temperature dependence of methyl-coenzyme M reductase activity and of the formation of the methyl-coenzyme M reductase red2 state induced by coenzyme B. J Biol Inorg Chem 2005; 10:333-42. [PMID: 15846525 DOI: 10.1007/s00775-005-0636-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2004] [Accepted: 02/18/2005] [Indexed: 10/25/2022]
Abstract
Methyl-coenzyme M reductase (MCR) catalyses the formation of methane from methyl-coenzyme M (CH(3)-S-CoM) and coenzyme B (HS-CoB) in methanogenic archaea. The enzyme has an alpha(2)beta(2)gamma(2) subunit structure forming two structurally interlinked active sites each with a molecule F(430) as a prosthetic group. The nickel porphinoid must be in the Ni(I) oxidation state for the enzyme to be active. The active enzyme exhibits an axial Ni(I)-based electron paramagnetic resonance (EPR) signal and a UV-vis spectrum with an absorption maximum at 385 nm. This state is called the MCR-red1 state. In the presence of coenzyme M (HS-CoM) and coenzyme B the MCR-red1 state is in part converted reversibly into the MCR-red2 state, which shows a rhombic Ni(I)-based EPR signal and a UV-vis spectrum with an absorption maximum at 420 nm. We report here for MCR from Methanothermobacter marburgensis that the MCR-red2 state is also induced by several coenzyme B analogues and that the degree of induction by coenzyme B is temperature-dependent. When the temperature was lowered below 20 degrees C the percentage of MCR in the red2 state decreased and that in the red1 state increased. These changes with temperature were fully reversible. It was found that at most 50% of the enzyme was converted to the MCR-red2 state under all experimental conditions. These findings indicate that in the presence of both coenzyme M and coenzyme B only one of the two active sites of MCR can be in the red2 state (half-of-the-sites reactivity). On the basis of this interpretation a two-stroke engine mechanism for MCR is proposed.
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Affiliation(s)
- Meike Goenrich
- Max-Planck-Institut für terrestrische Mikrobiologie and Laboratorium für Mikrobiologie, Fachbereich Biologie, Philipps-Universität, Karl-von-Frisch-Strasse, 35043 Marburg, Germany
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31
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Zilbermann I, Maimon E, Cohen H, Meyerstein D. Redox Chemistry of Nickel Complexes in Aqueous Solutions. Chem Rev 2005; 105:2609-25. [PMID: 15941223 DOI: 10.1021/cr030717f] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Israel Zilbermann
- Chemistry Department, Nuclear Research Centre Negev, Beer-Sheva, Israel.
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32
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Abstract
Methyl-coenzyme M reductase (MCR) catalyzes the reaction of methyl-coenzyme M (CH3-SCoM) and coenzyme B (HS-CoB) to methane and the corresponding heterodisulfide CoM-S-S-CoB. This unique reaction proceeds under strictly anaerobic conditions in the presence of coenzyme F430, a Ni-porphinoid. MCR is a large (alphabetagamma)2 heterohexameric protein complex containing two 50 A long active sites channels. Coenzyme F430 is embedded at the channel bottom and the substrates CH3-SCoM and HS-CoB bind in front of F430 into a solvent free and hydrophobic channel segment. Two principally different catalytic mechanisms are currently discussed. Mechanism I is based on a nucleophilic attack of Ni(I) onto the methyl group of CH3-SCoM yielding methyl-Ni(III) and mechanism II on an attack of Ni(I) onto the thioether sulfur of CH3-SCoM generating a Ni(II)-SCoM intermediate. Both mechanisms are discussed in the light of a large number of data collected about MCR over the last twenty years.
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Affiliation(s)
- Ulrich Ermler
- Max-Planck-Institut für Biophysik, Max-von-Laue-Str. 3, D-60438, Frankfurt am Main, Germany.
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