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Guden RM, Haegeman A, Ruttink T, Moens T, Derycke S. Nematodes alter the taxonomic and functional profiles of benthic bacterial communities: A metatranscriptomic approach. Mol Ecol 2024; 33:e17331. [PMID: 38533629 DOI: 10.1111/mec.17331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 02/25/2024] [Accepted: 03/18/2024] [Indexed: 03/28/2024]
Abstract
Marine sediments cover 70% of the Earth's surface, and harbour diverse bacterial communities critical for marine biogeochemical processes, which affect climate change, biodiversity and ecosystem functioning. Nematodes, the most abundant and species-rich metazoan organisms in marine sediments, in turn, affect benthic bacterial communities and bacterial-mediated ecological processes, but the underlying mechanisms by which they affect biogeochemical cycles remain poorly understood. Here, we demonstrate using a metatranscriptomic approach that nematodes alter the taxonomic and functional profiles of benthic bacterial communities. We found particularly strong stimulation of nitrogen-fixing and methane-oxidizing bacteria in the presence of nematodes, as well as increased functional activity associated with methane metabolism and degradation of various carbon compounds. This study provides empirical evidence that the presence of nematodes results in taxonomic and functional shifts in active bacterial communities, indicating that nematodes may play an important role in benthic ecosystem processes.
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Affiliation(s)
- Rodgee Mae Guden
- Marine Biology Unit, Department of Biology, Ghent University, Ghent, Belgium
| | - Annelies Haegeman
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | - Tom Ruttink
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | - Tom Moens
- Marine Biology Unit, Department of Biology, Ghent University, Ghent, Belgium
| | - Sofie Derycke
- Marine Biology Unit, Department of Biology, Ghent University, Ghent, Belgium
- Aquatic Environment and Quality, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Oostende, Belgium
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2
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Tucci FJ, Rosenzweig AC. Direct Methane Oxidation by Copper- and Iron-Dependent Methane Monooxygenases. Chem Rev 2024; 124:1288-1320. [PMID: 38305159 PMCID: PMC10923174 DOI: 10.1021/acs.chemrev.3c00727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
Methane is a potent greenhouse gas that contributes significantly to climate change and is primarily regulated in Nature by methanotrophic bacteria, which consume methane gas as their source of energy and carbon, first by oxidizing it to methanol. The direct oxidation of methane to methanol is a chemically difficult transformation, accomplished in methanotrophs by complex methane monooxygenase (MMO) enzyme systems. These enzymes use iron or copper metallocofactors and have been the subject of detailed investigation. While the structure, function, and active site architecture of the copper-dependent particulate methane monooxygenase (pMMO) have been investigated extensively, its putative quaternary interactions, regulation, requisite cofactors, and mechanism remain enigmatic. The iron-dependent soluble methane monooxygenase (sMMO) has been characterized biochemically, structurally, spectroscopically, and, for the most part, mechanistically. Here, we review the history of MMO research, focusing on recent developments and providing an outlook for future directions of the field. Engineered biological catalysis systems and bioinspired synthetic catalysts may continue to emerge along with a deeper understanding of the molecular mechanisms of biological methane oxidation. Harnessing the power of these enzymes will necessitate combined efforts in biochemistry, structural biology, inorganic chemistry, microbiology, computational biology, and engineering.
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Affiliation(s)
- Frank J Tucci
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Amy C Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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3
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Chan SI, Wang VC, Chen PP, Yu SS. Methane oxidation by the copper methane monooxygenase: Before and after the cryogenic electron microscopy structure of particulate methane monooxygenase from
Methylococcus capsulatus
(Bath). J CHIN CHEM SOC-TAIP 2022. [DOI: 10.1002/jccs.202200166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Sunney I Chan
- Institute of Chemistry, Academia Sinica Taipei City Taiwan
- Department of Chemistry National Taiwan University Taipei City Taiwan
| | - Vincent C.‐C Wang
- Department of Chemistry National Sun Yat‐Sen University Kaohsiung City Taiwan
| | - Peter P.‐Y. Chen
- Department of Chemistry National Chung Hsing University Taichung City Taiwan
| | - Steve S.‐F. Yu
- Institute of Chemistry, Academia Sinica Taipei City Taiwan
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4
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Abstract
Methanobactins (MBs) are small (<1,300-Da) posttranslationally modified copper-binding peptides and represent the extracellular component of a copper acquisition system in some methanotrophs. Interestingly, MBs can bind a range of metal ions, with some being reduced after binding, e.g., Cu2+ reduced to Cu+. Other metal ions, however, are bound but not reduced, e.g., K+. The source of electrons for selective metal ion reduction has been speculated to be water but never empirically shown. Here, using H218O, we show that when MBs from Methylocystis sp. strain SB2 (MB-SB2) and Methylosinus trichosporium OB3b (MB-OB3) were incubated in the presence of either Au3+, Cu2, or Ag+, 18,18O2 and free protons were released. No 18,18O2 production was observed in the presence of either MB-SB2 or MB-OB3b alone, gold alone, copper alone, or silver alone or when K+ or Mo2+ was incubated with MB-SB2. In contrast to MB-OB3b, MB-SB2 binds Fe3+ with an N2S2 coordination and will also reduce Fe3+ to Fe2+. Iron reduction was also found to be coupled to the oxidation of 2H2O and the generation of O2. MB-SB2 will also couple Hg2+, Ni2+, and Co2+ reduction to the oxidation of 2H2O and the generation of O2, but MB-OB3b will not, ostensibly as MB-OB3b binds but does not reduce these metal ions. To determine if the O2 generated during metal ion reduction by MB could be coupled to methane oxidation, 13CH4 oxidation by Methylosinus trichosporium OB3b was monitored under anoxic conditions. The results demonstrate that O2 generation from metal ion reduction by MB-OB3b can support methane oxidation. IMPORTANCE The discovery that MB will couple the oxidation of H2O to metal ion reduction and the release of O2 suggests that methanotrophs expressing MB may be able to maintain their activity under hypoxic/anoxic conditions through the “self-generation” of dioxygen required for the initial oxidation of methane to methanol. Such an ability may be an important factor in enabling methanotrophs to not only colonize the oxic-anoxic interface where methane concentrations are highest but also tolerate significant temporal fluctuations of this interface. Given that genomic surveys often show evidence of aerobic methanotrophs within anoxic zones, the ability to express MB (and thereby generate dioxygen) may be an important parameter in facilitating their ability to remove methane, a potent greenhouse gas, before it enters the atmosphere.
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Khider MLK, Brautaset T, Irla M. Methane monooxygenases: central enzymes in methanotrophy with promising biotechnological applications. World J Microbiol Biotechnol 2021; 37:72. [PMID: 33765207 PMCID: PMC7994243 DOI: 10.1007/s11274-021-03038-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 03/09/2021] [Indexed: 12/02/2022]
Abstract
Worldwide, the use of methane is limited to generating power, electricity, heating, and for production of chemicals. We believe this valuable gas can be employed more widely. Here we review the possibility of using methane as a feedstock for biotechnological processes based on the application of synthetic methanotrophs. Methane monooxygenase (MMO) enables aerobic methanotrophs to utilize methane as a sole carbon and energy source, in contrast to industrial microorganisms that grow on carbon sources, such as sugar cane, which directly compete with the food market. However, naturally occurring methanotrophs have proven to be difficult to manipulate genetically and their current industrial use is limited to generating animal feed biomass. Shifting the focus from genetic engineering of methanotrophs, towards introducing metabolic pathways for methane utilization in familiar industrial microorganisms, may lead to construction of efficient and economically feasible microbial cell factories. The applications of a technology for MMO production are not limited to methane-based industrial synthesis of fuels and value-added products, but are also of interest in bioremediation where mitigating anthropogenic pollution is an increasingly relevant issue. Published research on successful functional expression of MMO does not exist, but several attempts provide promising future perspectives and a few recent patents indicate that there is an ongoing research in this field. Combining the knowledge on genetics and metabolism of methanotrophy with tools for functional heterologous expression of MMO-encoding genes in non-methanotrophic bacterial species, is a key step for construction of synthetic methanotrophs that holds a great biotechnological potential.
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Affiliation(s)
- May L K Khider
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
| | - Trygve Brautaset
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
| | - Marta Irla
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway.
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6
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Semrau JD, DiSpirito AA. Methanobactin: A Novel Copper-Binding Compound Produced by Methanotrophs. ACTA ACUST UNITED AC 2019. [DOI: 10.1007/978-3-030-23261-0_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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7
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The PmoB subunit of particulate methane monooxygenase (pMMO) in Methylococcus capsulatus (Bath): The CuI sponge and its function. J Inorg Biochem 2019; 196:110691. [DOI: 10.1016/j.jinorgbio.2019.04.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 02/28/2019] [Accepted: 04/08/2019] [Indexed: 11/19/2022]
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8
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Ross MO, MacMillan F, Wang J, Nisthal A, Lawton TJ, Olafson BD, Mayo SL, Rosenzweig AC, Hoffman BM. Particulate methane monooxygenase contains only mononuclear copper centers. Science 2019; 364:566-570. [PMID: 31073062 PMCID: PMC6664434 DOI: 10.1126/science.aav2572] [Citation(s) in RCA: 175] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 04/15/2019] [Indexed: 12/23/2022]
Abstract
Bacteria that oxidize methane to methanol are central to mitigating emissions of methane, a potent greenhouse gas. The nature of the copper active site in the primary metabolic enzyme of these bacteria, particulate methane monooxygenase (pMMO), has been controversial owing to seemingly contradictory biochemical, spectroscopic, and crystallographic results. We present biochemical and electron paramagnetic resonance spectroscopic characterization most consistent with two monocopper sites within pMMO: one in the soluble PmoB subunit at the previously assigned active site (CuB) and one ~2 nanometers away in the membrane-bound PmoC subunit (CuC). On the basis of these results, we propose that a monocopper site is able to catalyze methane oxidation in pMMO.
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Affiliation(s)
- Matthew O Ross
- Department of Molecular Biosciences, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Fraser MacMillan
- Henry Wellcome Unit for Biological Electron Paramagnetic Resonance Spectroscopy, School of Chemistry, University of East Anglia, Norwich NR4 7TJ, UK
| | - Jingzhou Wang
- Division of Biology, California Institute of Technology, MC 114-96, 1200 East California Boulevard, Pasadena, CA 91125, USA
- Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 114-96, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Alex Nisthal
- Division of Biology, California Institute of Technology, MC 114-96, 1200 East California Boulevard, Pasadena, CA 91125, USA
- Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 114-96, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Thomas J Lawton
- Department of Molecular Biosciences, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Barry D Olafson
- Protabit, 1010 E. Union Street, Suite 110, Pasadena, CA 91106, USA
| | - Stephen L Mayo
- Division of Biology, California Institute of Technology, MC 114-96, 1200 East California Boulevard, Pasadena, CA 91125, USA
- Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 114-96, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Amy C Rosenzweig
- Department of Molecular Biosciences, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA.
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Brian M Hoffman
- Department of Molecular Biosciences, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA.
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
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9
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Kim HJ, Huh J, Kwon YW, Park D, Yu Y, Jang YE, Lee BR, Jo E, Lee EJ, Heo Y, Lee W, Lee J. Biological conversion of methane to methanol through genetic reassembly of native catalytic domains. Nat Catal 2019. [DOI: 10.1038/s41929-019-0255-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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10
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11
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Miyaji A, Nitta M, Baba T. Influence of copper ions removal from membrane-bound form of particulate methane monooxygenase from Methylosinus trichosporium OB3b on its activity for methane hydroxylation. J Biotechnol 2019; 306S:100001. [PMID: 34112370 DOI: 10.1016/j.btecx.2018.100001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 12/11/2018] [Accepted: 12/14/2018] [Indexed: 11/26/2022]
Abstract
The influence of metal removal with a chelating reagent, ethylenediaminetetraacetic acid (EDTA), and metal reconstitution on the activity of particulate methane monooxygenase (pMMO) from Methylosinus trichosporium OB3b toward methane oxidation to methanol was investigated. For this study, a membrane fraction containing pMMO and bacterial cell membrane components was prepared. pMMO activity was assessed with two different reductants, nicotinamide adenine dinucleotide (NADH) and 2,3,5,6-tetramethyl hydroquinone (duroquinol). The partial removal of metal ions with EDTA resulted in the selective inhibition of NADH-driven activity. The NADH-driven activity was restored by exogenous copper ions, but not by other divalent metal cations. Furthermore, both NADH- and duroquinol-driven activities were lost completely by increasing the amount of metal removed. Duroquinol-driven activity of the metal-deficient membrane fraction increased with increasing the amount of copper ions added, while NADH-driven activity increased when more than 5 mol of copper ions per mol of pMMO monomer was added. These results suggest that NADH-driven pMMO activity requires not only the catalytic copper center of pMMO but also copper ions outside the catalytic site.
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Affiliation(s)
- Akimitsu Miyaji
- Department of Environmental Chemistry and Engineering, Tokyo Institute of Technology, G1-14, Nagatsuta-cho, Midori-ku, Yokohama 226-8502, Japan.
| | - Muneyuki Nitta
- Department of Environmental Chemistry and Engineering, Tokyo Institute of Technology, G1-14, Nagatsuta-cho, Midori-ku, Yokohama 226-8502, Japan
| | - Toshihide Baba
- Department of Environmental Chemistry and Engineering, Tokyo Institute of Technology, G1-14, Nagatsuta-cho, Midori-ku, Yokohama 226-8502, Japan
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12
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Dennison C. The Coordination Chemistry of Copper Uptake and Storage for Methane Oxidation. Chemistry 2018; 25:74-86. [PMID: 30281847 DOI: 10.1002/chem.201803444] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Indexed: 11/09/2022]
Abstract
Methanotrophs are remarkable bacteria that utilise large quantities of copper (Cu) to oxidize the potent greenhouse gas methane. To assist in providing the Cu they require for this process some methanotrophs can secrete the Cu-sequestering modified peptide methanobactin. These small molecules bind CuI with very high affinity and crystal structures have given insight into why this is the case, and also how the metal ion may be released within the cell. A much greater proportion of methanotrophs, genomes of which have been sequenced, possess a member of a newly discovered bacterial family of copper storage proteins (the Csps). These are tetramers of four-helix bundles whose cores are lined with Cys residues enabling the binding of large numbers of CuI ions. In methanotrophs, a Csp exported from the cytosol stores CuI for the active site of the ubiquitous enzyme that catalyses the oxidation of methane. The presence of cytosolic Csps, not only in methanotrophs but in a wide range of bacteria, challenges the dogma that these organisms have no requirement for Cu in this location. The properties of the Csps, with an emphasis on CuI binding and the structures of the sites formed, are the primary focus of this review.
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Affiliation(s)
- Christopher Dennison
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
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13
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Deng YW, Ro SY, Rosenzweig AC. Structure and function of the lanthanide-dependent methanol dehydrogenase XoxF from the methanotroph Methylomicrobium buryatense 5GB1C. J Biol Inorg Chem 2018; 23:1037-1047. [PMID: 30132076 PMCID: PMC6370294 DOI: 10.1007/s00775-018-1604-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 08/16/2018] [Indexed: 01/07/2023]
Abstract
In methylotrophic bacteria, which use one-carbon (C1) compounds as a carbon source, methanol is oxidized by pyrroloquinoline quinone (PQQ)-dependent methanol dehydrogenase (MDH) enzymes. Methylotrophic genomes generally encode two distinct MDHs, MxaF and XoxF. MxaF is a well-studied, calcium-dependent heterotetrameric enzyme whereas XoxF is a lanthanide-dependent homodimer. Recent studies suggest that XoxFs are likely the functional MDHs in many environments. In methanotrophs, methylotrophs that utilize methane, interactions between particulate methane monooxygenase (pMMO) and MxaF have been detected. To investigate the possibility of interactions between pMMO and XoxF, XoxF was isolated from the methanotroph Methylomicrobium buryatense 5GB1C (5G-XoxF). Purified 5G-XoxF exhibits a specific activity of 0.16 μmol DCPIP reduced min-1 mg-1. The 1.85 Å resolution crystal structure reveals a La(III) ion in the active site, in contrast to the calcium ion in MxaF. The overall fold is similar to other MDH structures, but 5G-XoxF is a monomer in solution. An interaction between 5G-XoxF and its cognate pMMO was detected by biolayer interferometry, with a KD value of 50 ± 17 μM. These results suggest an alternative model of MDH-pMMO association, in which a XoxF monomer may bind to pMMO, and underscore the potential importance of lanthanide-dependent MDHs in biological methane oxidation.
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Affiliation(s)
- Yue Wen Deng
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA
- Department of Chemistry, Northwestern University, Evanston, IL, 60208, USA
| | - Soo Y Ro
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA
- Department of Chemistry, Northwestern University, Evanston, IL, 60208, USA
| | - Amy C Rosenzweig
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA.
- Department of Chemistry, Northwestern University, Evanston, IL, 60208, USA.
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14
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Pankhurst JR, Curcio M, Sproules S, Lloyd-Jones GC, Love JB. Earth-Abundant Mixed-Metal Catalysts for Hydrocarbon Oxygenation. Inorg Chem 2018; 57:5915-5928. [DOI: 10.1021/acs.inorgchem.8b00420] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- James R. Pankhurst
- EaStCHEM School of Chemistry, The University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, U.K
| | - Massimiliano Curcio
- EaStCHEM School of Chemistry, The University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, U.K
| | - Stephen Sproules
- WestCHEM School of Chemistry, University of Glasgow, Glasgow G12 8QQ, U.K
| | - Guy C. Lloyd-Jones
- EaStCHEM School of Chemistry, The University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, U.K
| | - Jason B. Love
- EaStCHEM School of Chemistry, The University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, U.K
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15
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Sonogashira-type cross-coupling reactions catalyzed by copper complexes of pincer N-heterocyclic carbenes. J Organomet Chem 2018. [DOI: 10.1016/j.jorganchem.2018.02.028] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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16
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Abstract
Aerobic methanotrophs have long been known to play a critical role in the global carbon cycle, being capable of converting methane to biomass and carbon dioxide. Interestingly, these microbes exhibit great sensitivity to copper and rare-earth elements, with the expression of key genes involved in the central pathway of methane oxidation controlled by the availability of these metals. That is, these microbes have a "copper switch" that controls the expression of alternative methane monooxygenases and a "rare-earth element switch" that controls the expression of alternative methanol dehydrogenases. Further, it has been recently shown that some methanotrophs can detoxify inorganic mercury and demethylate methylmercury; this finding is remarkable, as the canonical organomercurial lyase does not exist in these methanotrophs, indicating that a novel mechanism is involved in methylmercury demethylation. Here, we review recent findings on methanotrophic interactions with metals, with a particular focus on these metal switches and the mechanisms used by methanotrophs to bind and sequester metals.
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17
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Han L, Vuksanovic N, Oehm SA, Fenske TG, Schwabacher AW, Silvaggi NR. Streptomyces wadayamensis MppP is a PLP-Dependent Oxidase, Not an Oxygenase. Biochemistry 2018; 57:3252-3264. [DOI: 10.1021/acs.biochem.8b00130] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lanlan Han
- Department of Chemistry and Biochemistry, University of Wisconsin−Milwaukee, Milwaukee, Wisconsin 53201, United States
| | - Nemanja Vuksanovic
- Department of Chemistry and Biochemistry, University of Wisconsin−Milwaukee, Milwaukee, Wisconsin 53201, United States
| | - Sarah A. Oehm
- Department of Chemistry and Biochemistry, University of Wisconsin−Milwaukee, Milwaukee, Wisconsin 53201, United States
| | - Tyler G. Fenske
- Department of Chemistry and Biochemistry, University of Wisconsin−Milwaukee, Milwaukee, Wisconsin 53201, United States
| | - Alan W. Schwabacher
- Department of Chemistry and Biochemistry, University of Wisconsin−Milwaukee, Milwaukee, Wisconsin 53201, United States
| | - Nicholas R. Silvaggi
- Department of Chemistry and Biochemistry, University of Wisconsin−Milwaukee, Milwaukee, Wisconsin 53201, United States
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18
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Ross MO, Rosenzweig AC. A tale of two methane monooxygenases. J Biol Inorg Chem 2017; 22:307-319. [PMID: 27878395 PMCID: PMC5352483 DOI: 10.1007/s00775-016-1419-y] [Citation(s) in RCA: 153] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 11/15/2016] [Indexed: 11/24/2022]
Abstract
Methane monooxygenase (MMO) enzymes activate O2 for oxidation of methane. Two distinct MMOs exist in nature, a soluble form that uses a diiron active site (sMMO) and a membrane-bound form with a catalytic copper center (pMMO). Understanding the reaction mechanisms of these enzymes is of fundamental importance to biologists and chemists, and is also relevant to the development of new biocatalysts. The sMMO catalytic cycle has been elucidated in detail, including O2 activation intermediates and the nature of the methane-oxidizing species. By contrast, many aspects of pMMO catalysis remain unclear, most notably the nuclearity and molecular details of the copper active site. Here, we review the current state of knowledge for both enzymes, and consider pMMO O2 activation intermediates suggested by computational and synthetic studies in the context of existing biochemical data. Further work is needed on all fronts, with the ultimate goal of understanding how these two remarkable enzymes catalyze a reaction not readily achieved by any other metalloenzyme or biomimetic compound.
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Affiliation(s)
- Matthew O Ross
- 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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19
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Wang VCC, Maji S, Chen PPY, Lee HK, Yu SSF, Chan SI. Alkane Oxidation: Methane Monooxygenases, Related Enzymes, and Their Biomimetics. Chem Rev 2017; 117:8574-8621. [PMID: 28206744 DOI: 10.1021/acs.chemrev.6b00624] [Citation(s) in RCA: 249] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Methane monooxygenases (MMOs) mediate the facile conversion of methane into methanol in methanotrophic bacteria with high efficiency under ambient conditions. Because the selective oxidation of methane is extremely challenging, there is considerable interest in understanding how these enzymes carry out this difficult chemistry. The impetus of these efforts is to learn from the microbes to develop a biomimetic catalyst to accomplish the same chemical transformation. Here, we review the progress made over the past two to three decades toward delineating the structures and functions of the catalytic sites in two MMOs: soluble methane monooxygenase (sMMO) and particulate methane monooxygenase (pMMO). sMMO is a water-soluble three-component protein complex consisting of a hydroxylase with a nonheme diiron catalytic site; pMMO is a membrane-bound metalloenzyme with a unique tricopper cluster as the site of hydroxylation. The metal cluster in each of these MMOs harnesses O2 to functionalize the C-H bond using different chemistry. We highlight some of the common basic principles that they share. Finally, the development of functional models of the catalytic sites of MMOs is described. These efforts have culminated in the first successful biomimetic catalyst capable of efficient methane oxidation without overoxidation at room temperature.
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Affiliation(s)
- Vincent C-C Wang
- Institute of Chemistry, Academia Sinica , 128, Section 2, Academia Road, Nankang, Taipei 11529, Taiwan
| | - Suman Maji
- School of Chemical Engineering and Physical Sciences, Lovely Professional University , Jalandhar-Delhi G. T. Road (NH-1), Phagwara, Punjab India 144411
| | - Peter P-Y Chen
- Department of Chemistry, National Chung Hsing University , 250 Kuo Kuang Road, Taichung 402, Taiwan
| | - Hung Kay Lee
- Department of Chemistry, The Chinese University of Hong Kong , Shatin, New Territories, Hong Kong
| | - Steve S-F Yu
- Institute of Chemistry, Academia Sinica , 128, Section 2, Academia Road, Nankang, Taipei 11529, Taiwan
| | - Sunney I Chan
- Institute of Chemistry, Academia Sinica , 128, Section 2, Academia Road, Nankang, Taipei 11529, Taiwan.,Department of Chemistry, National Taiwan University , No. 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan.,Noyes Laboratory, 127-72, California Institute of Technology , 1200 East California Boulevard, Pasadena, California 91125, United States
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DiSpirito AA, Semrau JD, Murrell JC, Gallagher WH, Dennison C, Vuilleumier S. Methanobactin and the Link between Copper and Bacterial Methane Oxidation. Microbiol Mol Biol Rev 2016; 80:387-409. [PMID: 26984926 PMCID: PMC4867365 DOI: 10.1128/mmbr.00058-15] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Methanobactins (mbs) are low-molecular-mass (<1,200 Da) copper-binding peptides, or chalkophores, produced by many methane-oxidizing bacteria (methanotrophs). These molecules exhibit similarities to certain iron-binding siderophores but are expressed and secreted in response to copper limitation. Structurally, mbs are characterized by a pair of heterocyclic rings with associated thioamide groups that form the copper coordination site. One of the rings is always an oxazolone and the second ring an oxazolone, an imidazolone, or a pyrazinedione moiety. The mb molecule originates from a peptide precursor that undergoes a series of posttranslational modifications, including (i) ring formation, (ii) cleavage of a leader peptide sequence, and (iii) in some cases, addition of a sulfate group. Functionally, mbs represent the extracellular component of a copper acquisition system. Consistent with this role in copper acquisition, mbs have a high affinity for copper ions. Following binding, mbs rapidly reduce Cu(2+) to Cu(1+). In addition to binding copper, mbs will bind most transition metals and near-transition metals and protect the host methanotroph as well as other bacteria from toxic metals. Several other physiological functions have been assigned to mbs, based primarily on their redox and metal-binding properties. In this review, we examine the current state of knowledge of this novel type of metal-binding peptide. We also explore its potential applications, how mbs may alter the bioavailability of multiple metals, and the many roles mbs may play in the physiology of methanotrophs.
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Affiliation(s)
- Alan A DiSpirito
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA
| | - Jeremy D Semrau
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - J Colin Murrell
- Earth and Life Systems Alliance, School of Environmental Sciences, University of East Anglia, Norwich, United Kingdom
| | - Warren H Gallagher
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin, USA
| | - Christopher Dennison
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Stéphane Vuilleumier
- Department of Microbiology, Genomics and the Environment, UMR 7156 UNISTRA-CNRS, Université de Strasbourg, Strasbourg, France
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Da Silva JCS, Pennifold RCR, Harvey JN, Rocha WR. A radical rebound mechanism for the methane oxidation reaction promoted by the dicopper center of a pMMO enzyme: a computational perspective. Dalton Trans 2016; 45:2492-504. [DOI: 10.1039/c5dt02638e] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Hydrogen Atom Transfer (HAT) promoted by a triplet state of the bis-oxoCu2(iii) core generates a new radical rebound mechanism for the hydroxylation of methane catalyzed by the binuclear copper site of a pMMO enzyme.
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Affiliation(s)
- Júlio C. S. Da Silva
- BioMat: Biomaterial Modeling Group
- Departamento de Química Fundamental
- CCEN
- Universidade Federal de Pernambuco
- Cidade Universitária
| | | | | | - Willian R. Rocha
- LQC-MM: Laboratório de Química Computacional e Modelagem Molecular
- Departamento de Química
- ICEX
- Universidade Federal de Minas Gerais
- Belo Horizonte
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22
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Abstract
Methane monooxygenases (MMOs) are enzymes that catalyze the oxidation of methane to methanol in methanotrophic bacteria. As potential targets for new gas-to-liquid methane bioconversion processes, MMOs have attracted intense attention in recent years. There are two distinct types of MMO, a soluble, cytoplasmic MMO (sMMO) and a membrane-bound, particulate MMO (pMMO). Both oxidize methane at metal centers within a complex, multisubunit scaffold, but the structures, active sites, and chemical mechanisms are completely different. This Current Topic review article focuses on the overall architectures, active site structures, substrate reactivities, protein-protein interactions, and chemical mechanisms of both MMOs, with an emphasis on fundamental aspects. In addition, recent advances, including new details of interactions between the sMMO components, characterization of sMMO intermediates, and progress toward understanding the pMMO metal centers are highlighted. The work summarized here provides a guide for those interested in exploiting MMOs for biotechnological applications.
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Affiliation(s)
- Sarah Sirajuddin
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Amy C. Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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23
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Sazinsky MH, Lippard SJ. Methane Monooxygenase: Functionalizing Methane at Iron and Copper. Met Ions Life Sci 2015; 15:205-56. [DOI: 10.1007/978-3-319-12415-5_6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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24
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Culpepper MA, Rosenzweig AC. Structure and protein-protein interactions of methanol dehydrogenase from Methylococcus capsulatus (Bath). Biochemistry 2014; 53:6211-9. [PMID: 25185034 PMCID: PMC4188263 DOI: 10.1021/bi500850j] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
![]()
In
the initial steps of their metabolic pathway, methanotrophic
bacteria oxidize methane to methanol with methane monooxygenases (MMOs)
and methanol to formaldehyde with methanol dehydrogenases (MDHs).
Several lines of evidence suggest that the membrane-bound or particulate
MMO (pMMO) and MDH interact to form a metabolic supercomplex. To further
investigate the possible existence of such a supercomplex, native
MDH from Methylococcus capsulatus (Bath) has been
purified and characterized by size exclusion chromatography with multi-angle
light scattering and X-ray crystallography. M. capsulatus (Bath) MDH is primarily a dimer in solution, although an oligomeric
species with a molecular mass of ∼450–560 kDa forms
at higher protein concentrations. The 2.57 Å resolution crystal
structure reveals an overall fold and α2β2 dimeric architecture similar to those of other MDH structures.
In addition, biolayer interferometry studies demonstrate specific
protein–protein interactions between MDH and M. capsulatus (Bath) pMMO as well as between MDH and the truncated recombinant
periplasmic domains of M. capsulatus (Bath) pMMO
(spmoB). These interactions exhibit KD values of 833 ± 409 nM and 9.0 ± 7.7 μM, respectively.
The biochemical data combined with analysis of the crystal lattice
interactions observed in the MDH structure suggest a model in which
MDH and pMMO associate not as a discrete, stoichiometric complex but
as a larger assembly scaffolded by the intracytoplasmic membranes.
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Affiliation(s)
- Megen A Culpepper
- Departments of Molecular Biosciences and Chemistry, Northwestern University , Evanston, Illinois 60208, United States
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25
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Culpepper MA, Cutsail GE, Gunderson WA, Hoffman BM, Rosenzweig AC. Identification of the valence and coordination environment of the particulate methane monooxygenase copper centers by advanced EPR characterization. J Am Chem Soc 2014; 136:11767-75. [PMID: 25059917 PMCID: PMC4140498 DOI: 10.1021/ja5053126] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Particulate methane monooxygenase (pMMO) catalyzes the oxidation of methane to methanol in methanotrophic bacteria. As a copper-containing enzyme, pMMO has been investigated extensively by electron paramagnetic resonance (EPR) spectroscopy, but the presence of multiple copper centers has precluded correlation of EPR signals with the crystallographically identified monocopper and dicopper centers. A soluble recombinant fragment of the pmoB subunit of pMMO, spmoB, like pMMO itself, contains two distinct copper centers and exhibits methane oxidation activity. The spmoB protein, spmoB variants designed to disrupt one or the other or both copper centers, as well as native pMMO have been investigated by EPR, ENDOR, and ESEEM spectroscopies in combination with metal content analysis. The data are remarkably similar for spmoB and pMMO, validating the use of spmoB as a model system. The results indicate that one EPR-active Cu(II) ion is present per pMMO and that it is associated with the active-site dicopper center in the form of a valence localized Cu(I)Cu(II) pair; the Cu(II), however, is scrambled between the two locations within the dicopper site. The monocopper site observed in the crystal structures of pMMO can be assigned as Cu(I). (14)N ENDOR and ESEEM data are most consistent with one of these dicopper-site signals involving coordination of the Cu(II) ion by residues His137 and His139, the other with Cu(II) coordinated by His33 and the N-terminal amino group. (1)H ENDOR measurements indicate there is no aqua (HxO) ligand bound to the Cu(II), either terminally or as a bridge to Cu(I).
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Affiliation(s)
- Megen A Culpepper
- Departments of ‡Molecular Biosciences and of §Chemistry, Northwestern University , Evanston, Illinois 60208, United States
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26
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Solomon EI, Heppner DE, Johnston EM, Ginsbach JW, Cirera J, Qayyum M, Kieber-Emmons MT, Kjaergaard CH, Hadt RG, Tian L. Copper active sites in biology. Chem Rev 2014; 114:3659-853. [PMID: 24588098 PMCID: PMC4040215 DOI: 10.1021/cr400327t] [Citation(s) in RCA: 1147] [Impact Index Per Article: 114.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
| | - David E. Heppner
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | | | - Jake W. Ginsbach
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | - Jordi Cirera
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | - Munzarin Qayyum
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | | | | | - Ryan G. Hadt
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | - Li Tian
- Department of Chemistry, Stanford University, Stanford, CA, 94305
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27
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Argüello JM, Raimunda D, Padilla-Benavides T. Mechanisms of copper homeostasis in bacteria. Front Cell Infect Microbiol 2013; 3:73. [PMID: 24205499 PMCID: PMC3817396 DOI: 10.3389/fcimb.2013.00073] [Citation(s) in RCA: 149] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2013] [Accepted: 10/17/2013] [Indexed: 01/27/2023] Open
Abstract
Copper is an important micronutrient required as a redox co-factor in the catalytic centers of enzymes. However, free copper is a potential hazard because of its high chemical reactivity. Consequently, organisms exert a tight control on Cu(+) transport (entry-exit) and traffic through different compartments, ensuring the homeostasis required for cuproprotein synthesis and prevention of toxic effects. Recent studies based on biochemical, bioinformatics, and metalloproteomics approaches, reveal a highly regulated system of transcriptional regulators, soluble chaperones, membrane transporters, and target cuproproteins distributed in the various bacterial compartments. As a result, new questions have emerged regarding the diversity and apparent redundancies of these components, their irregular presence in different organisms, functional interactions, and resulting system architectures.
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Affiliation(s)
- José M Argüello
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute Worcester, MA, USA
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28
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Yoshizawa K. Quantum Chemical Studies on Dioxygen Activation and Methane Hydroxylation by Diiron and Dicopper Species as well as Related Metal–Oxo Species. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2013. [DOI: 10.1246/bcsj.20130127] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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29
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Ji Y, Mao G, Wang Y, Bartlam M. Structural insights into diversity and n-alkane biodegradation mechanisms of alkane hydroxylases. Front Microbiol 2013; 4:58. [PMID: 23519435 PMCID: PMC3604635 DOI: 10.3389/fmicb.2013.00058] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 02/28/2013] [Indexed: 11/13/2022] Open
Abstract
Environmental microbes utilize four degradation pathways for the oxidation of n-alkanes. Although the enzymes degrading n-alkanes in different microbes may vary, enzymes functioning in the first step in the aerobic degradation of alkanes all belong to the alkane hydroxylases. Alkane hydroxylases are a class of enzymes that insert oxygen atoms derived from molecular oxygen into different sites of the alkane terminus (or termini) depending on the type of enzymes. In this review, we summarize the different types of alkane hydroxylases, their degrading steps, and compare typical enzymes from various classes with regard to their three-dimensional structures, in order to provide insights into how the enzymes mediate their different roles in the degradation of n-alkanes and what determines their different substrate ranges. Through the above analyzes, the degrading mechanisms of enzymes can be elucidated and molecular biological methods can be utilized to expand their catalytic roles in the petrochemical industry or in bioremediation of oil-contaminated environments.
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Affiliation(s)
- Yurui Ji
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai UniversityTianjin, China
- State Key Laboratory of Medicinal Chemical Biology, Nankai UniversityTianjin, China
| | - Guannan Mao
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai UniversityTianjin, China
| | - Yingying Wang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai UniversityTianjin, China
| | - Mark Bartlam
- State Key Laboratory of Medicinal Chemical Biology, Nankai UniversityTianjin, China
- College of Life Sciences, Nankai UniversityTianjin, China
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30
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Biotechnologies for greenhouse gases (CH4, N2O, and CO2) abatement: state of the art and challenges. Appl Microbiol Biotechnol 2013; 97:2277-303. [DOI: 10.1007/s00253-013-4734-z] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 01/20/2013] [Accepted: 01/21/2013] [Indexed: 12/17/2022]
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31
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Abstract
Particulate methane monooxygenase (pMMO) is an integral membrane metalloenzyme that oxidizes methane to methanol in methanotrophic bacteria, organisms that live on methane gas as their sole carbon source. Understanding pMMO function has important implications for bioremediation applications and for the development of new, environmentally friendly catalysts for the direct conversion of methane to methanol. Crystal structures of pMMOs from three different methanotrophs reveal a trimeric architecture, consisting of three copies each of the pmoB, pmoA, and pmoC subunits. There are three distinct metal centers in each protomer of the trimer, mononuclear and dinuclear copper sites in the periplasmic regions of pmoB and a mononuclear site within the membrane that can be occupied by copper or zinc. Various models for the pMMO active site have been proposed within these structural constraints, including dicopper, tricopper, and diiron centers. Biochemical and spectroscopic data on pMMO and recombinant soluble fragments, denoted spmoB proteins, indicate that the active site involves copper and is located at the site of the dicopper center in the pmoB subunit. Initial spectroscopic evidence for O(2) binding at this site has been obtained. Despite these findings, questions remain about the active site identity and nuclearity and will be the focus of future studies.
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Affiliation(s)
- Megen A. Culpepper
- 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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32
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Ve T, Mathisen K, Helland R, Karlsen OA, Fjellbirkeland A, Røhr ÅK, Andersson KK, Pedersen RB, Lillehaug JR, Jensen HB. The Methylococcus capsulatus (Bath) secreted protein, MopE*, binds both reduced and oxidized copper. PLoS One 2012; 7:e43146. [PMID: 22916218 PMCID: PMC3423442 DOI: 10.1371/journal.pone.0043146] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Accepted: 07/17/2012] [Indexed: 11/18/2022] Open
Abstract
Under copper limiting growth conditions the methanotrophic bacterium Methylococcus capsulatus (Bath) secrets essentially only one protein, MopE*, to the medium. MopE* is a copper-binding protein whose structure has been determined by X-ray crystallography. The structure of MopE* revealed a unique high affinity copper binding site consisting of two histidine imidazoles and one kynurenine, the latter an oxidation product of Trp130. In this study, we demonstrate that the copper ion coordinated by this strong binding site is in the Cu(I) state when MopE* is isolated from the growth medium of M. capsulatus. The conclusion is based on X-ray Near Edge Absorption spectroscopy (XANES), and Electron Paramagnetic Resonance (EPR) studies. EPR analyses demonstrated that MopE*, in addition to the strong copper-binding site, also binds Cu(II) at two weaker binding sites. Both Cu(II) binding sites have properties typical of non-blue type II Cu (II) centres, and the strongest of the two Cu(II) sites is characterised by a relative high hyperfine coupling of copper (A|| = 20 mT). Immobilized metal affinity chromatography binding studies suggests that residues in the N-terminal part of MopE* are involved in forming binding site(s) for Cu(II) ions. Our results support the hypothesis that MopE plays an important role in copper uptake, possibly making use of both its high (Cu(I) and low Cu(II) affinity properties.
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Affiliation(s)
- Thomas Ve
- Department of Molecular Biology, University of Bergen, Bergen, Norway
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Karina Mathisen
- Department of Chemistry, Norwegian University of Science and Technology, Trondheim, Norway
| | - Ronny Helland
- Norwegian Structural Biology Centre, Faculty of Science, University of Tromso, Tromso, Norway
| | - Odd A. Karlsen
- Department of Molecular Biology, University of Bergen, Bergen, Norway
| | | | - Åsmund K. Røhr
- Department of Molecular Biosciences, University of Oslo, Oslo, Norway
| | | | - Rolf-Birger Pedersen
- Department of Earth Science–Centre for Geobiology, University of Bergen, Bergen, Norway
| | | | - Harald B. Jensen
- Department of Molecular Biology, University of Bergen, Bergen, Norway
- * E-mail:
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33
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Smith SM, Rawat S, Telser J, Hoffman BM, Stemmler TL, Rosenzweig AC. Crystal structure and characterization of particulate methane monooxygenase from Methylocystis species strain M. Biochemistry 2011; 50:10231-40. [PMID: 22013879 PMCID: PMC3364217 DOI: 10.1021/bi200801z] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Particulate methane monooxygenase (pMMO) is an integral membrane metalloenzyme that oxidizes methane to methanol in methanotrophic bacteria. Previous biochemical and structural studies of pMMO have focused on preparations from Methylococcus capsulatus (Bath) and Methylosinus trichosporium OB3b. A pMMO from a third organism, Methylocystis species strain M, has been isolated and characterized. Both membrane-bound and solubilized Methylocystis sp. strain M pMMO contain ~2 copper ions per 100 kDa protomer and exhibit copper-dependent propylene epoxidation activity. Spectroscopic data indicate that Methylocystis sp. strain M pMMO contains a mixture of Cu(I) and Cu(II), of which the latter exhibits two distinct type 2 Cu(II) electron paramagnetic resonance (EPR) signals. Extended X-ray absorption fine structure (EXAFS) data are best fit with a mixture of Cu-O/N and Cu-Cu ligand environments with a Cu-Cu interaction at 2.52-2.64 Å. The crystal structure of Methylocystis sp. strain M pMMO was determined to 2.68 Å resolution and is the best quality pMMO structure obtained to date. It provides a revised model for the pmoA and pmoC subunits and has led to an improved model of M. capsulatus (Bath) pMMO. In these new structures, the intramembrane zinc/copper binding site has a different coordination environment from that in previous models.
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Affiliation(s)
- Stephen M. Smith
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Swati Rawat
- Department of Biochemistry and Molecular Biology, Wayne State University, School of Medicine, Detroit, Michigan 48201, United States
| | - Joshua Telser
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Brian M. Hoffman
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Timothy L. Stemmler
- Department of Biochemistry and Molecular Biology, Wayne State University, School of Medicine, Detroit, Michigan 48201, United States
| | - Amy C. Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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34
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Proteomic and targeted qPCR analyses of subsurface microbial communities for presence of methane monooxygenase. Biodegradation 2011; 22:1045-59. [DOI: 10.1007/s10532-011-9462-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Accepted: 02/17/2011] [Indexed: 01/21/2023]
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35
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Gvozdev RI, Tukhvatullin IA, Tumanova LV. Purification and properties of membrane-bound methane hydroxylase from Methylococcus capsulatus (Strain M). BIOL BULL+ 2011. [DOI: 10.1134/s1062359008020106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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36
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Tumanova LV, Tukhvatullin IA, Burbaev DS, Gvozdev RI, Andersson KK. The binuclear iron site of membrane-bound methane hydroxylase from Methylococcus capsulatus (Strain M). RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2011; 34:194-203. [DOI: 10.1134/s1068162008020064] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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37
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Smith SM, Balasubramanian R, Rosenzweig AC. Metal reconstitution of particulate methane monooxygenase and heterologous expression of the pmoB subunit. Methods Enzymol 2011; 495:195-210. [PMID: 21419923 PMCID: PMC3361753 DOI: 10.1016/b978-0-12-386905-0.00013-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Particulate methane monooxygenase (pMMO) is a multisubunit metalloenzyme complex used by methanotrophic bacteria to oxidize methane in the first step of carbon assimilation and energy production. In this chapter, we detail methods to prepare metal free (apo) membrane-bound pMMO and to reconstitute apo pMMO with metal ions. We also describe protocols to clone, express, and refold metal-loaded soluble domain constructs of the pmoB subunit. These approaches were used to address fundamental questions concerning the metal content and location of the pMMO active site.
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Affiliation(s)
- Stephen M Smith
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA
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38
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Chan SI, Nguyen HHT, Chen KHC, Yu SSF. Overexpression and Purification of the Particulate Methane Monooxygenase from Methylococcus capsulatus (Bath). Methods Enzymol 2011; 495:177-93. [DOI: 10.1016/b978-0-12-386905-0.00012-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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39
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Abstract
Methanotrophs, cells that consume methane (CH(4)) as their sole source of carbon and energy, play key roles in the global carbon cycle, including controlling anthropogenic and natural emissions of CH(4), the second-most important greenhouse gas after carbon dioxide. These cells have also been widely used for bioremediation of chlorinated solvents, and help sustain diverse microbial communities as well as higher organisms through the conversion of CH(4) to complex organic compounds (e.g. in deep ocean and subterranean environments with substantial CH(4) fluxes). It has been well-known for over 30 years that copper (Cu) plays a key role in the physiology and activity of methanotrophs, but it is only recently that we have begun to understand how these cells collect Cu, the role Cu plays in CH(4) oxidation by the particulate CH(4) monooxygenase, the effect of Cu on the proteome, and how Cu affects the ability of methanotrophs to oxidize different substrates. Here we summarize the current state of knowledge of the phylogeny, environmental distribution, and potential applications of methanotrophs for regional and global issues, as well as the role of Cu in regulating gene expression and proteome in these cells, its effects on enzymatic and whole-cell activity, and the novel Cu uptake system used by methanotrophs.
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Affiliation(s)
- Jeremy D Semrau
- Department of Civil and Environmental Engineering, The University of Michigan, Ann Arbor, MI, USA.
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40
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Gilch S, Meyer O, Schmidt I. A soluble form of ammonia monooxygenase in Nitrosomonas europaea. Biol Chem 2009; 390:863-73. [DOI: 10.1515/bc.2009.085] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractAmmonia monooxygenase (AMO) ofNitrosomonas europaeais a metalloenzyme that catalyzes the oxidation of ammonia to hydroxylamine. This study shows that AMO resides in the cytoplasm of the bacteria in addition to its location in the membrane and is distributed approximately equally in both subcellular fractions. AMO in both fractions catalyzes the oxidation of ammonia and binds [14C]acetylene, a mechanism-based inhibitor which specifically interacts with catalytically active AMO. Soluble AMO was purified 12-fold to electrophoretic homogeneity with a yield of 8%. AMO has a molecular mass of approximately 283 kDa with subunits of ca. 27 kDa (α-subunit, AmoA), ca. 42 kDa (β-subunit, AmoB), and ca. 24 kDa (γ-subunit, cytochromec1) in an α3β3γ3sub-unit structure. Different from the β-subunit of membrane-bound AMO, AmoB of soluble AMO possesses an N-terminal signal sequence. AMO contains Cu (9.4±0.6 mol per mol AMO), Fe (3.9±0.3 mol per mol AMO), and Zn (0.5 to 2.6 mol per mol AMO). Upon reduction the visible absorption spectrum of AMO reveals absorption bands characteristic of cytochromec. Electron para-magnetic resonance spectroscopy of air-oxidized AMO at 50 K shows a paramagnetic signal originating from Cu2+and at 10 K a paramagnetic signal characteristic of heme-Fe.
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41
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Abstract
pMMO (particulate methane mono-oxygenase) is an integral membrane metalloenzyme that catalyses the oxidation of methane to methanol. The pMMO metal active site has not been identified, precluding detailed investigation of the reaction mechanism. Models for the metal centres proposed by various research groups have evolved as crystallographic and spectroscopic data have become available. The present review traces the evolution of these active-site models before and after the 2005 Methylococcus capsulatus (Bath) pMMO crystal structure determination.
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Helm J, Wendlandt KD, Jechorek M, Stottmeister U. Potassium deficiency results in accumulation of ultra-high molecular weight poly-β-hydroxybutyrate in a methane-utilizing mixed culture. J Appl Microbiol 2008; 105:1054-61. [DOI: 10.1111/j.1365-2672.2008.03831.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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43
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Abstract
Ammonia oxidizing bacteria extract energy for growth from the oxidation of ammonia to nitrite. Ammonia monooxygenase, which initiates ammonia oxidation, remains enigmatic given the lack of purified preparations. Genetic and biochemical studies support a model for the enzyme consisting of three subunits and metal centers of copper and iron. Knowledge of hydroxylamine oxidoreductase, which oxidizes hydroxylamine formed by ammonia monooxygenase to nitrite, is informed by a crystal structure and detailed spectroscopic and catalytic studies. Other inorganic nitrogen compounds, including NO, N2O, NO2, and N2 can be consumed and/or produced by ammonia-oxidizing bacteria. NO and N2O can be produced as byproducts of hydroxylamine oxidation or through nitrite reduction. NO2 can serve as an alternative oxidant in place of O2 in some ammonia-oxidizing strains. Our knowledge of the diversity of inorganic N metabolism by ammonia-oxidizing bacteria continues to grow. Nonetheless, many questions remain regarding the enzymes and genes involved in these processes and the role of these pathways in ammonia oxidizers.
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Affiliation(s)
- Daniel J Arp
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA.
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44
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Belousoff MJ, Graham B, Spiccia L. Copper(II) Complexes ofN-Methylated Derivatives ofortho- andmeta-Xylyl-Bridged Bis(1,4,7-triazacyclononane) Ligands: Synthesis, X-ray Structure and Reactivity as Artificial Nucleases. Eur J Inorg Chem 2008. [DOI: 10.1002/ejic.200800533] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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45
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Oxidase, superoxide dismutase, and hydrogen peroxide reductase activities of methanobactin from types I and II methanotrophs. J Inorg Biochem 2008; 102:1571-80. [DOI: 10.1016/j.jinorgbio.2008.02.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2007] [Revised: 02/04/2008] [Accepted: 02/08/2008] [Indexed: 11/20/2022]
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46
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Chan SI, Yu SSF. Controlled oxidation of hydrocarbons by the membrane-bound methane monooxygenase: the case for a tricopper cluster. Acc Chem Res 2008; 41:969-79. [PMID: 18605740 DOI: 10.1021/ar700277n] [Citation(s) in RCA: 147] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[Figure: see text]. The growing need for inexpensive methods to convert methane to methanol has sparked considerable interest in methods that catalyze this process. The integral membrane protein particulate methane monooxygenase (pMMO) mediates the facile conversion of methane to methanol in methanotrophic bacteria. Most evidence indicates that pMMO is a multicopper enzyme, and these copper ions support redox, dioxygen, and oxo-transfer chemistry. However, the exact identity of the copper species that mediates the oxo-transfer chemistry remains an area of intense debate. This highly complex enzyme is notoriously difficult to purify because of its instability outside the lipid bilayer and tendency to lose its essential metal cofactors. For this reason, pMMO has resisted both initial identification and subsequent isolation and purification for biochemical and biophysical characterization. In this Account, we describe evidence that pMMO is a multicopper protein. Its unique trinuclear copper cluster mediates dioxygen chemistry and O-atom transfer during alkane hydroxylation. Although a recent crystal structure did not show this tricopper cluster, we provide compelling evidence for such a cluster through redox potentiometry and EPR experiments on the "holo" enzyme in pMMO-enriched membranes. We also identify a site in the structure of pMMO that could accommodate this cluster. A hydrophobic pocket capable of harboring pentane, the enzyme's largest known substrate, lies adjacent to this site. In addition, we have designed and synthesized model tricopper clusters to provide further chemical evidence that a tricopper cluster mediates the enzyme's oxo-transfer chemistry. These biomimetic models exhibit similar spectroscopic properties and chemical reactivity to the putative tricopper cluster in pMMO. Based on computational analysis using density functional theory (DFT), triangular tricopper clusters are capable of harnessing a "singlet oxene" upon activation by dioxygen. An oxygen atom is then inserted via a concerted process into the C-H bond of an alkane in the transition state during hydroxylation. The turnover frequency and kinetic isotope effect predicted by DFT show excellent agreement with experimental data.
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Affiliation(s)
- Sunney I. Chan
- Institute of Chemistry, Academia Sinica, Nankang, Taipei 11509, Taiwan
- A. A. Noyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena, CA 91125
| | - Steve S.-F. Yu
- Institute of Chemistry, Academia Sinica, Nankang, Taipei 11509, Taiwan
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Hakemian AS, Kondapalli KC, Telser J, Hoffman BM, Stemmler TL, Rosenzweig AC. The metal centers of particulate methane monooxygenase from Methylosinus trichosporium OB3b. Biochemistry 2008; 47:6793-801. [PMID: 18540635 PMCID: PMC2664655 DOI: 10.1021/bi800598h] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Particulate methane monooxygenase (pMMO) is a membrane-bound metalloenzyme that oxidizes methane to methanol in methanotrophic bacteria. The nature of the pMMO active site and the overall metal content are controversial, with spectroscopic and crystallographic data suggesting the presence of a mononuclear copper center, a dinuclear copper center, a trinuclear center, and a diiron center or combinations thereof. Most studies have focused on pMMO from Methylococcus capsulatus (Bath). pMMO from a second organism, Methylosinus trichosporium OB3b, has been purified and characterized by spectroscopic and crystallographic methods. Purified M. trichosporium OB3b pMMO contains approximately 2 copper ions per 100 kDa protomer. Electron paramagnetic resonance (EPR) spectroscopic parameters indicate that type 2 Cu(II) is present as two distinct species. Extended X-ray absorption fine structure (EXAFS) data are best fit with oxygen/nitrogen ligands and reveal a Cu-Cu interaction at 2.52 A. Correspondingly, X-ray crystallography of M. trichosporium OB3b pMMO shows a dinuclear copper center, similar to that observed previously in the crystal structure of M. capsulatus (Bath) pMMO. There are, however, significant differences between the pMMO structures from the two organisms. A mononuclear copper center present in M. capsulatus (Bath) pMMO is absent in M. trichosporium OB3b pMMO, whereas a metal center occupied by zinc in the M. capsulatus (Bath) pMMO structure is occupied by copper in M. trichosporium OB3b pMMO. These findings extend previous work on pMMO from M. capsulatus (Bath) and provide new insight into the functional importance of the different metal centers.
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Affiliation(s)
| | | | | | | | - Timothy L. Stemmler
- To whom correspondence may be addressed. A.C.R.: tel, 847-467-5301; fax, 847-467-6489; e-mail, . T.L.S.: tel, 313-577-5712; fax, 313-577-2765; e-mail,
| | - Amy C. Rosenzweig
- To whom correspondence may be addressed. A.C.R.: tel, 847-467-5301; fax, 847-467-6489; e-mail, . T.L.S.: tel, 313-577-5712; fax, 313-577-2765; e-mail,
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48
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Trotsenko YA, Murrell JC. Metabolic aspects of aerobic obligate methanotrophy. ADVANCES IN APPLIED MICROBIOLOGY 2008; 63:183-229. [PMID: 18395128 DOI: 10.1016/s0065-2164(07)00005-6] [Citation(s) in RCA: 248] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Yuri A Trotsenko
- G.K.Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow 142290, Russia
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49
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Martinho M, Choi DW, DiSpirito AA, Antholine WE, Semrau JD, Münck E. Mössbauer studies of the membrane-associated methane monooxygenase from Methylococcus capsulatus bath: evidence for a Diiron center. J Am Chem Soc 2007; 129:15783-5. [PMID: 18052283 PMCID: PMC2533734 DOI: 10.1021/ja077682b] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Two methane monooxygenase (MMO) systems have been identified in methanotrophic bacteria, namely, a soluble or cytoplasmic MMO and a membrane-associated or particulate MMO. The active site of the well-characterized soluble MMO contains a bis-mu-hydroxo-bridged diiron cluster. X-ray crystallographic studies of the particulate enzyme, pMMO, have identified two copper centers on the alpha subunit (pmoB) of the alphabetagamma trimer and a site at the interface of the betagamma subunits filled by a Zn, apparently from the crystallization buffer. In our hands, pMMO preparations containing 1-2 iron atoms per alphabetagamma show the highest catalytic activity. We have employed Mössbauer spectroscopy to characterize the iron in our preparations. Interestingly, we find in pMMO a component with the same spectral properties as the antiferromagnetically coupled diiron(III) cluster in the soluble enzyme. In whole cells, we find nearly 1 diiron center per alphabetagamma of pMMO; in purified enzyme preparations, only 10% of the sites appear to be occupied. These occupancies correlate well with the measured specific activities of purified pMMO and pMMO in whole cells. We suggest that it is the "Zn site" that accommodates the diiron center in active pMMO.
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Affiliation(s)
- Marlène Martinho
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213
| | - Dong W. Choi
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011-3211
| | - Alan A. DiSpirito
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011-3211
| | | | - Jeremy D. Semrau
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI 58109-2125
| | - Eckard Münck
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213
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50
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Zhang HP, Zhou H, Pan ZQ, Meng XG, Song Y. Synthesis, crystal structure and magnetic characterization of a novel linear trinuclear copper(II) complex bridged by phenoxy and benzyloxy oxygen atoms. TRANSIT METAL CHEM 2007. [DOI: 10.1007/s11243-007-9018-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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