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Qiu L, Lok KS, Lu Q, Zhong H, Guo X, Shim H. Zinc and copper supplements enhance trichloroethylene removal by Pseudomonas plecoglossicida in water. ENVIRONMENTAL TECHNOLOGY 2023; 44:3698-3709. [PMID: 35451932 DOI: 10.1080/09593330.2022.2069518] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
The effects of two microelements, zinc and copper, on the aerobic co-metabolic removal of trichloroethylene (10 mg/L) by the isolate Pseudomonas plecoglossicida were investigated. The strain was previously isolated from a petroleum-contaminated site using toluene (150 mg/L) as substrate. Different concentrations (1, 10 and 100 mg/L) of microelements provided with SO42- and Cl- were tested. The results showed the supplement of Zn2+ and Cu2+ at the low concentration (1 mg/L) significantly enhanced cell growth. The removal efficiencies for toluene and trichloroethylene were also enhanced at the low concentration (1 mg/L) of Zn2+ and Cu2+. Compared to the control without zinc supplement, higher concentrations of zinc (10 and 100 mg/L) enhanced the removal efficiencies for both toluene and trichloroethylene in the first three days but showed some inhibitory effect afterward. However, the higher concentrations of Cu2+ (10 and 100 mg/L) always showed inhibitory to the toluene removal while showing inhibitory to the TCE removal after three days. For both Zn2+ and Cu2+, the anions SO42- and Cl- did not show significant difference in their effects on the toluene removal. A possible mechanism for Zn2+ and Cu2+ to enhance the removal of toluene and trichloroethylene would be their involvement in toluene oxygenase-based transformation processes. In addition, high concentrations of Zn2+ and Cu2+ ions could be removed from the liquid by the cells accordingly. The results imply a potential of supplementing low concentrations of zinc and copper to enhance bioremediation of the sites co-contaminated with toluene and trichloroethylene.
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Affiliation(s)
- Lan Qiu
- Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau SAR, People's Republic of China
| | - Keng Seng Lok
- Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau SAR, People's Republic of China
| | - Qihong Lu
- Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau SAR, People's Republic of China
| | - Hua Zhong
- Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau SAR, People's Republic of China
| | - Xiaoyuan Guo
- Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau SAR, People's Republic of China
| | - Hojae Shim
- Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau SAR, People's Republic of China
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2
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Khramenkova E, Medvedev MG, Li G, Pidko EA. Unraveling the Nature of Extraframework Catalytic Ensembles in Zeolites: Flexibility and Dynamics of the Copper-Oxo Trimers in Mordenite. J Phys Chem Lett 2021; 12:10906-10913. [PMID: 34731568 PMCID: PMC8591661 DOI: 10.1021/acs.jpclett.1c03288] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Extraframework cations define the chemical versatility of zeolite catalysts. Addressing their structural complexity and dynamic behavior represents one of the main fundamental challenges in the field. Herein, we present a computational approach for the identification and analysis of the accessible pool of intrazeolite extraframework complexes with a Cu/MOR catalyst as an industrially important model system. We employ ab initio molecular dynamics for capturing the ensemble of reactive isomers with the [Cu3O3]2+ stoichiometry confined in the mordenite channels. The high structural diversity of the generated isomers was ensured by concentrating the kinetic energy along the low-curvature directions of the potential energy surface (PES). Geometrically distinct [Cu3O3]2+ complexes were identified via a series of clustering procedures ensuring that one structure of each local minima is retained. The proposed procedure has resulted in a set of previously unknown peroxo-complexes, which are >50 kJ/mol more stable than the recently hypothesized chair-shaped structure. Our analysis demonstrates that the most stable peroxo-containing clusters can be formed under operando conditions from molecular oxygen and the Cu3O unit, similar to that in methane monooxygenase (MMO) enzymes.
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Affiliation(s)
- Elena
V. Khramenkova
- Inorganic
Systems Engineering (ISE), Department of Chemical Engineering, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Michael G. Medvedev
- Zelinsky
Institute of Organic Chemistry RAS, Leninsky Prospect, 47, Moscow 119991, Russia
| | - Guanna Li
- Biobased
Chemistry & Technology, Wageningen University
& Research, 6708 PB Wageningen, The Netherlands
- Organic
Chemistry, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Evgeny A. Pidko
- Inorganic
Systems Engineering (ISE), Department of Chemical Engineering, Delft University of Technology, 2629 HZ Delft, The Netherlands
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3
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Aoto YA, Bargholz A, Kats D, Werner HJ, Köhn A. Perturbation Expansion of Internally Contracted Coupled-Cluster Theory up to Third Order. J Chem Theory Comput 2019; 15:2291-2305. [DOI: 10.1021/acs.jctc.8b01301] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yuri Alexandre Aoto
- Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
- Center for Mathematics Computing and Cognition, Federal University of ABC (UFABC), Avenida dos Estados 5001, Santo André, Brazil
| | - Arne Bargholz
- Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
| | - Daniel Kats
- Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
- Max Planck Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany
| | - Hans-Joachim Werner
- Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
| | - Andreas Köhn
- Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
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4
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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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5
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Hakobyan A, Liesack W, Glatter T. Crude-MS Strategy for in-Depth Proteome Analysis of the Methane-Oxidizing Methylocystis sp. strain SC2. J Proteome Res 2018; 17:3086-3103. [DOI: 10.1021/acs.jproteome.8b00216] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - Werner Liesack
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Karl-von-Frisch-Str. 16, D-35043 Marburg, Germany
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6
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Sushkevich VL, Palagin D, Ranocchiari M, van Bokhoven JA. Selective anaerobic oxidation of methane enables direct synthesis of methanol. Science 2017; 356:523-527. [DOI: 10.1126/science.aam9035] [Citation(s) in RCA: 459] [Impact Index Per Article: 65.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 04/13/2017] [Indexed: 01/20/2023]
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7
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Palagin D, Knorpp AJ, Pinar AB, Ranocchiari M, van Bokhoven JA. Assessing the relative stability of copper oxide clusters as active sites of a CuMOR zeolite for methane to methanol conversion: size matters? NANOSCALE 2017; 9:1144-1153. [PMID: 28009911 DOI: 10.1039/c6nr07723d] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Copper-containing zeolites exhibit high activity in the direct partial oxidation of methane into methanol at relatively low temperatures. Di- and tricopper species have been proposed as active catalytic sites, with recent experimental evidence also suggesting the possibility of the formation of larger copper oxide species. Using density functional theory based global geometry optimization, we were able to identify a general trend of the copper oxide cluster stability increasing with size. For instance, the identified ground-state structures of tetra- and pentamer copper clusters of CunOn2+ and CunOn-12+ stoichiometries embedded in an 8-ring channel of mordenite exhibit higher relative stability compared to smaller clusters. Moreover, the aluminium content and localization in the zeolite pore influence the cluster's stability and its geometrical motif, which offers a perspective of tuning the properties of copper-exchanged zeolites by creating copper oxide clusters of a given structure and size. With the activity of the cluster towards methane being connected to its stability, such tuning will potentially allow the design of catalysts with engineered properties.
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Affiliation(s)
- Dennis Palagin
- Laboratory for Catalysis and Sustainable Chemistry, Paul Scherrer Institut, 5232 Villigen, Switzerland.
| | - Amy J Knorpp
- Institute for Chemistry and Bioengineering, ETH Zurich, Vladimir-Prelog-Weg 1, 8093 Zürich, Switzerland
| | - Ana B Pinar
- Laboratory for Catalysis and Sustainable Chemistry, Paul Scherrer Institut, 5232 Villigen, Switzerland.
| | - Marco Ranocchiari
- Laboratory for Catalysis and Sustainable Chemistry, Paul Scherrer Institut, 5232 Villigen, Switzerland.
| | - Jeroen A van Bokhoven
- Laboratory for Catalysis and Sustainable Chemistry, Paul Scherrer Institut, 5232 Villigen, Switzerland. and Institute for Chemistry and Bioengineering, ETH Zurich, Vladimir-Prelog-Weg 1, 8093 Zürich, Switzerland
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8
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Lawton TJ, Rosenzweig AC. Methane-Oxidizing Enzymes: An Upstream Problem in Biological Gas-to-Liquids Conversion. J Am Chem Soc 2016; 138:9327-40. [PMID: 27366961 PMCID: PMC5242187 DOI: 10.1021/jacs.6b04568] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Biological conversion of natural gas to liquids (Bio-GTL) represents an immense economic opportunity. In nature, aerobic methanotrophic bacteria and anaerobic archaea are able to selectively oxidize methane using methane monooxygenase (MMO) and methyl coenzyme M reductase (MCR) enzymes. Although significant progress has been made toward genetically manipulating these organisms for biotechnological applications, the enzymes themselves are slow, complex, and not recombinantly tractable in traditional industrial hosts. With turnover numbers of 0.16-13 s(-1), these enzymes pose a considerable upstream problem in the biological production of fuels or chemicals from methane. Methane oxidation enzymes will need to be engineered to be faster to enable high volumetric productivities; however, efforts to do so and to engineer simpler enzymes have been minimally successful. Moreover, known methane-oxidizing enzymes have different expression levels, carbon and energy efficiencies, require auxiliary systems for biosynthesis and function, and vary considerably in terms of complexity and reductant requirements. The pros and cons of using each methane-oxidizing enzyme for Bio-GTL are considered in detail. The future for these enzymes is bright, but a renewed focus on studying them will be critical to the successful development of biological processes that utilize methane as a feedstock.
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Affiliation(s)
- Thomas J Lawton
- 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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9
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Sheppard T, Daly H, Goguet A, Thompson JM. Improved Efficiency for Partial Oxidation of Methane by Controlled Copper Deposition on Surface-Modified ZSM-5. ChemCatChem 2015; 8:562-570. [PMID: 26925172 PMCID: PMC4755137 DOI: 10.1002/cctc.201500980] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 10/10/2015] [Indexed: 11/20/2022]
Abstract
The mono(μ‐oxo) dicopper cores present in the pores of Cu‐ZSM‐5 are active for the partial oxidation of methane to methanol. However, copper on the external surface reduces the ratio of active, selective sites to unselective sites. More efficient catalysts are obtained by controlling the copper deposition during synthesis. Herein, the external exchange sites of ZSM‐5 samples were passivated by bis(trimethylsilyl) trifluoroacetamide (BSTFA) followed by calcination, promoting selective deposition of intraporous copper during aqueous copper ion exchange. At an optimum level of 1–2 wt % SiO2, IR studies showed a 64 % relative reduction in external copper species and temperature‐programmed oxidation analysis showed an associated increase in the formation of methanol compared with unmodified Cu‐ZSM‐5 samples. It is, therefore, reported that the modified zeolites contained a significantly higher proportion of active, selective copper species than their unmodified counterparts with activity for partial methane oxidation to methanol.
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Affiliation(s)
- Thomas Sheppard
- School of Chemistry and Chemical EngineeringQueen's UniversityStranmillis RoadBelfastBT9 5AGNorthern Ireland
- Institute of Catalysis Research and Technology (IKFT)Karlsruhe Institute of Technology (KIT)Kaiserstrasse 1276131KarlsruheGermany
| | - Helen Daly
- School of Chemistry and Chemical EngineeringQueen's UniversityStranmillis RoadBelfastBT9 5AGNorthern Ireland
| | - Alex Goguet
- School of Chemistry and Chemical EngineeringQueen's UniversityStranmillis RoadBelfastBT9 5AGNorthern Ireland
| | - Jillian M. Thompson
- School of Chemistry and Chemical EngineeringQueen's UniversityStranmillis RoadBelfastBT9 5AGNorthern Ireland
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10
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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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11
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Vinogradov MM, Kozlov YN, Bilyachenko AN, Nesterov DS, Shul'pina LS, Zubavichus YV, Pombeiro AJL, Levitsky MM, Yalymov AI, Shul'pin GB. Alkane oxidation with peroxides catalyzed by cage-like copper(ii) silsesquioxanes. NEW J CHEM 2015. [DOI: 10.1039/c4nj01163e] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Copper(ii) silsesquioxanes [(PhSiO1.5)12(CuO)4(NaO0.5)4] or [(PhSiO1.5)10(CuO)2(NaO0.5)2] are catalysts for alkane oxidation with H2O2ort-BuOOH.
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Affiliation(s)
- Mikhail M. Vinogradov
- Nesmeyanov Institute of Organoelement Compounds
- Russian Academy of Sciences
- Moscow 119991
- Russia
- Centro de Química Estrutural
| | - Yuriy N. Kozlov
- Semenov Institute of Chemical Physics
- Russian Academy of Sciences
- Moscow 119991
- Russia
| | - Alexey N. Bilyachenko
- Nesmeyanov Institute of Organoelement Compounds
- Russian Academy of Sciences
- Moscow 119991
- Russia
| | - Dmytro S. Nesterov
- Centro de Química Estrutural
- Complexo I
- Instituto Superior Técnico
- Universidade de Lisboa
- 1049-001 Lisboa
| | - Lidia S. Shul'pina
- Nesmeyanov Institute of Organoelement Compounds
- Russian Academy of Sciences
- Moscow 119991
- Russia
| | - Yan V. Zubavichus
- Nesmeyanov Institute of Organoelement Compounds
- Russian Academy of Sciences
- Moscow 119991
- Russia
- National Research Center “Kurchatov Institute”
| | - Armando J. L. Pombeiro
- Centro de Química Estrutural
- Complexo I
- Instituto Superior Técnico
- Universidade de Lisboa
- 1049-001 Lisboa
| | - Mikhail M. Levitsky
- Nesmeyanov Institute of Organoelement Compounds
- Russian Academy of Sciences
- Moscow 119991
- Russia
| | - Alexey I. Yalymov
- Nesmeyanov Institute of Organoelement Compounds
- Russian Academy of Sciences
- Moscow 119991
- Russia
| | - Georgiy B. Shul'pin
- Semenov Institute of Chemical Physics
- Russian Academy of Sciences
- Moscow 119991
- Russia
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12
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Sirajuddin S, Barupala D, Helling S, Marcus K, Stemmler TL, Rosenzweig AC. Effects of zinc on particulate methane monooxygenase activity and structure. J Biol Chem 2014; 289:21782-94. [PMID: 24942740 PMCID: PMC4118136 DOI: 10.1074/jbc.m114.581363] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 06/11/2014] [Indexed: 11/06/2022] Open
Abstract
Particulate methane monooxygenase (pMMO) is a membrane-bound metalloenzyme that oxidizes methane to methanol in methanotrophic bacteria. Zinc is a known inhibitor of pMMO, but the details of zinc binding and the mechanism of inhibition are not understood. Metal binding and activity assays on membrane-bound pMMO from Methylococcus capsulatus (Bath) reveal that zinc inhibits pMMO at two sites that are distinct from the copper active site. The 2.6 Å resolution crystal structure of Methylocystis species strain Rockwell pMMO reveals two previously undetected bound lipids, and metal soaking experiments identify likely locations for the two zinc inhibition sites. The first is the crystallographic zinc site in the pmoC subunit, and zinc binding here leads to the ordering of 10 previously unobserved residues. A second zinc site is present on the cytoplasmic side of the pmoC subunit. Parallels between these results and zinc inhibition studies of several respiratory complexes suggest that zinc might inhibit proton transfer in pMMO.
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Affiliation(s)
- Sarah Sirajuddin
- From the Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208
| | - Dulmini Barupala
- the Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan 48201, and
| | - Stefan Helling
- the Medical Proteome Center, Department of Functional Proteomics, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Katrin Marcus
- the Medical Proteome Center, Department of Functional Proteomics, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Timothy L Stemmler
- the Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan 48201, and
| | - Amy C Rosenzweig
- From the Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208,
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13
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Sheppard T, Hamill CD, Goguet A, Rooney DW, Thompson JM. A low temperature, isothermal gas-phase system for conversion of methane to methanol over Cu–ZSM-5. Chem Commun (Camb) 2014; 50:11053-5. [DOI: 10.1039/c4cc02832e] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A low temperature, recyclable process for partial methane oxidation is described over Cu–ZSM-5 using NO as the oxidant.
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Affiliation(s)
- T. Sheppard
- School of Chemistry and Chemical Engineering
- Queen's University
- Belfast, UK
| | - C. D. Hamill
- School of Chemistry and Chemical Engineering
- Queen's University
- Belfast, UK
| | - A. Goguet
- School of Chemistry and Chemical Engineering
- Queen's University
- Belfast, UK
| | - D. W. Rooney
- School of Chemistry and Chemical Engineering
- Queen's University
- Belfast, UK
| | - J. M. Thompson
- School of Chemistry and Chemical Engineering
- Queen's University
- Belfast, UK
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14
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Khenkin AM, Efremenko I, Martin JML, Neumann R. Polyoxometalate-Catalyzed Insertion of Oxygen from O2 into Tin–Alkyl Bonds. J Am Chem Soc 2013; 135:19304-10. [DOI: 10.1021/ja409559h] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Alexander M. Khenkin
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel 76100
| | - Irena Efremenko
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel 76100
| | - Jan M. L. Martin
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel 76100
| | - Ronny Neumann
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel 76100
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15
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Mohanty SR, Kollah B, Sharma VK, Singh AB, Singh M, Rao AS. Methane oxidation and methane driven redox process during sequential reduction of a flooded soil ecosystem. ANN MICROBIOL 2013. [DOI: 10.1007/s13213-013-0633-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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16
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Bordiga S, Groppo E, Agostini G, van Bokhoven JA, Lamberti C. Reactivity of Surface Species in Heterogeneous Catalysts Probed by In Situ X-ray Absorption Techniques. Chem Rev 2013; 113:1736-850. [DOI: 10.1021/cr2000898] [Citation(s) in RCA: 488] [Impact Index Per Article: 44.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Silvia Bordiga
- Department of Chemistry and NIS Centre of Excellence, Università di Torino and INSTM Reference Center, Via P. Giuria 7, 10125 Torino, Italy
| | - Elena Groppo
- Department of Chemistry and NIS Centre of Excellence, Università di Torino and INSTM Reference Center, Via P. Giuria 7, 10125 Torino, Italy
| | - Giovanni Agostini
- Department of Chemistry and NIS Centre of Excellence, Università di Torino and INSTM Reference Center, Via P. Giuria 7, 10125 Torino, Italy
| | - Jeroen A. van Bokhoven
- ETH Zurich, Institute for Chemical and Bioengineering, HCI E127 8093 Zurich, Switzerland
- Laboratory for Catalysis and Sustainable Chemistry (LSK) Swiss Light Source, Paul Scherrer Instituteaul Scherrer Institute, Villigen, Switzerland
| | - Carlo Lamberti
- Department of Chemistry and NIS Centre of Excellence, Università di Torino and INSTM Reference Center, Via P. Giuria 7, 10125 Torino, Italy
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17
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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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18
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Cotruvo JA, Stubbe J. Metallation and mismetallation of iron and manganese proteins in vitro and in vivo: the class I ribonucleotide reductases as a case study. Metallomics 2012; 4:1020-36. [PMID: 22991063 PMCID: PMC3488304 DOI: 10.1039/c2mt20142a] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
How cells ensure correct metallation of a given protein and whether a degree of promiscuity in metal binding has evolved are largely unanswered questions. In a classic case, iron- and manganese-dependent superoxide dismutases (SODs) catalyze the disproportionation of superoxide using highly similar protein scaffolds and nearly identical active sites. However, most of these enzymes are active with only one metal, although both metals can bind in vitro and in vivo. Iron(ii) and manganese(ii) bind weakly to most proteins and possess similar coordination preferences. Their distinct redox properties suggest that they are unlikely to be interchangeable in biological systems except when they function in Lewis acid catalytic roles, yet recent work suggests this is not always the case. This review summarizes the diversity of ways in which iron and manganese are substituted in similar or identical protein frameworks. As models, we discuss (1) enzymes, such as epimerases, thought to use Fe(II) as a Lewis acid under normal growth conditions but which switch to Mn(II) under oxidative stress; (2) extradiol dioxygenases, which have been found to use both Fe(II) and Mn(II), the redox role of which in catalysis remains to be elucidated; (3) SODs, which use redox chemistry and are generally metal-specific; and (4) the class I ribonucleotide reductases (RNRs), which have evolved unique biosynthetic pathways to control metallation. The primary focus is the class Ib RNRs, which can catalyze formation of a stable radical on a tyrosine residue in their β2 subunits using either a di-iron or a recently characterized dimanganese cofactor. The physiological roles of enzymes that can switch between iron and manganese cofactors are discussed, as are insights obtained from the studies of many groups regarding iron and manganese homeostasis and the divergent and convergent strategies organisms use for control of protein metallation. We propose that, in many of the systems discussed, "discrimination" between metals is not performed by the protein itself, but it is instead determined by the environment in which the protein is expressed.
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Affiliation(s)
- Joseph A. Cotruvo
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA.; Fax: +1 617 324-0505; Tel: +1 617 253-1814
| | - JoAnne Stubbe
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA.; Fax: +1 617 324-0505; Tel: +1 617 253-1814
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA
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Hammond C, Conrad S, Hermans I. Oxidative methane upgrading. CHEMSUSCHEM 2012; 5:1668-1686. [PMID: 22848012 DOI: 10.1002/cssc.201200299] [Citation(s) in RCA: 171] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Indexed: 06/01/2023]
Abstract
The economically viable oxidative upgrading of methane presents one of the most difficult but rewarding challenges within catalysis research. Its potential to revolutionalise the chemical value chain, coupled with the associated supremely challenging scientific aspects, has ensured this topic's high popularity over the preceeding decades. Herein, we report a non-exhaustive account of the current developments within the field of oxidative methane upgrading and summarise the pertaining challenges that have yet to be solved.
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Affiliation(s)
- Ceri Hammond
- Department of Chemistry and Applied Biosciences, ETH Zurich, Switzerland
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Culpepper MA, Cutsail GE, Hoffman BM, Rosenzweig AC. Evidence for oxygen binding at the active site of particulate methane monooxygenase. J Am Chem Soc 2012; 134:7640-3. [PMID: 22540911 DOI: 10.1021/ja302195p] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Particulate methane monooxygenase (pMMO) is an integral membrane metalloenzyme that converts methane to methanol in methanotrophic bacteria. The enzyme consists of three subunits, pmoB, pmoA, and pmoC, organized in an α(3)β(3)γ(3) trimer. Studies of intact pMMO and a recombinant soluble fragment of the pmoB subunit (denoted as spmoB) indicate that the active site is located within the soluble region of pmoB at the site of a crystallographically modeled dicopper center. In this work, we have investigated the reactivity of pMMO and spmoB with oxidants. Upon reduction and treatment of spmoB with O(2) or H(2)O(2) or pMMO with H(2)O(2), an absorbance feature at 345 nm is generated. The energy and intensity of this band are similar to those of the μ-η(2):η(2)-peroxo-Cu(II)(2) species formed in several dicopper enzymes and model compounds. The feature is not observed in inactive spmoB variants in which the dicopper center is disrupted, consistent with O(2) binding to the proposed active site. Reaction of the 345 nm species with CH(4) results in the disappearance of the spectroscopic feature, suggesting that this O(2) intermediate is mechanistically relevant. Taken together, these observations provide strong new support for the identity and location of the pMMO active site.
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Affiliation(s)
- Megen A Culpepper
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA
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The divergent AmoC3 subunit of ammonia monooxygenase functions as part of a stress response system in Nitrosomonas europaea. J Bacteriol 2012; 194:3448-56. [PMID: 22544266 DOI: 10.1128/jb.00133-12] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ammonia monooxygenase of chemolithotrophic ammonia-oxidizing bacteria (AOB) catalyzes the first step in ammonia oxidation by converting ammonia to hydroxylamine. The monooxygenase of Nitrosomonas europaea is encoded by two nearly identical operon copies (amoCAB(1,2)). Several AOB, including N. europaea, also possess a divergent monocistronic copy of amoC (amoC(3)) of unknown function. Previous work suggested a possible functional role for amoC(3) as part of the σ(E) stress response regulon during the recovery of N. europaea from extended ammonia starvation, thus indicating its importance during the exit of cells from starvation. We here used global transcription analysis to show that expression of amoC(3) is part of a general poststarvation cellular response system in N. europaea. We also found that amoC(3) is required for an efficient response to some stress conditions, as deleting this gene impaired growth at elevated temperatures and recovery following starvation under high oxygen tensions. Deletion of the σ(32) global stress response regulator demonstrated that the heat shock regulon plays a significant role in mediating the recovery of N. europaea from starvation. These findings provide the first described phenotype associated with the divergent AmoC(3) subunit which appears to function as a stress-responsive subunit capable of maintaining ammonia oxidation activity under stress conditions. While this study was limited to starvation and heat shock, it is possible that the AmoC(3) subunit may be responsive to other membrane stressors (e.g., solvent or osmotic shocks) that are prevalent in the environments of AOB.
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Pesch ML, Christl I, Barmettler K, Kraemer SM, Kretzschmar R. Isolation and purification of Cu-free methanobactin from Methylosinus trichosporium OB3b. GEOCHEMICAL TRANSACTIONS 2011; 12:2. [PMID: 21299876 PMCID: PMC3044663 DOI: 10.1186/1467-4866-12-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Accepted: 02/07/2011] [Indexed: 05/30/2023]
Abstract
BACKGROUND The isolation of highly pure copper-free methanobactin is a prerequisite for the investigation of the biogeochemical functions of this chalkophore molecule produced by methane oxidizing bacteria. Here, we report a purification method for methanobactin from Methylosinus trichosporium OB3b cultures based on reversed-phase HPLC fractionation used in combination with a previously reported resin extraction. HPLC eluent fractions of the resin extracted product were collected and characterized with UV-vis, FT-IR, and C-1s NEXAFS spectroscopy, as well as with elemental analysis and ESI-MS. RESULTS The results showed that numerous compounds other than methanobactin were present in the isolate obtained with resin extraction. Molar C/N ratios, mass spectrometry measurements, and UV-vis spectra indicated that methanobactin was only present in one of the HPLC fractions. On a mass basis, methanobactin carbon contributed only 32% to the total organic carbon isolated with resin extraction. Our spectroscopic results implied that besides methanobactin, the organic compounds in the resin extract comprised breakdown products of methanobactin as well as polysaccharide-like substances. CONCLUSION Our results demonstrate that a purification step is indispensable in addition to resin extraction in order to obtain pure methanobactin. The proposed HPLC purification procedure is suitable for semi-preparative work and provides copper-free methanobactin.
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Affiliation(s)
- Marie-Laure Pesch
- Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Sciences, ETH Zurich, CHN, Universitätstrasse 16, 8092 Zurich, Switzerland
| | - Iso Christl
- Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Sciences, ETH Zurich, CHN, Universitätstrasse 16, 8092 Zurich, Switzerland
| | - Kurt Barmettler
- Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Sciences, ETH Zurich, CHN, Universitätstrasse 16, 8092 Zurich, Switzerland
| | - Stephan M Kraemer
- Department of Environmental Geosciences, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Ruben Kretzschmar
- Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Sciences, ETH Zurich, CHN, Universitätstrasse 16, 8092 Zurich, Switzerland
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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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The geochemical record of the ancient nitrogen cycle, nitrogen isotopes, and metal cofactors. Methods Enzymol 2011; 486:483-506. [PMID: 21185450 DOI: 10.1016/b978-0-12-381294-0.00022-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The nitrogen (N) cycle is the only global biogeochemical cycle that is driven by biological functions involving the interaction of many microorganisms. The N cycle has evolved over geological time and its interaction with the oxygen cycle has had profound effects on the evolution and timing of Earth's atmosphere oxygenation (Falkowski and Godfrey, 2008). Almost every enzyme that microorganisms use to manipulate N contains redox-sensitive metals. Bioavailability of these metals has changed through time as a function of varying redox conditions, and likely influenced the biological underpinnings of the N cycle. It is possible to construct a record through geological time using N isotopes and metal concentrations in sediments to determine when the different stages of the N cycle evolved and the role metal availability played in the development of key enzymes. The same techniques are applicable to understanding the operation and changes in the N cycle through geological time. However, N and many of the redox-sensitive metals in some of their oxidation states are mobile and the isotopic composition or distribution can be altered by subsequent processes leading to erroneous conclusions. This chapter reviews the enzymology and metal cofactors of the N cycle and describes proper utilization of methods used to reconstruct evolution of the N cycle through time.
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25
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Abstract
Whole-cell biocatalysis utilizes native or recombinant enzymes produced by cellular metabolism to perform synthetically interesting reactions. Besides hydrolases, oxidoreductases represent the most applied enzyme class in industry. Oxidoreductases are attributed a high future potential, especially for applications in the chemical and pharmaceutical industries, as they enable highly interesting chemistry (e.g., the selective oxyfunctionalization of unactivated C-H bonds). Redox reactions are characterized by electron transfer steps that often depend on redox cofactors as additional substrates. Their regeneration typically is accomplished via the metabolism of whole-cell catalysts. Traditionally, studies towards productive redox biocatalysis focused on the biocatalytic enzyme, its activity, selectivity, and specificity, and several successful examples of such processes are running commercially. However, redox cofactor regeneration by host metabolism was hardly considered for the optimization of biocatalytic rate, yield, and/or titer. This article reviews molecular mechanisms of oxidoreductases with synthetic potential and the host redox metabolism that fuels biocatalytic reactions with redox equivalents. The tools discussed in this review for investigating redox metabolism provide the basis for studies aiming at a deeper understanding of the interplay between synthetically active enzymes and metabolic networks. The ultimate goal of rational whole-cell biocatalyst engineering and use for fine chemical production is discussed.
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Dioxygen activation responsible for oxidation of aliphatic and aromatic hydrocarbon compounds: current state and variants. Appl Microbiol Biotechnol 2010; 87:1595-603. [DOI: 10.1007/s00253-010-2715-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Revised: 06/03/2010] [Accepted: 06/05/2010] [Indexed: 10/19/2022]
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Balasubramanian R, Smith SM, Rawat S, Yatsunyk LA, Stemmler TL, Rosenzweig AC. Oxidation of methane by a biological dicopper centre. Nature 2010; 465:115-9. [PMID: 20410881 PMCID: PMC2999467 DOI: 10.1038/nature08992] [Citation(s) in RCA: 381] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2009] [Accepted: 03/05/2010] [Indexed: 11/23/2022]
Abstract
Vast world reserves of methane gas are underutilized as a feedstock for the production of liquid fuels and chemicals owing to the lack of economical and sustainable strategies for the selective oxidation of methane to methanol. Current processes to activate the strong C-H bond (104 kcal mol(-1)) in methane require high temperatures, are costly and inefficient, and produce waste. In nature, methanotrophic bacteria perform this reaction under ambient conditions using metalloenzymes called methane monooxygenases (MMOs). MMOs thus provide the optimal model for an efficient, environmentally sound catalyst. There are two types of MMO. Soluble MMO (sMMO) is expressed by several strains of methanotroph under copper-limited conditions and oxidizes methane with a well-characterized catalytic di-iron centre. Particulate MMO (pMMO) is an integral membrane metalloenzyme produced by all methanotrophs and is composed of three subunits, pmoA, pmoB and pmoC, arranged in a trimeric alpha(3)beta(3)gamma(3) complex. Despite 20 years of research and the availability of two crystal structures, the metal composition and location of the pMMO metal active site are not known. Here we show that pMMO activity is dependent on copper, not iron, and that the copper active site is located in the soluble domains of the pmoB subunit rather than within the membrane. Recombinant soluble fragments of pmoB (spmoB) bind copper and have propylene and methane oxidation activities. Disruption of each copper centre in spmoB by mutagenesis indicates that the active site is a dicopper centre. These findings help resolve the pMMO controversy and provide a promising new approach to developing environmentally friendly C-H oxidation catalysts.
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Affiliation(s)
- Ramakrishnan Balasubramanian
- Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, Evanston, Illinois 60208, USA
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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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