1
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Peng W, Wang Z, Zhang Q, Yan S, Wang B. Unraveling the Valence State and Reactivity of Copper Centers in Membrane-Bound Particulate Methane Monooxygenase. J Am Chem Soc 2023; 145:25304-25317. [PMID: 37955571 DOI: 10.1021/jacs.3c08834] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
Particulate methane monooxygenase (pMMO) plays a critical role in catalyzing the conversion of methane to methanol, constituting the initial step in the C1 metabolic pathway within methanotrophic bacteria. However, the membrane-bound pMMO's structure and catalytic mechanism, notably the copper's valence state and genuine active site for methane oxidation, have remained elusive. Based on the recently characterized structure of membrane-bound pMMO, extensive computational studies were conducted to address these long-standing issues. A comprehensive analysis comparing the quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulated structures with cryo-EM data indicates that both the CuC and CuD sites tend to stay in the Cu(I) valence state within the membrane environment. Additionally, the concurrent presence of Cu(I) at both CuC and CuD sites leads to the significant reduction of the ligand-binding cavity situated between them, making it less likely to accommodate a reductant molecule such as durohydroquinone (DQH2). Subsequent QM/MM calculations reveal that the CuD(I) site is more reactive than the CuC(I) site in oxygen activation, en route to H2O2 formation and the generation of Cu(II)-O•- species. Finally, our simulations demonstrate that the natural reductant ubiquinol (CoQH2) assumes a productive binding conformation at the CuD(I) site but not at the CuC(I) site. This provides evidence that the true active site of membrane-bound pMMOs may be CuD rather than CuC. These findings clarify pMMO's catalytic mechanism and emphasize the membrane environment's pivotal role in modulating the coordination structure and the activity of copper centers within pMMO.
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Affiliation(s)
- Wei Peng
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, P. R. China
- Key Laboratory of Aerosol Chemistry and Physics, State Key Laboratory of Loess and Quaternary Geology (SKLLQG), Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710061, P. R. China
| | - Zikuan Wang
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an der Ruhr 45470, Germany
| | - Qiaoyu Zhang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, P. R. China
| | - Shengheng Yan
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, P. R. China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, P. R. China
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2
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Thi Quynh Le H, Yeol Lee E. Methanotrophs: Metabolic versatility from utilization of methane to multi-carbon sources and perspectives on current and future applications. BIORESOURCE TECHNOLOGY 2023:129296. [PMID: 37302766 DOI: 10.1016/j.biortech.2023.129296] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 05/29/2023] [Accepted: 06/07/2023] [Indexed: 06/13/2023]
Abstract
The development of biorefineries for a sustainable bioeconomy has been driven by the concept of utilizing environmentally friendly and cost-effective renewable energy sources. Methanotrophic bacteria with a unique capacity to utilize methane as a carbon and energy source can serve as outstanding biocatalysts to develop C1 bioconversion technology. By establishing the utilization of diverse multi-carbon sources, integrated biorefinery platforms can be created for the concept of the circular bioeconomy. An understanding of physiology and metabolism could help to overcome challenges for biomanufacturing. This review summaries fundamental gaps for methane oxidation and the capability to utilize multi-carbon sources in methanotrophic bacteria. Subsequently, breakthroughs and challenges in harnessing methanotrophs as robust microbial chassis for industrial biotechnology were compiled and overviewed. Finally, capabilities to exploit the inherent advantages of methanotrophs to synthesize various target products in higher titers are proposed.
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Affiliation(s)
- Hoa Thi Quynh Le
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin 17104, Republic of Korea
| | - Eun Yeol Lee
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin 17104, Republic of Korea.
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3
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Amrutha K, Kathirvelu V. Interpretation of EPR and optical spectra of Ni(II) ions in crystalline lattices at ambient temperature. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2022; 60:414-421. [PMID: 34859492 DOI: 10.1002/mrc.5237] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/24/2021] [Accepted: 11/25/2021] [Indexed: 06/13/2023]
Abstract
Many biologically important paramagnetic metal ions are characterized by electron paramagnetic resonance (EPR) spectroscopy to use as spin probes to investigate the structure and function of biomolecules. Though nickel(II) ions are an essential trace element and part of many biomolecules, the EPR properties are least understood. Herein, the EPR and optical absorption spectra measured at 300 K for Ni(II) ions diluted in two different diamagnetic hosts are investigated and reported. The EPR spectrum of a polycrystalline Ni/Mg(3-methylpyrazole)6 (ClO4 )2 [Ni/MMPC] shows two transitions at X-band frequency (~9.5 GHz), suggesting the zero-field splitting parameter (D) is larger than the resonance field of the free electron (Ho ). This incomplete and complex spectrum is successfully analyzed to obtain EPR parameters. The EPR spectrum of the polycrystalline Ni/Zn(pyrazole)6 (NO3 )2 [Ni/ZPN] shows a triplet spectrum indicating D < Ho . A detailed analysis of single-crystal EPR data yielded the spin Hamiltonian parameters. The optical absorption spectra are deconvoluted to understand the symmetry of the coordination environment in the complex.
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Affiliation(s)
- Kamalon Amrutha
- Department of Applied Sciences, National Institute of Technology Goa, Ponda, India
| | - Velavan Kathirvelu
- Department of Applied Sciences, National Institute of Technology Goa, Ponda, India
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4
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Jaiswal KK, Dutta S, Banerjee I, Pohrmen CB, Singh RK, Das HT, Dubey S, Kumar V. Impact of aquatic microplastics and nanoplastics pollution on ecological systems and sustainable remediation strategies of biodegradation and photodegradation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:151358. [PMID: 34736954 DOI: 10.1016/j.scitotenv.2021.151358] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 06/13/2023]
Abstract
The extreme degree of microplastics contamination and its negative impact on ecosystems has become a serious and emerging global concern. Microplastics are mainly generated from products that are used primarily in our everyday lives and are also generated from the fragmentation of larger plastic wastes. It easily penetrates the food chain and, when ingested by aquatic animals or humans, can pose serious health problems. Recently, several technologies have been developed to control the unrestricted spread of microplastics and possibly eradicate them; however, still under investigation. In this review, we have illustrated the types of microplastics, their harmful effect on living things, and the progress to degrade them to protect the environment and life on earth. Several promising and eco-friendly technologies including microbial and enzymatic approaches are enticing to eliminate the microplastics. Also, the photodegradation of microplastics contaminations appeals as a more fascinating approach. The metal oxide-assisted photodegradation of microplastics has also been taken into account. This work presented an impact on the comprehensive research for the effective degradation of different microplastic compositions as well as emerging green approaches for a sustainable environment and a healthier life.
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Affiliation(s)
- Krishna Kumar Jaiswal
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban 4000, South Africa.
| | - Swapnamoy Dutta
- Department of Green Energy Technology, Pondicherry University, Puducherry 605014, India
| | - Ishita Banerjee
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996, United States
| | | | - Ram Kishore Singh
- Department of Nanoscience and Technology, Central University of Jharkhand, Ranchi, Jharkhand 835222, India
| | - Himadri Tanaya Das
- Centers of Excellence for Advanced Materials and Application, Utkal University, Bhubaneswar, Odisha 751004, India
| | - Swati Dubey
- Academy of Scientific and innovative research, CSIR - Advanced Materials and Process Research Institutes, Bhopal, Madhya Pradesh 462026, India
| | - Vinod Kumar
- Department of Life Sciences, Graphic Era (Deemed to Be University), Dehradun, Uttarakhand, 248002, India; Peoples' Friendship University of Russia (RUDN University), Moscow 117198, Russian Federation.
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5
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Peifer R, Müller L, Hoof S, Beckmann F, Cula B, Limberg C. Mimicking of the histidine brace structural motif in molecular copper(I) compounds. Z Anorg Allg Chem 2021. [DOI: 10.1002/zaac.202100145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- R. Peifer
- Institut für Chemie Humboldt-Universität zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
| | - L. Müller
- Institut für Chemie Humboldt-Universität zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
| | - S. Hoof
- Institut für Chemie Humboldt-Universität zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
| | - F. Beckmann
- Institut für Chemie Humboldt-Universität zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
| | - B. Cula
- Institut für Chemie Humboldt-Universität zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
| | - C. Limberg
- Institut für Chemie Humboldt-Universität zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
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6
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Jodts RJ, Ross MO, Koo CW, Doan PE, Rosenzweig AC, Hoffman BM. Coordination of the Copper Centers in Particulate Methane Monooxygenase: Comparison between Methanotrophs and Characterization of the Cu C Site by EPR and ENDOR Spectroscopies. J Am Chem Soc 2021; 143:15358-15368. [PMID: 34498465 DOI: 10.1021/jacs.1c07018] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In nature, methane is oxidized to methanol by two enzymes, the iron-dependent soluble methane monooxygenase (sMMO) and the copper-dependent particulate MMO (pMMO). While sMMO's diiron metal active site is spectroscopically and structurally well-characterized, pMMO's copper sites are not. Recent EPR and ENDOR studies have established the presence of two monocopper sites, but the coordination environment of only one has been determined, that within the PmoB subunit and denoted CuB. Moreover, this recent work only focused on a type I methanotrophic pMMO, while previous observations of the type II enzyme were interpreted in terms of the presence of a dicopper site. First, this report shows that the type II Methylocystis species strain Rockwell pMMO, like the type I pMMOs, contains two monocopper sites and that its CuB site has a coordination environment identical to that of type I enzymes. As such, for the full range of pMMOs this report completes the refutation of prior and ongoing suggestions of multicopper sites. Second, and of primary importance, EPR/ENDOR measurements (a) for the first time establish the coordination environment of the spectroscopically observed site, provisionally denoted CuC, in both types of pMMO, thereby (b) establishing the assignment of this site observed by EPR to the crystallographically observed metal-binding site in the PmoC subunit. Finally, these results further indicate that CuC is the likely site of biological methane oxidation by pMMO, a conclusion that will serve as a foundation for proposals regarding the mechanism of this reaction.
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Affiliation(s)
- Richard J Jodts
- Departments of Chemistry and Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Matthew O Ross
- Departments of Chemistry and Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Christopher W Koo
- Departments of Chemistry and Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Peter E Doan
- Departments of Chemistry and Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Amy C Rosenzweig
- Departments of Chemistry and Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Brian M Hoffman
- Departments of Chemistry and Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
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7
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Affiliation(s)
- Judith Münch
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Saale, Germany
| | - Pascal Püllmann
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Saale, Germany
| | - Wuyuan Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West seventh Avenue, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, 32 West seventh Avenue, Tianjin 300308, China
| | - Martin J. Weissenborn
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Saale, Germany
- Institute of Chemistry, MartinLuther-University Halle-Wittenberg, Kurt-Mothes-Strasse 2, 06120, Halle, Saale, Germany
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8
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Stöhr F, Kulhanek N, Becker J, Göttlich R, Schindler S. Reactivity of Copper(I) Complexes Containing Ligands Derived from (1
S
,3
R
)‐Camphoric Acid with Dioxygen. Eur J Inorg Chem 2021. [DOI: 10.1002/ejic.202100187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Fabian Stöhr
- Institute for Inorganic and Analytical Chemistry Justus-Liebig-University Gießen Heinrich-Buff-Ring 17 35392 Gießen Germany
- Institute for Organic Chemistry Justus-Liebig-University Gießen Heinrich-Buff-Ring 17 35392 Gießen Germany
| | - Niclas Kulhanek
- Institute for Organic Chemistry Justus-Liebig-University Gießen Heinrich-Buff-Ring 17 35392 Gießen Germany
| | - Jonathan Becker
- Institute for Inorganic and Analytical Chemistry Justus-Liebig-University Gießen Heinrich-Buff-Ring 17 35392 Gießen Germany
| | - Richard Göttlich
- Institute for Organic Chemistry Justus-Liebig-University Gießen Heinrich-Buff-Ring 17 35392 Gießen Germany
| | - Siegfried Schindler
- Institute for Inorganic and Analytical Chemistry Justus-Liebig-University Gießen Heinrich-Buff-Ring 17 35392 Gießen Germany
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9
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Lashanizadegan M, Asna Ashari H, Sarkheil M, Anafcheh M, Jahangiry S. New Cu(II), Co(II) and Ni(II) azo-Schiff base complexes: Synthesis, characterization, catalytic oxidation of alkenes and DFT study. Polyhedron 2021. [DOI: 10.1016/j.poly.2021.115148] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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10
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Peng W, Qu X, Shaik S, Wang B. Deciphering the oxygen activation mechanism at the CuC site of particulate methane monooxygenase. Nat Catal 2021. [DOI: 10.1038/s41929-021-00591-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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11
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Cutsail GE, Ross MO, Rosenzweig AC, DeBeer S. Towards a unified understanding of the copper sites in particulate methane monooxygenase: an X-ray absorption spectroscopic investigation. Chem Sci 2021; 12:6194-6209. [PMID: 33996018 PMCID: PMC8098663 DOI: 10.1039/d1sc00676b] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The enzymatic conversion of the greenhouse gas, methane, to a liquid fuel, methanol, is performed by methane monooxygenases (MMOs) under mild conditions. The copper stoichiometry of particulate MMO (pMMO) has been long debated, with a dicopper site previously proposed on the basis of a 2.51 Å Cu–Cu feature in extended X-ray absorption fine structure (EXAFS) data. However, recent crystallographic data and advanced electron paramagnetic resonance (EPR) characterization support the presence of only mononuclear copper sites. To reconcile these data, we have collected high-energy resolution fluorescence detected (HERFD) and partial fluorescence yield (PFY) EXAFS spectra of Methylococcus (M.) capsulatus (Bath) pMMO. Both methods reveal only monocopper sites. These data were compared to previously published pMMO PFY-EXAFS data from M. capsulatus (Bath) and Methylomicrobium alcaliphilum 20Z, supporting dicopper and monocopper sites, respectively. The FT-EXAFS feature previously attributed to a dicopper site can be reproduced by the inclusion of a metallic copper background signal. The exact position of this feature is dependent on the nature of the sample and the percentage of background contamination, indicating that visual inspection is not sufficient for identifying background metallic contributions. Additionally, an undamaged X-ray absorption spectrum was obtained, consistent with the copper oxidation-state speciation determined by EPR quantification. X-ray photodamage studies suggest that the previously observed Cu(i) XAS features are in part attributable to photodamage. This study illustrates the complex array of factors involved in EXAFS measurement and modeling of pMMO and more generally, dilute metalloproteins with multiple metal centers. Extended X-ray absorption fine structure spectroscopic analysis of particulate methane monooxygenase reveals only monocopper sites and investigates the possible origins of the previous observed dicopper signals.![]()
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Affiliation(s)
- George E Cutsail
- Max Planck Institute for Chemical Energy Conversion Stiftstrasse 34-36 D-45470 Mülheim an der Ruhr Germany .,University of Duisburg-Essen Universitätsstrasse 7 D-45151 Essen Germany
| | - Matthew O Ross
- Departments of Molecular Biosciences and Chemistry, Northwestern University Evanston 60208 IL USA
| | - Amy C Rosenzweig
- Departments of Molecular Biosciences and Chemistry, Northwestern University Evanston 60208 IL USA
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion Stiftstrasse 34-36 D-45470 Mülheim an der Ruhr Germany
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12
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Ikeda K, Mahyuddin MH, Shiota Y, Yoshizawa K. Active Catalyst for Methane Hydroxylation by an Iridium–Oxo Complex. ACS Catal 2020. [DOI: 10.1021/acscatal.0c01610] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Kei Ikeda
- Institute for Materials Chemistry and Engineering and Integrated Research Consortium on Chemical Science (IRCCS), Kyushu University, Fukuoka 819-0395, Japan
| | - Muhammad Haris Mahyuddin
- Research Group of Advanced Functional Materials, Faculty of Industrial Technology, Institut Teknologi Bandung, Jl. Ganesha 10, Bandung 40132, Indonesia
- Research Center for Nanoscience and Nanotechnology, Institut Teknologi Bandung, Jl. Ganesha 10, Bandung 40132, Indonesia
| | - Yoshihito Shiota
- Institute for Materials Chemistry and Engineering and Integrated Research Consortium on Chemical Science (IRCCS), Kyushu University, Fukuoka 819-0395, Japan
| | - Kazunari Yoshizawa
- Institute for Materials Chemistry and Engineering and Integrated Research Consortium on Chemical Science (IRCCS), Kyushu University, Fukuoka 819-0395, Japan
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13
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Shteinman AA. Bioinspired Oxidation of Methane: From Academic Models of Methane Monooxygenases to Direct Conversion of Methane to Methanol. KINETICS AND CATALYSIS 2020. [DOI: 10.1134/s0023158420030180] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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14
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Ikeda K, Mahyuddin MH, Shiota Y, Staykov A, Matsumoto T, Ogo S, Yoshizawa K. Computational Study on the Light-Induced Oxidation of Iridium-Aqua Complex to Iridium-Oxo Complex over WO 3(001) Surface. Inorg Chem 2019; 59:415-422. [PMID: 31829576 DOI: 10.1021/acs.inorgchem.9b02704] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
An iridium aqua complex [IrIII(η5-C5Me5){bpy(COOH)2}(H2O)]2+ under visible light irradiation has been experimentally reported to form an iridium-oxo (Ir-oxo) complex [IrV(η5-C5Me5){bpy(COOH)2}(O)]2+, which oxidizes H2O to O2. However, the mechanism for the formation of this Ir-oxo complex remains unclear, due to the difficulties in observing the unstable Ir-oxo complex and computing light-induced systems having different numbers of electrons. In this study, we perform density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations to investigate more in detail our previously proposed deprotonation and light-induced oxidation reactions composing the formation of the Ir-oxo complex. In particular, we discuss effects of light irradiation and WO3 support on the formation of the Ir-oxo complex. We suggest two distinct mechanisms, that is, direct and indirect for the light-induced oxidation. In the direct mechanism electrons are directly transferred from the occupied π* orbitals of IrIII-OH or IrIV=O• to the conduction band of the WO3 surface, whereas in the indirect mechanism electrons are first excited from the valence band to the conduction band of the WO3 surface due to the UV light, and then the resultant electron hole oxidizes the Ir complex. In the direct mechanism, in particular, we found that the lowest energy of the anode's conduction band determines the adsorption wavelength of the light irradiation, enabling us to predict alternative semiconductor anodes for more efficient formation of the Ir-oxo complex.
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Affiliation(s)
- Kei Ikeda
- Institute for Materials Chemistry and Engineering , Kyushu University , Fukuoka 819-0395 , Japan
| | - Muhammad Haris Mahyuddin
- Institute for Materials Chemistry and Engineering , Kyushu University , Fukuoka 819-0395 , Japan
| | - Yoshihito Shiota
- Institute for Materials Chemistry and Engineering , Kyushu University , Fukuoka 819-0395 , Japan
| | - Aleksandar Staykov
- International Institute for Carbon-Neutral Energy Research (WPI-I2CNER) , Kyushu University , Fukuoka 819-0395 , Japan
| | - Takahiro Matsumoto
- International Institute for Carbon-Neutral Energy Research (WPI-I2CNER) , Kyushu University , Fukuoka 819-0395 , Japan.,Department of Chemistry and Biochemistry, Graduate School of Engineering , Kyushu University , Fukuoka 819-0395 , Japan.,Center for Small Molecule Energy , Kyushu University , Fukuoka 819-0395 , Japan
| | - Seiji Ogo
- International Institute for Carbon-Neutral Energy Research (WPI-I2CNER) , Kyushu University , Fukuoka 819-0395 , Japan.,Department of Chemistry and Biochemistry, Graduate School of Engineering , Kyushu University , Fukuoka 819-0395 , Japan.,Center for Small Molecule Energy , Kyushu University , Fukuoka 819-0395 , Japan
| | - Kazunari Yoshizawa
- Institute for Materials Chemistry and Engineering , Kyushu University , Fukuoka 819-0395 , Japan.,International Institute for Carbon-Neutral Energy Research (WPI-I2CNER) , Kyushu University , Fukuoka 819-0395 , Japan.,Department of Chemistry and Biochemistry, Graduate School of Engineering , Kyushu University , Fukuoka 819-0395 , Japan.,Center for Small Molecule Energy , Kyushu University , Fukuoka 819-0395 , Japan
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15
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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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16
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Abstract
Copper is a redox-active transition metal ion required for the function of many essential human proteins. For biosynthesis of proteins coordinating copper, the metal may bind before, during or after folding of the polypeptide. If the metal binds to unfolded or partially folded structures of the protein, such coordination may modulate the folding reaction. The molecular understanding of how copper is incorporated into proteins requires descriptions of chemical, thermodynamic, kinetic and structural parameters involved in the formation of protein-metal complexes. Because free copper ions are toxic, living systems have elaborate copper-transport systems that include particular proteins that facilitate efficient and specific delivery of copper ions to target proteins. Therefore, these pathways become an integral part of copper protein folding in vivo. This review summarizes biophysical-molecular in vitro work assessing the role of copper in folding and stability of copper-binding proteins as well as protein-protein copper exchange reactions between human copper transport proteins. We also describe some recent findings about the participation of copper ions and copper proteins in protein misfolding and aggregation reactions in vitro.
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17
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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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18
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Tao W, Bower JK, Moore CE, Zhang S. Dicopper μ-Oxo, μ-Nitrosyl Complex from the Activation of NO or Nitrite at a Dicopper Center. J Am Chem Soc 2019; 141:10159-10164. [PMID: 31244169 DOI: 10.1021/jacs.9b03635] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Wenjie Tao
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Jamey K. Bower
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Curtis E. Moore
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Shiyu Zhang
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
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19
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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: 171] [Impact Index Per Article: 34.2] [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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20
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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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21
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Baek J, Rungtaweevoranit B, Pei X, Park M, Fakra SC, Liu YS, Matheu R, Alshmimri SA, Alshehri S, Trickett CA, Somorjai GA, Yaghi OM. Bioinspired Metal–Organic Framework Catalysts for Selective Methane Oxidation to Methanol. J Am Chem Soc 2018; 140:18208-18216. [DOI: 10.1021/jacs.8b11525] [Citation(s) in RCA: 200] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
| | | | | | - Myeongkee Park
- Department of Chemistry, College of Natural Science, Dong-A University, Busan 49315, Republic of Korea
| | | | | | | | | | - Saeed Alshehri
- King Abdulaziz City for Science and Technology, Riyadh 12354, Saudi Arabia
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22
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23
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Ro SY, Ross MO, Deng YW, Batelu S, Lawton TJ, Hurley JD, Stemmler TL, Hoffman BM, Rosenzweig AC. From micelles to bicelles: Effect of the membrane on particulate methane monooxygenase activity. J Biol Chem 2018; 293:10457-10465. [PMID: 29739854 DOI: 10.1074/jbc.ra118.003348] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Revised: 05/06/2018] [Indexed: 11/06/2022] Open
Abstract
Particulate methane monooxygenase (pMMO) is a copper-dependent integral membrane metalloenzyme that converts methane to methanol in methanotrophic bacteria. Studies of isolated pMMO have been hindered by loss of enzymatic activity upon its removal from the native membrane. To characterize pMMO in a membrane-like environment, we reconstituted pMMOs from Methylococcus (Mcc.) capsulatus (Bath) and Methylomicrobium (Mm.) alcaliphilum 20Z into bicelles. Reconstitution into bicelles recovers methane oxidation activity lost upon detergent solubilization and purification without substantial alterations to copper content or copper electronic structure, as observed by electron paramagnetic resonance (EPR) spectroscopy. These findings suggest that loss of pMMO activity upon isolation is due to removal from the membranes rather than caused by loss of the catalytic copper ions. A 2.7 Å resolution crystal structure of pMMO from Mm. alcaliphilum 20Z reveals a mononuclear copper center in the PmoB subunit and indicates that the transmembrane PmoC subunit may be conformationally flexible. Finally, results from extended X-ray absorption fine structure (EXAFS) analysis of pMMO from Mm. alcaliphilum 20Z were consistent with the observed monocopper center in the PmoB subunit. These results underscore the importance of studying membrane proteins in a membrane-like environment and provide valuable insight into pMMO function.
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Affiliation(s)
- Soo Y Ro
- From the Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, Illinois 60208 and
| | - Matthew O Ross
- From the Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, Illinois 60208 and
| | - Yue Wen Deng
- From the Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, Illinois 60208 and
| | - Sharon Batelu
- the Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan 48201
| | - Thomas J Lawton
- From the Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, Illinois 60208 and
| | - Joseph D Hurley
- From the Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, Illinois 60208 and
| | - Timothy L Stemmler
- the Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan 48201
| | - Brian M Hoffman
- From the Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, Illinois 60208 and
| | - Amy C Rosenzweig
- From the Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, Illinois 60208 and
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24
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Matsuo T, Kono T, Shobu I, Ishida M, Gonda K, Hirota S. Global Structural Flexibility of Metalloproteins Regulates Reactivity of Transition Metal Ion in the Protein Core: An Experimental Study Using Thiol-subtilisin as a Model Protein. Chemistry 2018; 24:2767-2775. [DOI: 10.1002/chem.201705920] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Takashi Matsuo
- Graduate School of Materials Science; Nara Institute of Science and Technology (NAIST); 8916-5 Takayama-cho Ikoma Nara 630-0192 Japan
| | - Takamasa Kono
- Graduate School of Materials Science; Nara Institute of Science and Technology (NAIST); 8916-5 Takayama-cho Ikoma Nara 630-0192 Japan
| | - Isamu Shobu
- Graduate School of Materials Science; Nara Institute of Science and Technology (NAIST); 8916-5 Takayama-cho Ikoma Nara 630-0192 Japan
| | - Masaya Ishida
- Graduate School of Materials Science; Nara Institute of Science and Technology (NAIST); 8916-5 Takayama-cho Ikoma Nara 630-0192 Japan
| | - Katsuya Gonda
- Graduate School of Materials Science; Nara Institute of Science and Technology (NAIST); 8916-5 Takayama-cho Ikoma Nara 630-0192 Japan
| | - Shun Hirota
- Graduate School of Materials Science; Nara Institute of Science and Technology (NAIST); 8916-5 Takayama-cho Ikoma Nara 630-0192 Japan
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25
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Snyder BER, Bols ML, Schoonheydt RA, Sels BF, Solomon EI. Iron and Copper Active Sites in Zeolites and Their Correlation to Metalloenzymes. Chem Rev 2017; 118:2718-2768. [DOI: 10.1021/acs.chemrev.7b00344] [Citation(s) in RCA: 193] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Benjamin E. R. Snyder
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Max L. Bols
- Department of Microbial and Molecular Systems, Centre for Surface Chemistry and Catalysis, KU Leuven—University of Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Robert A. Schoonheydt
- Department of Microbial and Molecular Systems, Centre for Surface Chemistry and Catalysis, KU Leuven—University of Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Bert F. Sels
- Department of Microbial and Molecular Systems, Centre for Surface Chemistry and Catalysis, KU Leuven—University of Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Edward I. Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Photon Science, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
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26
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Stumpf TDJ, Steinbach M, Würtele C, Becker J, Becker S, Fröhlich R, Göttlich R, Schindler S. Reactivity of Copper Complexes with Bis(piperidinyl)methane and Bis(quinolinyl)methane Ligands. Eur J Inorg Chem 2017. [DOI: 10.1002/ejic.201700755] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Tim-Daniel J. Stumpf
- Institute for Inorganic and Analytical Chemistry; Justus-Liebig-University Gießen; Heinrich-Buff-Ring 17 35392 Gießen Germany
- Institute for Organic Chemistry; Justus-Liebig-University Gießen; Heinrich-Buff-Ring 17 35392 Gießen Germany
| | - Manfred Steinbach
- Institute for Inorganic and Analytical Chemistry; Justus-Liebig-University Gießen; Heinrich-Buff-Ring 17 35392 Gießen Germany
- Institute for Organic Chemistry; Justus-Liebig-University Gießen; Heinrich-Buff-Ring 17 35392 Gießen Germany
| | - Christian Würtele
- Institute for Inorganic and Analytical Chemistry; Justus-Liebig-University Gießen; Heinrich-Buff-Ring 17 35392 Gießen Germany
| | - Jonathan Becker
- Institute for Inorganic and Analytical Chemistry; Justus-Liebig-University Gießen; Heinrich-Buff-Ring 17 35392 Gießen Germany
| | - Sabine Becker
- Institute for Inorganic and Analytical Chemistry; Justus-Liebig-University Gießen; Heinrich-Buff-Ring 17 35392 Gießen Germany
| | - Roland Fröhlich
- Institute for Organic Chemistry; WWU Münster; Corrensstraße 40 48149 Münster Germany
| | - Richard Göttlich
- Institute for Organic Chemistry; Justus-Liebig-University Gießen; Heinrich-Buff-Ring 17 35392 Gießen Germany
| | - Siegfried Schindler
- Institute for Inorganic and Analytical Chemistry; Justus-Liebig-University Gießen; Heinrich-Buff-Ring 17 35392 Gießen Germany
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27
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Ipek B, Wulfers MJ, Kim H, Göltl F, Hermans I, Smith JP, Booksh KS, Brown CM, Lobo RF. Formation of [Cu2O2]2+ and [Cu2O]2+ toward C–H Bond Activation in Cu-SSZ-13 and Cu-SSZ-39. ACS Catal 2017. [DOI: 10.1021/acscatal.6b03005] [Citation(s) in RCA: 160] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | - Hacksung Kim
- Department
of Chemistry, Center for Catalysis and Surface Science, Northwestern University, Evanston, Illinois 60208, United States
- Chemical
Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | | | | | | | | | - Craig M. Brown
- Center
for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
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28
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Mahyuddin MH, Staykov A, Shiota Y, Miyanishi M, Yoshizawa K. Roles of Zeolite Confinement and Cu–O–Cu Angle on the Direct Conversion of Methane to Methanol by [Cu2(μ-O)]2+-Exchanged AEI, CHA, AFX, and MFI Zeolites. ACS Catal 2017. [DOI: 10.1021/acscatal.7b00588] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- M. Haris Mahyuddin
- Institute
for Materials Chemistry and Engineering and IRCCS, Kyushu University, Fukuoka 819-0395, Japan
- Department
of Physics-Energy Engineering, Surya University, Tangerang 15810, Indonesia
| | - Aleksandar Staykov
- International
Institute for Carbon-Neutral Energy Research, Kyushu University, Fukuoka 819-0395, Japan
| | - Yoshihito Shiota
- Institute
for Materials Chemistry and Engineering and IRCCS, Kyushu University, Fukuoka 819-0395, Japan
| | - Mayuko Miyanishi
- Institute
for Materials Chemistry and Engineering and IRCCS, Kyushu University, Fukuoka 819-0395, Japan
| | - Kazunari Yoshizawa
- Institute
for Materials Chemistry and Engineering and IRCCS, Kyushu University, Fukuoka 819-0395, Japan
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29
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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: 148] [Impact Index Per Article: 21.1] [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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30
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Kochem A, Gennarini F, Yemloul M, Orio M, Le Poul N, Rivière E, Giorgi M, Faure B, Le Mest Y, Réglier M, Simaan AJ. Characterization of a Dinuclear Copper(II) Complex and Its Fleeting Mixed-Valent Copper(II)/Copper(III) Counterpart. Chempluschem 2017; 82:615-624. [DOI: 10.1002/cplu.201600636] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 02/14/2017] [Indexed: 01/06/2023]
Affiliation(s)
- Amélie Kochem
- Aix Marseille Université, CNRS; Centrale Marseille, iSm2; 13397 Marseille France
| | | | - Mehdi Yemloul
- Aix Marseille Université, CNRS; Centrale Marseille, iSm2; 13397 Marseille France
| | - Maylis Orio
- Aix Marseille Université, CNRS; Centrale Marseille, iSm2; 13397 Marseille France
| | - Nicolas Le Poul
- Université de Bretagne occidentale; CEMCA, UMR CNRS; 6521 Brest France
| | - Eric Rivière
- Institut de Chimie Moléculaire et des Matériaux d'Orsay; Univ Paris Sud, Université Paris-Saclay, CNRS; 91400 Orsay France
| | - Michel Giorgi
- Aix Marseille Université, CNRS; Spectropole FR1739; 13397 Marseille France
| | - Bruno Faure
- Aix Marseille Université, CNRS; Centrale Marseille, iSm2; 13397 Marseille France
| | - Yves Le Mest
- Université de Bretagne occidentale; CEMCA, UMR CNRS; 6521 Brest France
| | - Marius Réglier
- Aix Marseille Université, CNRS; Centrale Marseille, iSm2; 13397 Marseille France
| | - A. Jalila Simaan
- Aix Marseille Université, CNRS; Centrale Marseille, iSm2; 13397 Marseille France
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31
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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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32
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Lawton TJ, Rosenzweig AC. Biocatalysts for methane conversion: big progress on breaking a small substrate. Curr Opin Chem Biol 2016; 35:142-149. [PMID: 27768948 PMCID: PMC5161620 DOI: 10.1016/j.cbpa.2016.10.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 09/30/2016] [Accepted: 10/03/2016] [Indexed: 01/08/2023]
Abstract
Nature utilizes two groups of enzymes to catalyze methane conversions, methyl-coenzyme M reductases (MCRs) and methane monooxygenases (MMOs). These enzymes have been difficult to incorporate into industrial processes due to their complexity, poor stability, and lack of recombinant tractability. Despite these issues, new ways of preparing and stabilizing these enzymes have recently been discovered, and new mechanistic insight into how MCRs and MMOs break the C-H bond in nature's most inert hydrocarbon have been obtained. This review focuses on recent findings in the methane biocatalysis field, and discusses the impact of these finding on designing MMO and MCR-based biotechnologies.
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Affiliation(s)
- Thomas J Lawton
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Amy C Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL 60208, USA.
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33
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McMoran EP, Powell DR, Perez F, Rowe GT, Yang L. Synthesis and Characterization of Copper Complexes with CuICuI, Cu1.5Cu1.5m and CuIICuII Core Structures Supported by a Flexible Dipyridylamide Ligand. Inorg Chem 2016; 55:11462-11472. [DOI: 10.1021/acs.inorgchem.6b02006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ethan P. McMoran
- Department
of Chemistry, University of Central Arkansas, Conway, Arkansas 72035, United States
| | - Douglas R. Powell
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Felio Perez
- Integrated Microscopy Center, University of Memphis, Memphis, Tennessee 38152, United States
| | - Gerard T. Rowe
- Department
of Chemistry and Physics, University of South Carolina—Aiken, Aiken, South Carolina 29801, United States
| | - Lei Yang
- Department
of Chemistry, University of Central Arkansas, Conway, Arkansas 72035, United States
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34
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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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35
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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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36
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37
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Itoyama S, Doitomi K, Kamachi T, Shiota Y, Yoshizawa K. Possible Peroxo State of the Dicopper Site of Particulate Methane Monooxygenase from Combined Quantum Mechanics and Molecular Mechanics Calculations. Inorg Chem 2016; 55:2771-5. [DOI: 10.1021/acs.inorgchem.5b02603] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shuhei Itoyama
- Institute
for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan
| | - Kazuki Doitomi
- Institute
for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan
| | - Takashi Kamachi
- Institute
for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan
| | - Yoshihito Shiota
- Institute
for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan
| | - Kazunari Yoshizawa
- Institute
for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan
- Elements
Strategy Initiative for Catalysts and Batteries, Kyoto University, Kyoto 615-8245, Japan
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38
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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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39
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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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40
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Lee JY, Karlin KD. Elaboration of copper-oxygen mediated C-H activation chemistry in consideration of future fuel and feedstock generation. Curr Opin Chem Biol 2015; 25:184-93. [PMID: 25756327 DOI: 10.1016/j.cbpa.2015.02.014] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 02/12/2015] [Accepted: 02/16/2015] [Indexed: 12/21/2022]
Abstract
To contribute solutions to current energy concerns, improvements in the efficiency of dioxygen mediated C-H bond cleavage chemistry, for example, selective oxidation of methane to methanol, could minimize losses in natural gas usage or produce feedstocks for fuels. Oxidative C-H activation is also a component of polysaccharide degradation, potentially affording alternative biofuels from abundant biomass. Thus, an understanding of active-site chemistry in copper monooxygenases, those activating strong C-H bonds is briefly reviewed. Then, recent advances in the synthesis-generation and study of various copper-oxygen intermediates are highlighted. Of special interest are cupric-superoxide, Cu-hydroperoxo and Cu-oxy complexes. Such investigations can contribute to an enhanced future application of C-H oxidation or oxygenation processes using air, as concerning societal energy goals.
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Affiliation(s)
- Jung Yoon Lee
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Kenneth D Karlin
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA.
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