1
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Siegbahn PEM. Mechanisms for Methane and Ammonia Oxidation by Particulate Methane Monooxygenase. J Phys Chem B 2024; 128:5840-5845. [PMID: 38850249 PMCID: PMC11194816 DOI: 10.1021/acs.jpcb.4c01807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/18/2024] [Accepted: 05/28/2024] [Indexed: 06/10/2024]
Abstract
Particulate MMO (pMMO) catalyzes the oxidation of methane to methanol and also ammonia to hydroxylamine. Experimental characterization of the active site has been very difficult partly because the enzyme is membrane-bound. However, recently, there has been major progress mainly through the use of cryogenic electron microscopy (cryoEM). Electron paramagnetic resonance (EPR) and X-ray spectroscopy have also been employed. Surprisingly, the active site has only one copper. There are two histidine ligands and one asparagine ligand, and the active site is surrounded by phenyl alanines but no charged amino acids in the close surrounding. The present study is the first quantum chemical study using a model of that active site (CuD). Low barrier mechanisms have been found, where an important part is that there are two initial proton-coupled electron transfer steps to a bound O2 ligand before the substrate enters. Surprisingly, this leads to large radical character for the oxygens even though they are protonated. That result is very important for the ability to accept a proton from the substrates. Methods have been used which have been thoroughly tested for redox enzyme mechanisms.
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Affiliation(s)
- Per E. M. Siegbahn
- Department of Organic Chemistry,
Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
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2
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Tucci FJ, Rosenzweig AC. Direct Methane Oxidation by Copper- and Iron-Dependent Methane Monooxygenases. Chem Rev 2024; 124:1288-1320. [PMID: 38305159 PMCID: PMC10923174 DOI: 10.1021/acs.chemrev.3c00727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
Methane is a potent greenhouse gas that contributes significantly to climate change and is primarily regulated in Nature by methanotrophic bacteria, which consume methane gas as their source of energy and carbon, first by oxidizing it to methanol. The direct oxidation of methane to methanol is a chemically difficult transformation, accomplished in methanotrophs by complex methane monooxygenase (MMO) enzyme systems. These enzymes use iron or copper metallocofactors and have been the subject of detailed investigation. While the structure, function, and active site architecture of the copper-dependent particulate methane monooxygenase (pMMO) have been investigated extensively, its putative quaternary interactions, regulation, requisite cofactors, and mechanism remain enigmatic. The iron-dependent soluble methane monooxygenase (sMMO) has been characterized biochemically, structurally, spectroscopically, and, for the most part, mechanistically. Here, we review the history of MMO research, focusing on recent developments and providing an outlook for future directions of the field. Engineered biological catalysis systems and bioinspired synthetic catalysts may continue to emerge along with a deeper understanding of the molecular mechanisms of biological methane oxidation. Harnessing the power of these enzymes will necessitate combined efforts in biochemistry, structural biology, inorganic chemistry, microbiology, computational biology, and engineering.
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Affiliation(s)
- Frank J Tucci
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Amy C Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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3
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Spatola Rossi T, Fricker M, Kriechbaumer V. Gene Stacking and Stoichiometric Expression of ER-Targeted Constructs Using "2A" Self-Cleaving Peptides. Methods Mol Biol 2024; 2772:337-351. [PMID: 38411827 DOI: 10.1007/978-1-0716-3710-4_26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Simultaneous stoichiometric expression of multiple genes plays a major part in modern research and biotechnology. Traditional methods for incorporating multiple transgenes (or "gene stacking") have drawbacks such as long time frames, uneven gene expression, gene silencing, and segregation derived from the use of multiple promoters. 2A self-cleaving peptides have emerged over the last two decades as a functional gene stacking method and have been used in plants for the co-expression of multiple genes under a single promoter. Here we describe design features of multicistronic polyproteins using 2A peptides for co-expression in plant cells and targeting to the endoplasmic reticulum (ER). We designed up to quad-cistronic vectors that could target proteins in tandem to the ER. We also exemplify the incorporation of self-excising intein domains within 2A polypeptides, to remove residue additions. These features could aid in the design of stoichiometric protein co-expression strategies in plants in combination with targeting to different subcellular compartments.
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Affiliation(s)
- Tatiana Spatola Rossi
- Endomembrane Structure and Function Research Group, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Mark Fricker
- Department of Biology, University of Oxford, Oxford, UK
| | - Verena Kriechbaumer
- Endomembrane Structure and Function Research Group, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK.
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4
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Tucci FJ, Jodts RJ, Hoffman BM, Rosenzweig AC. Product analog binding identifies the copper active site of particulate methane monooxygenase. Nat Catal 2023; 6:1194-1204. [PMID: 38187819 PMCID: PMC10766429 DOI: 10.1038/s41929-023-01051-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 09/22/2023] [Indexed: 01/09/2024]
Abstract
Nature's primary methane-oxidizing enzyme, the membrane-bound particulate methane monooxygenase (pMMO), catalyzes the oxidation of methane to methanol. pMMO activity requires copper, and decades of structural and spectroscopic studies have sought to identify the active site among three candidates: the CuB, CuC, and CuD sites. Challenges associated with the isolation of active pMMO have hindered progress toward locating its catalytic center. However, reconstituting pMMO into native lipid nanodiscs stabilizes its structure and recovers its activity. Here, these active samples were incubated with 2,2,2,-trifluoroethanol (TFE), a product analog that serves as a readily visualized active-site probe. Interactions of TFE with the CuD site were observed by both pulsed ENDOR spectroscopy and cryoEM, implicating CuD and the surrounding hydrophobic pocket as the likely site of methane oxidation. Use of these orthogonal techniques on parallel samples is a powerful approach that can circumvent difficulties in interpreting metalloenzyme cryoEM maps.
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Affiliation(s)
- Frank J Tucci
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL, USA
- These authors contributed equally
| | - Richard J Jodts
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL, USA
- These authors contributed equally
| | - Brian M Hoffman
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL, USA
| | - Amy C Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL, USA
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5
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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: 6] [Impact Index Per Article: 6.0] [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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6
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Mohammed TP, George A, Sivaramakrishnan MP, Vadivelu P, Balasubramanian S, Sankaralingam M. Deciphering the effect of amine versus imine ligands of copper(II) complexes in 2-aminophenol oxidation. J Inorg Biochem 2023; 247:112309. [PMID: 37451084 DOI: 10.1016/j.jinorgbio.2023.112309] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/19/2023] [Accepted: 06/27/2023] [Indexed: 07/18/2023]
Abstract
A series of amine (1-6) and imine (5',6') based copper(II) complexes with tridentate (NNO) ligand donors were synthesized and characterized using modern analytical techniques. All the complexes were subjected to 2-aminophenol (OAP) oxidation to form 2-aminophenoxazin-3-one, as a functional analogue of an enzyme, phenoxazinone synthase. In addition, a critical comparison of the reactivity using the amine-based complexes with their respective imine counterparts was achieved in both experimental as well as theoretical studies. For instance, the kinetic measurement revealed that the imine-based copper(II) complexes (kcat, 2.4 × 105-6.2 × 106 h-1) are better than amine-based (kcat, 6.3 × 104-3.9 × 105 h-1) complexes. The complex-substrate adducts [Cu(L3)(OAP)] (7) and [Cu(L3')(OAP)] (7') were characterized for both systems by mass spectrometry. Further, the DFT study was performed with amine- (3) and imine- (3') based copper(II) complexes, to compare their efficacy in the oxidation of OAP. The mechanistic investigations reveal that the key elementary step to determine the reactivity of 3 and 3' is the proton-coupled electron transfer (PCET) step occurring from the intermediates 7/7'. Further, the computed HOMO-LUMO energy gap of 7' was smaller than 7 by 0.8 eV, which indicates the facile PCET compared to that of 7. Moreover, the coupling of the OAP moiety using imine-complexes (ΔGR.E = -5.8 kcal/mol) was found to be thermodynamically more favorable than amine complexes (ΔGR.E = +3.3 kcal/mol). Overall, the theoretical findings are in good agreement with the experimental results.
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Affiliation(s)
- Thasnim P Mohammed
- Bioinspired & Biomimetic Inorganic Chemistry Lab, Department of Chemistry, National Institute of Technology Calicut, Kozhikode, Kerala 673601, India
| | - Akhila George
- Bioinspired & Biomimetic Inorganic Chemistry Lab, Department of Chemistry, National Institute of Technology Calicut, Kozhikode, Kerala 673601, India
| | | | - Prabha Vadivelu
- Department of Chemistry, Central University of Tamil Nadu, Thiruvarur 610 005, India
| | - Sridhar Balasubramanian
- Centre for X-ray Crystallography, CSIR-Indian Institute of Chemical Technology, Hyderabad, Telangana 500007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Muniyandi Sankaralingam
- Bioinspired & Biomimetic Inorganic Chemistry Lab, Department of Chemistry, National Institute of Technology Calicut, Kozhikode, Kerala 673601, India.
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7
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Spatola Rossi T, Tolmie AF, Nichol T, Pain C, Harrison P, Smith TJ, Fricker M, Kriechbaumer V. Recombinant expression and subcellular targeting of the particulate methane monooxygenase (pMMO) protein components in plants. Sci Rep 2023; 13:15337. [PMID: 37714899 PMCID: PMC10504283 DOI: 10.1038/s41598-023-42224-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 09/07/2023] [Indexed: 09/17/2023] Open
Abstract
Methane is a potent greenhouse gas, which has contributed to approximately a fifth of global warming since pre-industrial times. The agricultural sector produces significant methane emissions, especially from livestock, waste management and rice cultivation. Rice fields alone generate around 9% of total anthropogenic emissions. Methane is produced in waterlogged paddy fields by methanogenic archaea, and transported to the atmosphere through the aerenchyma tissue of rice plants. Thus, bioengineering rice with catalysts to detoxify methane en route could contribute to an efficient emission mitigation strategy. Particulate methane monooxygenase (pMMO) is the predominant methane catalyst found in nature, and is an enzyme complex expressed by methanotrophic bacteria. Recombinant expression of pMMO has been challenging, potentially due to its membrane localization, multimeric structure, and polycistronic operon. Here we show the first steps towards the engineering of plants for methane detoxification with the three pMMO subunits expressed in the model systems tobacco and Arabidopsis. Membrane topology and protein-protein interactions were consistent with correct folding and assembly of the pMMO subunits on the plant ER. Moreover, a synthetic self-cleaving polypeptide resulted in simultaneous expression of all three subunits, although low expression levels precluded more detailed structural investigation. The work presents plant cells as a novel heterologous system for pMMO allowing for protein expression and modification.
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Affiliation(s)
- Tatiana Spatola Rossi
- Endomembrane Structure and Function Research Group, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
| | - A Frances Tolmie
- Endomembrane Structure and Function Research Group, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
| | - Tim Nichol
- Molecular Microbiology Research Group, Biomolecular Sciences Research Centre, Sheffield Hallam University, Sheffield, S1 1WB, UK
| | - Charlotte Pain
- Endomembrane Structure and Function Research Group, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
| | - Patrick Harrison
- Department of Biological and Marine Sciences, University of Hull, Hull, HU6 7RX, UK
| | - Thomas J Smith
- Molecular Microbiology Research Group, Biomolecular Sciences Research Centre, Sheffield Hallam University, Sheffield, S1 1WB, UK
| | - Mark Fricker
- Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Verena Kriechbaumer
- Endomembrane Structure and Function Research Group, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK.
- Centre for Bioimaging, Oxford Brookes University, Oxford, UK.
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8
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Weng C, Peng X, Han Y. From methane to value-added bioproducts: microbial metabolism, enzymes, and metabolic engineering. ADVANCES IN APPLIED MICROBIOLOGY 2023; 124:119-146. [PMID: 37597946 DOI: 10.1016/bs.aambs.2023.07.004] [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] [Indexed: 08/21/2023]
Abstract
Methane is abundant in nature, and excessive emissions will cause the greenhouse effect. Methane is also an ideal carbon and energy feedstock for biosynthesis. In the review, the microorganisms, metabolism, and enzymes for methane utilization, and the advances of conversion to value-added bioproducts were summarized. First, the physiological characteristics, classification, and methane oxidation process of methanotrophs were introduced. The metabolic pathways for methane utilization and key intermediate metabolites of native and synthetic methanotrophs were summarized. Second, the enzymatic properties, crystal structures, and catalytic mechanisms of methane-oxidizing and metabolizing enzymes in methanotrophs were described. Third, challenges and prospects in metabolic pathways and enzymatic catalysis for methane utilization and conversion to value-added bioproducts were discussed. Finally, metabolic engineering of microorganisms for methane biooxidation and bioproducts synthesis based on different pathways were summarized. Understanding the metabolism and challenges of microbial methane utilization will provide insights into possible strategies for efficient methane-based synthesis.
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Affiliation(s)
- Caihong Weng
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, P.R. China; School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Xiaowei Peng
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, P.R. China; School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Yejun Han
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, P.R. China; School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, P.R. China.
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9
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Wu H, Xu S, Du P, Liu Y, Li H, Yang H, Wang T, Wang ZG. A nucleotide-copper(II) complex possessing a monooxygenase-like catalytic function. J Mater Chem B 2023. [PMID: 37409588 DOI: 10.1039/d3tb00780d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023]
Abstract
The de novo design of artificial biocatalysts with enzyme-like active sites and catalytic functions has long been an attractive yet challenging goal. In this study, we present a nucleotide-Cu2+ complex, synthesized through a one-pot approach, capable of catalyzing ortho-hydroxylation reactions resembling those of minimalist monooxygenases. Both experimental and theoretical findings demonstrate that the catalyst, in which Cu2+ coordinates with both the nucleobase and phosphate moieties, forms a ternary-complex intermediate with H2O2 and tyramine substrates through multiple weak interactions. The subsequent electron transfer and hydrogen (or proton) transfer steps lead to the ortho-hydroxylation of tyramine, where the single copper center exhibits a similar function to natural dicopper sites. Moreover, Cu2+ bound to nucleotides or oligonucleotides exhibits thermophilic catalytic properties within the temperature range of 25 °C to 75 °C, while native enzymes are fully deactivated above 35 °C. This study may provide insights for the future design of oxidase-mimetic catalysts and serve as a guide for the design of primitive metallocentre-dependent enzymes.
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Affiliation(s)
- Haifeng Wu
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, P. R. China.
| | - Shichao Xu
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, P. R. China.
| | - Peidong Du
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, P. R. China.
| | - Yuanxi Liu
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, P. R. China.
| | - Hui Li
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, P. R. China.
| | - Haijun Yang
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Ting Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Zhen-Gang Wang
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, P. R. China.
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10
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Ali Eltayb W, Abdalla M, Ahmed EL-Arabey A, Boufissiou A, Azam M, Al-Resayes SI, Alam M. Exploring particulate methane monooxygenase (pMMO) proteins using experimentation and computational molecular docking. JOURNAL OF KING SAUD UNIVERSITY - SCIENCE 2023; 35:102634. [DOI: https:/doi.org/10.1016/j.jksus.2023.102634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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11
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Ali Eltayb W, Abdalla M, Ahmed EL-Arabey A, Boufissiou A, Azam M, Al-Resayes SI, Alam M. Exploring particulate methane monooxygenase (pMMO) proteins using experimentation and computational molecular docking. JOURNAL OF KING SAUD UNIVERSITY - SCIENCE 2023; 35:102634. [DOI: 10.1016/j.jksus.2023.102634] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2024]
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12
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Hodgskiss LH, Melcher M, Kerou M, Chen W, Ponce-Toledo RI, Savvides SN, Wienkoop S, Hartl M, Schleper C. Unexpected complexity of the ammonia monooxygenase in archaea. THE ISME JOURNAL 2023; 17:588-599. [PMID: 36721060 PMCID: PMC10030591 DOI: 10.1038/s41396-023-01367-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 01/09/2023] [Accepted: 01/12/2023] [Indexed: 02/02/2023]
Abstract
Ammonia oxidation, as the first step of nitrification, constitutes a critical process in the global nitrogen cycle. However, fundamental knowledge of its key enzyme, the copper-dependent ammonia monooxygenase, is lacking, in particular for the environmentally abundant ammonia-oxidizing archaea (AOA). Here the structure of the enzyme is investigated by blue-native gel electrophoresis and proteomics from native membrane complexes of two AOA. Besides the known AmoABC subunits and the earlier predicted AmoX, two new protein subunits, AmoY and AmoZ, were identified. They are unique to AOA, highly conserved and co-regulated, and their genes are linked to other AMO subunit genes in streamlined AOA genomes. Modeling and in-gel cross-link approaches support an overall protomer structure similar to the distantly related bacterial particulate methane monooxygenase but also reveals clear differences in extracellular domains of the enzyme. These data open avenues for further structure-function studies of this ecologically important nitrification complex.
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Affiliation(s)
- Logan H Hodgskiss
- Archaea Biology and Ecogenomics Unit, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Michael Melcher
- Archaea Biology and Ecogenomics Unit, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Melina Kerou
- Archaea Biology and Ecogenomics Unit, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Weiqiang Chen
- Mass Spectrometry Facility, Max Perutz Labs, Vienna BioCenter (VBC), Vienna, Austria
| | - Rafael I Ponce-Toledo
- Archaea Biology and Ecogenomics Unit, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Savvas N Savvides
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Stefanie Wienkoop
- Molecular Systems Biology Unit, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Markus Hartl
- Mass Spectrometry Facility, Max Perutz Labs, Vienna BioCenter (VBC), Vienna, Austria
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Christa Schleper
- Archaea Biology and Ecogenomics Unit, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria.
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13
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Andrade LS, Lima HH, Silva CT, Amorim WL, Poço JG, López-Castillo A, Kirillova MV, Carvalho WA, Kirillov AM, Mandelli D. Metal–organic frameworks as catalysts and biocatalysts for methane oxidation: The current state of the art. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2023.215042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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14
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Liu Z, Wang J, Xie J, Yao D, Yang S, Ge J. Interactions among heavy metals and methane-metabolizing microorganisms and their effects on methane emissions in Dajiuhu peatland. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:37415-37426. [PMID: 36572772 DOI: 10.1007/s11356-022-24868-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 12/15/2022] [Indexed: 06/18/2023]
Abstract
Peatlands play a crucial role in mediating the emissions of methane through active biogeochemical cycling of accumulated carbon driven by methane-metabolizing microorganisms; meanwhile, they serve as vital archives of atmospheric heavy metal deposition. Despite many edaphic factors confirmed as determinants to modulate the structure of methanotrophic and methanogenic communities, recognition of interactions among them is limited. In this study, peat soils were collected from Dajiuhu peatland to assess the presence of heavy metals, and methanotrophs and methanogens were investigated via high-throughput sequencing for functional genes mcrA and pmoA. Further analyses of the correlations between methane-related functional groups were conducted. The results demonstrated that both methane-metabolizing microorganisms and heavy metals have prominent vertical heterogeneity upward and downward along the depth of 20 cm. Pb, Cd, and Hg strongly correlated with methanotrophs and methanogens across all seasons and depths, serving as forceful factors in structural variations of methanogenic and methanotrophic communities. Particularly, Pb, Cd, and Hg were identified as excessive elements in Dajiuhu peatland. Furthermore, seasonal variations of networks among methane-related functional groups and environmental factors significantly affected the changes of methane fluxes across different seasons. Concretely, the complicated interactions were detrimental to methane emissions in the Dajiuhu peatland, leading to the minimum methane emissions in winter. Our study identified the key heavy metals affecting the composition of methane-metabolizing microorganisms and linkages between seasonal variations of methane emissions and interaction among heavy metals and methane-metabolizing microorganisms, which provided much new reference and theoretical basis for integrated management of natural peatlands.
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Affiliation(s)
- Ziwei Liu
- School of Environmental Studies, China University of Geosciences (Wuhan), 68 Jincheng Street, Hongshan District, Wuhan, 430078, Hubei Province, China
- Laboratory of Basin Hydrology and Wetland Eco-Restoration, China University of Geosciences (Wuhan), Wuhan, 430078, China
- Hubei Key Laboratory of Wetland Evolution and Ecological Restoration, China University of Geosciences (Wuhan), Wuhan, 430078, China
- Institution of Ecology and Environmental Sciences, China University of Geosciences (Wuhan), Wuhan, 430078, China
| | - Jiumei Wang
- School of Environmental Studies, China University of Geosciences (Wuhan), 68 Jincheng Street, Hongshan District, Wuhan, 430078, Hubei Province, China
- Laboratory of Basin Hydrology and Wetland Eco-Restoration, China University of Geosciences (Wuhan), Wuhan, 430078, China
- Hubei Key Laboratory of Wetland Evolution and Ecological Restoration, China University of Geosciences (Wuhan), Wuhan, 430078, China
- Institution of Ecology and Environmental Sciences, China University of Geosciences (Wuhan), Wuhan, 430078, China
| | - Jinlin Xie
- School of Environmental Studies, China University of Geosciences (Wuhan), 68 Jincheng Street, Hongshan District, Wuhan, 430078, Hubei Province, China
- Laboratory of Basin Hydrology and Wetland Eco-Restoration, China University of Geosciences (Wuhan), Wuhan, 430078, China
- Hubei Key Laboratory of Wetland Evolution and Ecological Restoration, China University of Geosciences (Wuhan), Wuhan, 430078, China
- Institution of Ecology and Environmental Sciences, China University of Geosciences (Wuhan), Wuhan, 430078, China
| | - Dong Yao
- School of Environmental Studies, China University of Geosciences (Wuhan), 68 Jincheng Street, Hongshan District, Wuhan, 430078, Hubei Province, China
- Laboratory of Basin Hydrology and Wetland Eco-Restoration, China University of Geosciences (Wuhan), Wuhan, 430078, China
- Hubei Key Laboratory of Wetland Evolution and Ecological Restoration, China University of Geosciences (Wuhan), Wuhan, 430078, China
- Institution of Ecology and Environmental Sciences, China University of Geosciences (Wuhan), Wuhan, 430078, China
| | - Shiyu Yang
- School of Environmental Studies, China University of Geosciences (Wuhan), 68 Jincheng Street, Hongshan District, Wuhan, 430078, Hubei Province, China
- Laboratory of Basin Hydrology and Wetland Eco-Restoration, China University of Geosciences (Wuhan), Wuhan, 430078, China
- Hubei Key Laboratory of Wetland Evolution and Ecological Restoration, China University of Geosciences (Wuhan), Wuhan, 430078, China
- Institution of Ecology and Environmental Sciences, China University of Geosciences (Wuhan), Wuhan, 430078, China
| | - Jiwen Ge
- School of Environmental Studies, China University of Geosciences (Wuhan), 68 Jincheng Street, Hongshan District, Wuhan, 430078, Hubei Province, China.
- Laboratory of Basin Hydrology and Wetland Eco-Restoration, China University of Geosciences (Wuhan), Wuhan, 430078, China.
- Hubei Key Laboratory of Wetland Evolution and Ecological Restoration, China University of Geosciences (Wuhan), Wuhan, 430078, China.
- Institution of Ecology and Environmental Sciences, China University of Geosciences (Wuhan), Wuhan, 430078, China.
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15
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Koo CW, Hershewe JM, Jewett MC, Rosenzweig AC. Cell-Free Protein Synthesis of Particulate Methane Monooxygenase into Nanodiscs. ACS Synth Biol 2022; 11:4009-4017. [PMID: 36417751 PMCID: PMC9910172 DOI: 10.1021/acssynbio.2c00366] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Particulate methane monooxygenase (pMMO) is a multi-subunit membrane metalloenzyme used by methanotrophic bacteria to convert methane to methanol. A major hurdle to studying pMMO is the lack of a recombinant expression system, precluding investigation of individual residues by mutagenesis and hampering a complete understanding of its mechanism. Here, we developed an Escherichia coli lysate-based cell-free protein synthesis (CFPS) system that can be used to express pMMO in vitro in the presence of nanodiscs. We used a SUMO fusion construct to generate the native PmoB subunit and showed that the SUMO protease (Ulp1) cleaves the protein in the reaction mixture. Using an affinity tag to isolate the complete pMMO complex, we demonstrated that the complex forms without the need for exogenous translocon machinery or chaperones, confirmed by negative stain electron microscopy. This work demonstrates the potential for using CFPS to express multi-subunit membrane-bound metalloenzymes directly into lipid bilayers.
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Affiliation(s)
- Christopher W. Koo
- Department of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Jasmine M. Hershewe
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering and Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Amy C. Rosenzweig
- Department of Molecular Biosciences and of Chemistry and Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
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16
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Guo K, Hakobyan A, Glatter T, Paczia N, Liesack W. Methylocystis sp. Strain SC2 Acclimatizes to Increasing NH 4+ Levels by a Precise Rebalancing of Enzymes and Osmolyte Composition. mSystems 2022; 7:e0040322. [PMID: 36154142 PMCID: PMC9600857 DOI: 10.1128/msystems.00403-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 08/26/2022] [Indexed: 12/24/2022] Open
Abstract
A high NH4+ load is known to inhibit bacterial methane oxidation. This is due to a competition between CH4 and NH3 for the active site of particulate methane monooxygenase (pMMO), which converts CH4 to CH3OH. Here, we combined global proteomics with amino acid profiling and nitrogen oxides measurements to elucidate the cellular acclimatization response of Methylocystis sp. strain SC2 to high NH4+ levels. Relative to 1 mM NH4+, a high (50 mM and 75 mM) NH4+ load under CH4-replete conditions significantly increased the lag phase duration required for proteome adjustment. The number of differentially regulated proteins was highly significantly correlated with an increasing NH4+ load. The cellular responses to increasing ionic and osmotic stress involved a significant upregulation of stress-responsive proteins, the K+ "salt-in" strategy, the synthesis of compatible solutes (glutamate and proline), and the induction of the glutathione metabolism pathway. A significant increase in the apparent Km value for CH4 oxidation during the growth phase was indicative of increased pMMO-based oxidation of NH3 to toxic hydroxylamine. The detoxifying activity of hydroxlyamine oxidoreductase (HAO) led to a significant accumulation of NO2- and, upon decreasing O2 tension, N2O. Nitric oxide reductase and hybrid cluster proteins (Hcps) were the candidate enzymes for the production of N2O. In summary, strain SC2 has the capacity to precisely rebalance enzymes and osmolyte composition in response to increasing NH4+ exposure, but the need to simultaneously combat both ionic-osmotic stress and the toxic effects of hydroxylamine may be the reason why its acclimatization capacity is limited to 75 mM NH4+. IMPORTANCE In addition to reducing CH4 emissions from wetlands and landfills, the activity of alphaproteobacterial methane oxidizers of the genus Methylocystis contributes to the sink capacity of forest and grassland soils for atmospheric methane. The methane-oxidizing activity of Methylocystis spp. is, however, sensitive to high NH4+ concentrations. This is due to the competition of CH4 and NH3 for the active site of particulate methane monooxygenase, thereby resulting in the production of toxic hydroxylamine with an increasing NH4+ load. An understanding of the physiological and molecular response mechanisms of Methylocystis spp. is therefore of great importance. Here, we combined global proteomics with amino acid profiling and NOx measurements to disentangle the cellular mechanisms underlying the acclimatization of Methylocystis sp. strain SC2 to an increasing NH4+ load.
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Affiliation(s)
- Kangli Guo
- Methanotrophic Bacteria and Environmental Genomics/Transcriptomics Research Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Anna Hakobyan
- Methanotrophic Bacteria and Environmental Genomics/Transcriptomics Research Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Timo Glatter
- Core Facility for Mass Spectrometry and Proteomics, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Nicole Paczia
- Core Facility for Metabolomics and Small Molecule Mass Spectrometry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Werner Liesack
- Methanotrophic Bacteria and Environmental Genomics/Transcriptomics Research Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany
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17
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Recent Insights into Cu-Based Catalytic Sites for the Direct Conversion of Methane to Methanol. Molecules 2022; 27:molecules27217146. [DOI: 10.3390/molecules27217146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/13/2022] [Accepted: 10/19/2022] [Indexed: 11/05/2022] Open
Abstract
Direct conversion of methane to methanol is an effective and practical process to improve the efficiency of natural gas utilization. Copper (Cu)-based catalysts have attracted great research attention, due to their unique ability to selectively catalyze the partial oxidation of methane to methanol at relatively low temperatures. In recent decades, many different catalysts have been studied to achieve a high conversion of methane to methanol, including the Cu-based enzymes, Cu-zeolites, Cu-MOFs (metal-organic frameworks) and Cu-oxides. In this mini review, we will detail the obtained evidence on the exact state of the active Cu sites on these various catalysts, which have arisen from the most recently developed techniques and the results of DFT calculations. We aim to establish the structure–performance relationship in terms of the properties of these materials and their catalytic functionalities, and also discuss the unresolved questions in the direct conversion of methane to methanol reactions. Finally, we hope to offer some suggestions and strategies for guiding the practical applications regarding the catalyst design and engineering for a high methanol yield in the methane oxidation reaction.
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18
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Zhu Y, Koo CW, Cassidy CK, Spink MC, Ni T, Zanetti-Domingues LC, Bateman B, Martin-Fernandez ML, Shen J, Sheng Y, Song Y, Yang Z, Rosenzweig AC, Zhang P. Structure and activity of particulate methane monooxygenase arrays in methanotrophs. Nat Commun 2022; 13:5221. [PMID: 36064719 PMCID: PMC9445010 DOI: 10.1038/s41467-022-32752-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 08/16/2022] [Indexed: 01/29/2023] Open
Abstract
Methane-oxidizing bacteria play a central role in greenhouse gas mitigation and have potential applications in biomanufacturing. Their primary metabolic enzyme, particulate methane monooxygenase (pMMO), is housed in copper-induced intracytoplasmic membranes (ICMs), of which the function and biogenesis are not known. We show by serial cryo-focused ion beam (cryoFIB) milling/scanning electron microscope (SEM) volume imaging and lamellae-based cellular cryo-electron tomography (cryoET) that these ICMs are derived from the inner cell membrane. The pMMO trimer, resolved by cryoET and subtomogram averaging to 4.8 Å in the ICM, forms higher-order hexagonal arrays in intact cells. Array formation correlates with increased enzymatic activity, highlighting the importance of studying the enzyme in its native environment. These findings also demonstrate the power of cryoET to structurally characterize native membrane enzymes in the cellular context.
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Affiliation(s)
- Yanan Zhu
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Christopher W Koo
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL, USA
| | - C Keith Cassidy
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Matthew C Spink
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Tao Ni
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Laura C Zanetti-Domingues
- Central Laser Facility, Science and Technology Facility Council, Rutherford Appleton Laboratory, Didcot, Oxfordshire, UK
| | - Benji Bateman
- Central Laser Facility, Science and Technology Facility Council, Rutherford Appleton Laboratory, Didcot, Oxfordshire, UK
| | - Marisa L Martin-Fernandez
- Central Laser Facility, Science and Technology Facility Council, Rutherford Appleton Laboratory, Didcot, Oxfordshire, UK
| | - Juan Shen
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Yuewen Sheng
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Yun Song
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Zhengyi Yang
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
- Imaging Centre, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Amy C Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL, USA.
| | - Peijun Zhang
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK.
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK.
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19
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Bete SC, May LK, Woite P, Roemelt M, Otte M. A Copper Cage‐Complex as Mimic of the pMMO Cu
C
Site. Angew Chem Int Ed Engl 2022; 61:e202206120. [PMID: 35731651 PMCID: PMC9544873 DOI: 10.1002/anie.202206120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Indexed: 12/05/2022]
Abstract
The active site of particulate methane monooxygenase (pMMO) and its mechanism of action are not known. Recently, the CuC site emerged as a potential active site, but to date it lacks any study on biomimetic resemblance of the coordination environment provided by the enzyme. Here, the synthesis of a cage ligand providing such an environment is reported. Copper is incorporated, and coordination occurs by the two imidazole and one carboxylate group offered by the ligand. Depending on the oxidation state, it can adopt different coordination modes, as evidenced by the solid‐state structures and computational investigation. The copper(I) state readily reacts with dioxygen and thereby undergoes CH activation. Moreover, the catalytic aerobic oxidation of hydroquinones as ubiquinol mimics is shown. Clean one‐electron oxidation occurs under mild conditions and EPR analysis of the copper(II) state in the presence of water reveals striking similarities to the data obtained from pMMO.
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Affiliation(s)
- Sarah C. Bete
- Institute of Inorganic Chemistry University of Goettingen Tammannstraße 4 37077 Göttingen Germany
| | - Leander K. May
- Institute of Inorganic Chemistry University of Goettingen Tammannstraße 4 37077 Göttingen Germany
| | - Philipp Woite
- Institut für Chemie Humboldt-Universität zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
| | - Michael Roemelt
- Institut für Chemie Humboldt-Universität zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
| | - Matthias Otte
- Institute of Inorganic Chemistry University of Goettingen Tammannstraße 4 37077 Göttingen Germany
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20
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Da Silva WDB, Dias RP, Da Silva JCS. Refining details of the structural and electronic properties of the Cu B site in pMMO enzyme through sequential molecular dynamics/CPKS-EPR calculations. Phys Chem Chem Phys 2022; 24:16611-16621. [PMID: 35730560 DOI: 10.1039/d2cp01217k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This work investigated the structural and electronic properties of the copper mononuclear site of the PmoB part of the pMMO enzyme at the molecular level. We propose that the CuB catalytic site in the soluble portion of pMMO at room temperature and under physiological conditions is a mononuclear copper complex in a distorted octahedral arrangement with the residues His33, His137, and His139 on the equatorial base and two water molecules on the axial axis. Our view was based on the molecular dynamics results and DFT calculations of the electronic paramagnetic resonance parameters and comparisons with experimental EPR data. This new proposed model for the CuB site brings additional support concerning the recent experimental evidence, which pointed out that a saturated coordination sphere of the copper ion in the CuB center is an essential factor that makes it less efficient than the CuC site in the methane oxidation. Therefore, according to the CuB site model proposed here, an additional step involving a displacement of at least one water molecule of the copper coordination sphere by the O2 molecule prior to its activation must be necessary. This scenario is less likely to occur in the CuC center once this one is buried in the alpha-helices, which are part of the pMMO structure bound to the membrane wall, and consequently located in a less solvent-exposed region. In addition, we also present a simple and efficient sequential S-MD/CPKS protocol to compute EPR parameters that can, in principle, be expanded for the study of other copper-containing proteins.
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Affiliation(s)
- William Daniel B Da Silva
- LQCBio: Laboratório de Química Computacional e Modelagem de Biomoléculas, Instituto de Química e Biotecnologia, IQB, Universidade Federal de Alagoas, Campus A. C. Simões, 57072-900, Maceió, AL, Brazil.
| | - Roberta P Dias
- GIMMM: Grupo Interdisciplinar de Modelagem Molecular e Simulação de Materiais, Núcleo Interdisciplinar de Ciências Exatas e da Natureza - NICEN, Campus do Agreste, Universidade Federal de Pernambuco, 55002-970, Caruaru, PE, Brazil
| | - Júlio C S Da Silva
- LQCBio: Laboratório de Química Computacional e Modelagem de Biomoléculas, Instituto de Química e Biotecnologia, IQB, Universidade Federal de Alagoas, Campus A. C. Simões, 57072-900, Maceió, AL, Brazil.
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21
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Bete SC, May LK, Woite P, Roemelt M, Otte M. A Copper Cage‐Complex as Mimic of the pMMO CuC Site. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202206120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Sarah C. Bete
- University of Göttingen: Georg-August-Universitat Gottingen Institut für Anorganische Chemie GERMANY
| | - Leander K. May
- Georg-August-Universität Göttingen: Georg-August-Universitat Gottingen Institut für Anorganische Chemie GERMANY
| | - Philipp Woite
- Humboldt-Universitat zu Berlin Institut für Chemie GERMANY
| | - Michael Roemelt
- Humboldt-Universitat zu Berlin Institut für Chemie Brook-Taylor-Straße 2 12489 Berlin GERMANY
| | - Matthias Otte
- Georg-August-Universität Göttingen Institut für Anorganische Chemie, Institut für Anorganische Chemie Tammannstraße 4 37077 Göttingen GERMANY
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22
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Chan SI, Wang VC, Chen PP, Yu SS. Methane oxidation by the copper methane monooxygenase: Before and after the cryogenic electron microscopy structure of particulate methane monooxygenase from
Methylococcus capsulatus
(Bath). J CHIN CHEM SOC-TAIP 2022. [DOI: 10.1002/jccs.202200166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Sunney I Chan
- Institute of Chemistry, Academia Sinica Taipei City Taiwan
- Department of Chemistry National Taiwan University Taipei City Taiwan
| | - Vincent C.‐C Wang
- Department of Chemistry National Sun Yat‐Sen University Kaohsiung City Taiwan
| | - Peter P.‐Y. Chen
- Department of Chemistry National Chung Hsing University Taichung City Taiwan
| | - Steve S.‐F. Yu
- Institute of Chemistry, Academia Sinica Taipei City Taiwan
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23
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Cutsail III GE, DeBeer S. Challenges and Opportunities for Applications of Advanced X-ray Spectroscopy in Catalysis Research. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01016] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- George E. Cutsail III
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
- Institute of Inorganic Chemistry, University of Duisburg-Essen, Universitätsstr. 5-7, 45117 Essen, Germany
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
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24
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Greening C, Grinter R. Microbial oxidation of atmospheric trace gases. Nat Rev Microbiol 2022; 20:513-528. [PMID: 35414013 DOI: 10.1038/s41579-022-00724-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2022] [Indexed: 02/06/2023]
Abstract
The atmosphere has recently been recognized as a major source of energy sustaining life. Diverse aerobic bacteria oxidize the three most abundant reduced trace gases in the atmosphere, namely hydrogen (H2), carbon monoxide (CO) and methane (CH4). This Review describes the taxonomic distribution, physiological role and biochemical basis of microbial oxidation of these atmospheric trace gases, as well as the ecological, environmental, medical and astrobiological importance of this process. Most soil bacteria and some archaea can survive by using atmospheric H2 and CO as alternative energy sources, as illustrated through genetic studies on Mycobacterium cells and Streptomyces spores. Certain specialist bacteria can also grow on air alone, as confirmed by the landmark characterization of Methylocapsa gorgona, which grows by simultaneously consuming atmospheric CH4, H2 and CO. Bacteria use high-affinity lineages of metalloenzymes, namely hydrogenases, CO dehydrogenases and methane monooxygenases, to utilize atmospheric trace gases for aerobic respiration and carbon fixation. More broadly, trace gas oxidizers enhance the biodiversity and resilience of soil and marine ecosystems, drive primary productivity in extreme environments such as Antarctic desert soils and perform critical regulatory services by mitigating anthropogenic emissions of greenhouse gases and toxic pollutants.
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Affiliation(s)
- Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia. .,Securing Antarctica's Environmental Future, Monash University, Clayton, Victoria, Australia. .,Centre to Impact AMR, Monash University, Clayton, Victoria, Australia.
| | - Rhys Grinter
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
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25
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Theoretical perspective on mononuclear copper-oxygen mediated C–H and O–H activations: A comparison between biological and synthetic systems. CHINESE JOURNAL OF CATALYSIS 2022. [DOI: 10.1016/s1872-2067(21)63974-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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26
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Koo CW, Tucci FJ, He Y, Rosenzweig AC. Recovery of particulate methane monooxygenase structure and activity in a lipid bilayer. Science 2022; 375:1287-1291. [PMID: 35298269 PMCID: PMC9357287 DOI: 10.1126/science.abm3282] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Bacterial methane oxidation using the enzyme particulate methane monooxygenase (pMMO) contributes to the removal of environmental methane, a potent greenhouse gas. Crystal structures determined using inactive, detergent-solubilized pMMO lack several conserved regions neighboring the proposed active site. We show that reconstituting pMMO in nanodiscs with lipids extracted from the native organism restores methane oxidation activity. Multiple nanodisc-embedded pMMO structures determined by cryo-electron microscopy to 2.14- to 2.46-angstrom resolution reveal the structure of pMMO in a lipid environment. The resulting model includes stabilizing lipids, regions of the PmoA and PmoC subunits not observed in prior structures, and a previously undetected copper-binding site in the PmoC subunit with an adjacent hydrophobic cavity. These structures provide a revised framework for understanding and engineering pMMO function.
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Affiliation(s)
- Christopher W. Koo
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Frank J. Tucci
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Yuan He
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Amy C. Rosenzweig
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
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27
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Wang Z, Fang W, Peng W, Wu P, Wang B. Recent Computational Insights into the Oxygen Activation by Copper-Dependent Metalloenzymes. Top Catal 2022. [DOI: 10.1007/s11244-021-01444-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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28
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Das B, Al-Hunaiti A, Carey A, Lidin S, Demeshko S, Repo T, Nordlander E. A di‑iron(III) μ-oxido complex as catalyst precursor in the oxidation of alkanes and alkenes. J Inorg Biochem 2022; 231:111769. [DOI: 10.1016/j.jinorgbio.2022.111769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 02/10/2022] [Accepted: 02/10/2022] [Indexed: 11/30/2022]
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29
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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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30
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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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31
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Chan SI, Chang WH, Huang SH, Lin HH, Yu SSF. Catalytic machinery of methane oxidation in particulate methane monooxygenase (pMMO). J Inorg Biochem 2021; 225:111602. [PMID: 34547604 DOI: 10.1016/j.jinorgbio.2021.111602] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 08/21/2021] [Accepted: 09/09/2021] [Indexed: 10/20/2022]
Abstract
In this focused review, we portray the recently reported 2.5 Å cyro-EM structure of the particulate methane monooxygenase (pMMO) from M. capsulatus (Bath). The structure of the functional holo-pMMO near atomic resolution has uncovered the sites of the copper cofactors including the location of the active site in the enzyme. The three coppers seen in the original X-ray crystal structures of the enzyme are now augmented by additional coppers in the transmembrane domain as well as in the water-exposed C-terminal subdomain of the PmoB subunit. The cryo-EM structure offers the first glimpse of the catalytic machinery capable of methane oxidation with high selectivity and efficiency. The findings are entirely consistent with the biochemical and biophysical findings previously reported in the literature, including the chemistry of hydrocarbon hydroxylation, regeneration of the catalyst for multiple turnovers, and the mechanism of aborting non-productive cycles to ensure kinetic competence.
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Affiliation(s)
- Sunney I Chan
- Institute of Chemistry, Academia Sinica, Nankang, Taipei 11529, Taiwan.
| | - Wei-Hau Chang
- Institute of Chemistry, Academia Sinica, Nankang, Taipei 11529, Taiwan.
| | - Shih-Hsin Huang
- Institute of Chemistry, Academia Sinica, Nankang, Taipei 11529, Taiwan
| | - Hsin-Hung Lin
- Institute of Chemistry, Academia Sinica, Nankang, Taipei 11529, Taiwan
| | - Steve S-F Yu
- Institute of Chemistry, Academia Sinica, Nankang, Taipei 11529, Taiwan.
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32
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Langerman M, Hetterscheid DGH. Mechanistic Study of the Activation and the Electrocatalytic Reduction of Hydrogen Peroxide by Cu-tmpa in Neutral Aqueous Solution. ChemElectroChem 2021; 8:2783-2791. [PMID: 34589379 PMCID: PMC8453753 DOI: 10.1002/celc.202100436] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/04/2021] [Indexed: 11/29/2022]
Abstract
Hydrogen peroxide plays an important role as an intermediate and product in the reduction of dioxygen by copper enzymes and mononuclear copper complexes. The copper(II) tris(2-pyridylmethyl)amine complex (Cu-tmpa) has been shown to produce H2O2 as an intermediate during the electrochemical 4-electron reduction of O2. We investigated the electrochemical hydrogen peroxide reduction reaction (HPRR) by Cu-tmpa in a neutral aqueous solution. The catalytic rate constant of the reaction was shown to be one order of magnitude lower than the reduction of dioxygen. A significant solvent kinetic isotope effect (KIE) of 1.4 to 1.7 was determined for the reduction of H2O2, pointing to a Fenton-like reaction pathway as the likely catalytic mechanism, involving a single copper site that produces an intermediate copper(II) hydroxo species and a free hydroxyl radical anion in the process.
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Affiliation(s)
- Michiel Langerman
- Leiden Institute of ChemistryLeiden UniversityP.O Box 95022300 RALeidenThe Netherlands
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33
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Chang WH, Lin HH, Tsai IK, Huang SH, Chung SC, Tu IP, Yu SSF, Chan SI. Copper Centers in the Cryo-EM Structure of Particulate Methane Monooxygenase Reveal the Catalytic Machinery of Methane Oxidation. J Am Chem Soc 2021; 143:9922-9932. [PMID: 34170126 DOI: 10.1021/jacs.1c04082] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The particulate methane monooxygenase (pMMO) is the first enzyme in the C1 metabolic pathway in methanotrophic bacteria. As this enzyme converts methane into methanol efficiently near room temperature, it has become the paradigm for developing an understanding of this difficult C1 chemistry. pMMO is a membrane-bound protein with three subunits (PmoB, PmoA, and PmoC) and 12-14 coppers distributed among different sites. X-ray crystal structures that have revealed only three mononuclear coppers at three sites have neither disclosed the location of the active site nor the catalytic mechanism of the enzyme. Here we report a cyro-EM structure of holo-pMMO from Methylococcus capsulatus (Bath) at 2.5 Å, and develop quantitative electrostatic-potential profiling to scrutinize the nonprotein densities for signatures of the copper cofactors. Our results confirm a mononuclear CuI at the A site, resolve two CuIs at the B site, and uncover additional CuI clusters at the PmoA/PmoC interface within the membrane (D site) and in the water-exposed C-terminal subdomain of the PmoB (E clusters). These findings complete the minimal set of copper factors required for catalytic turnover of pMMO, offering a glimpse of the catalytic machinery for methane oxidation according to the chemical principles underlying the mechanism proposed earlier.
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Affiliation(s)
- W-H Chang
- Institute of Chemistry, Academia Sinica, Nangang, Taipei 11529, Taiwan
| | - H-H Lin
- Institute of Chemistry, Academia Sinica, Nangang, Taipei 11529, Taiwan
| | - I-K Tsai
- Institute of Chemistry, Academia Sinica, Nangang, Taipei 11529, Taiwan
| | - S-H Huang
- Institute of Chemistry, Academia Sinica, Nangang, Taipei 11529, Taiwan
| | - S-C Chung
- Institute of Statistical Science, Academia Sinica, Nangang, Taipei 11529, Taiwan
| | - I-P Tu
- Institute of Statistical Science, Academia Sinica, Nangang, Taipei 11529, Taiwan
| | - S S-F Yu
- Institute of Chemistry, Academia Sinica, Nangang, Taipei 11529, Taiwan
| | - S I Chan
- Institute of Chemistry, Academia Sinica, Nangang, Taipei 11529, Taiwan
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34
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Murphy CL, Sheremet A, Dunfield PF, Spear JR, Stepanauskas R, Woyke T, Elshahed MS, Youssef NH. Genomic Analysis of the Yet-Uncultured Binatota Reveals Broad Methylotrophic, Alkane-Degradation, and Pigment Production Capacities. mBio 2021; 12:e00985-21. [PMID: 34006650 PMCID: PMC8262859 DOI: 10.1128/mbio.00985-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 04/07/2021] [Indexed: 01/18/2023] Open
Abstract
The recent leveraging of genome-resolved metagenomics has generated an enormous number of genomes from novel uncultured microbial lineages yet left many clades undescribed. Here, we present a global analysis of genomes belonging to Binatota (UBP10), a globally distributed, yet-uncharacterized bacterial phylum. All orders in Binatota encoded the capacity for aerobic methylotrophy using methanol, methylamine, sulfomethanes, and chloromethanes as the substrates. Methylotrophy in Binatota was characterized by order-specific substrate degradation preferences, as well as extensive metabolic versatility, i.e., the utilization of diverse sets of genes, pathways, and combinations to achieve a specific metabolic goal. The genomes also encoded multiple alkane hydroxylases and monooxygenases, potentially enabling growth on a wide range of alkanes and fatty acids. Pigmentation is inferred from a complete pathway for carotenoids (lycopene, β- and γ-carotenes, xanthins, chlorobactenes, and spheroidenes) production. Further, the majority of genes involved in bacteriochlorophyll a, c, and d biosynthesis were identified, although absence of key genes and failure to identify a photosynthetic reaction center preclude proposing phototrophic capacities. Analysis of 16S rRNA databases showed the preferences of Binatota to terrestrial and freshwater ecosystems, hydrocarbon-rich habitats, and sponges, supporting their potential role in mitigating methanol and methane emissions, breakdown of alkanes, and their association with sponges. Our results expand the lists of methylotrophic, aerobic alkane-degrading, and pigment-producing lineages. We also highlight the consistent encountering of incomplete biosynthetic pathways in microbial genomes, a phenomenon necessitating careful assessment when assigning putative functions based on a set-threshold of pathway completion.IMPORTANCE A wide range of microbial lineages remain uncultured, yet little is known regarding their metabolic capacities, physiological preferences, and ecological roles in various ecosystems. We conducted a thorough comparative genomic analysis of 108 genomes belonging to the Binatota (UBP10), a globally distributed, yet-uncharacterized bacterial phylum. We present evidence that members of the order Binatota specialize in methylotrophy and identify an extensive repertoire of genes and pathways mediating the oxidation of multiple one-carbon (C1) compounds in Binatota genomes. The occurrence of multiple alkane hydroxylases and monooxygenases in these genomes was also identified, potentially enabling growth on a wide range of alkanes and fatty acids. Pigmentation is inferred from a complete pathway for carotenoids production. We also report on the presence of incomplete chlorophyll biosynthetic pathways in all genomes and propose several evolutionary-grounded scenarios that could explain such a pattern. Assessment of the ecological distribution patterns of the Binatota indicates preference of its members to terrestrial and freshwater ecosystems characterized by high methane and methanol emissions, as well as multiple hydrocarbon-rich habitats and marine sponges.
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Affiliation(s)
- Chelsea L Murphy
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Andriy Sheremet
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Peter F Dunfield
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - John R Spear
- Civil and Environmental Engineering, Colorado School of Mines, Golden, Colorado, USA
| | | | - Tanja Woyke
- Department of Energy Joint Genome Institute, Berkley, California, USA
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
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35
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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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36
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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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37
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Abstract
Methanotrophic bacteria represent a potential route to methane utilization and mitigation of methane emissions. In the first step of their metabolic pathway, aerobic methanotrophs use methane monooxygenases (MMOs) to activate methane, oxidizing it to methanol. There are two types of MMOs: a particulate, membrane-bound enzyme (pMMO) and a soluble, cytoplasmic enzyme (sMMO). The two MMOs are completely unrelated, with different architectures, metal cofactors, and mechanisms. The more prevalent of the two, pMMO, is copper-dependent, but the identity of its copper active site remains unclear. By contrast, sMMO uses a diiron active site, the catalytic cycle of which is well understood. Here we review the current state of knowledge for both MMOs, with an emphasis on recent developments and emerging hypotheses. In addition, we discuss obstacles to developing expression systems, which are needed to address outstanding questions and to facilitate future protein engineering efforts.
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Affiliation(s)
- Christopher W Koo
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL 60208, USA.
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38
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Calisto F, Sousa FM, Sena FV, Refojo PN, Pereira MM. Mechanisms of Energy Transduction by Charge Translocating Membrane Proteins. Chem Rev 2021; 121:1804-1844. [PMID: 33398986 DOI: 10.1021/acs.chemrev.0c00830] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Life relies on the constant exchange of different forms of energy, i.e., on energy transduction. Therefore, organisms have evolved in a way to be able to harvest the energy made available by external sources (such as light or chemical compounds) and convert these into biological useable energy forms, such as the transmembrane difference of electrochemical potential (Δμ̃). Membrane proteins contribute to the establishment of Δμ̃ by coupling exergonic catalytic reactions to the translocation of charges (electrons/ions) across the membrane. Irrespectively of the energy source and consequent type of reaction, all charge-translocating proteins follow two molecular coupling mechanisms: direct- or indirect-coupling, depending on whether the translocated charge is involved in the driving reaction. In this review, we explore these two coupling mechanisms by thoroughly examining the different types of charge-translocating membrane proteins. For each protein, we analyze the respective reaction thermodynamics, electron transfer/catalytic processes, charge-translocating pathways, and ion/substrate stoichiometries.
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Affiliation(s)
- Filipa Calisto
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
| | - Filipe M Sousa
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
| | - Filipa V Sena
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
| | - Patricia N Refojo
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
| | - Manuela M Pereira
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
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39
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Choi C, Yoon S, Jung Y. Shifting the scaling relations of single-atom catalysts for facile methane activation by tuning the coordination number. Chem Sci 2021; 12:3551-3557. [PMID: 34163628 PMCID: PMC8179458 DOI: 10.1039/d0sc05632d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 01/11/2021] [Indexed: 11/21/2022] Open
Abstract
We investigate oxidative methane activation on a wide range of single transition metal atom catalysts embedded on N-doped graphene derivatives using density functional theory calculations. An inverse scaling relationship between *O formation and its hydrogen affinity is observed, consistent with a previous report. However, we find that the latter scaling line can be shifted towards a more reactive region by tuning the coordination number (CN) of the active metal sites. Specifically, we find that lowering the CN plays an important role in increasing the reactivity for methane activation via a radical-like transition state by moving the scaling lines. Thus, in the new design strategy suggested here, different from the conventional efforts focusing mainly on breaking the scaling relations, one maintains the scaling relations but moves them towards more reactive regions by controlling the coordination number of the active sites. With this design principle, we suggest several single atom catalysts with lower C-H activation barriers than some of the most active methane activation catalysts in the literature such as Cu-based zeolites.
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Affiliation(s)
- Changhyeok Choi
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea
| | - Sungho Yoon
- Department of Chemistry, Chung-Ang University Seoul 06974 Republic of Korea
| | - Yousung Jung
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea
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40
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Trace gas oxidizers are widespread and active members of soil microbial communities. Nat Microbiol 2021; 6:246-256. [PMID: 33398096 DOI: 10.1038/s41564-020-00811-w] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/08/2020] [Indexed: 01/24/2023]
Abstract
Soil microorganisms globally are thought to be sustained primarily by organic carbon sources. Certain bacteria also consume inorganic energy sources such as trace gases, but they are presumed to be rare community members, except within some oligotrophic soils. Here we combined metagenomic, biogeochemical and modelling approaches to determine how soil microbial communities meet energy and carbon needs. Analysis of 40 metagenomes and 757 derived genomes indicated that over 70% of soil bacterial taxa encode enzymes to consume inorganic energy sources. Bacteria from 19 phyla encoded enzymes to use the trace gases hydrogen and carbon monoxide as supplemental electron donors for aerobic respiration. In addition, we identified a fourth phylum (Gemmatimonadota) potentially capable of aerobic methanotrophy. Consistent with the metagenomic profiling, communities within soil profiles from diverse habitats rapidly oxidized hydrogen, carbon monoxide and to a lesser extent methane below atmospheric concentrations. Thermodynamic modelling indicated that the power generated by oxidation of these three gases is sufficient to meet the maintenance needs of the bacterial cells capable of consuming them. Diverse bacteria also encode enzymes to use trace gases as electron donors to support carbon fixation. Altogether, these findings indicate that trace gas oxidation confers a major selective advantage in soil ecosystems, where availability of preferred organic substrates limits microbial growth. The observation that inorganic energy sources may sustain most soil bacteria also has broad implications for understanding atmospheric chemistry and microbial biodiversity in a changing world.
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41
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Miyaji A, Satou K, Baba T. Influence of tryptic hydrolysis on the enzymatic function of the membrane-bound form of particulate methane monooxygenase from Methylosinus trichosporium OB3b. J Biotechnol 2020; 323:98-106. [PMID: 32828830 DOI: 10.1016/j.jbiotec.2020.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 07/30/2020] [Accepted: 08/17/2020] [Indexed: 11/29/2022]
Abstract
Particulate methane monooxygenase (pMMO) is a membrane protein embedded in the intracytoplasmic membrane of methane-oxidizing bacteria. Structural analysis of pMMO showed the existence of a hydrophilic region exposed outside of the bacterial membrane. To obtain information regarding the role of this hydrophilic region in the enzymatic function of pMMO, trypsin proteolysis of the membrane-bound form of pMMO from Methylosinus trichosporium OB3b was performed at 4 °C. The polypeptides produced by this hydrolysis were analyzed by polyacrylamide gel electrophoresis and MALDI-TOF/TOF. Furthermore, the influence of this tryptic digestion on the methane hydroxylation and propene epoxidation enzymatic activities of pMMO was investigated. Among the three subunits of pMMO, PmoB and PmoC were hydrolyzed by trypsin, but PmoA was not. With 10 mg L-1 trypsin, both terminal regions or the C-terminal region of PmoC polypeptide was selectively hydrolyzed. Furthermore, the stability of pMMO was decreased by this digestion. These results indicate that PmoC plays a role in maintaining the stability of pMMO in vitro. On the other hand, the digestion of PmoB with 100 mg L-1 trypsin produced several polypeptides, indicating that trypsin digestion occurs at several sites of the hydrophilic region of PmoB. Hydrolysis led to a decrease in pMMO activity towards methane hydroxylation and propene epoxidation. These results indicate that the hydrophilic region of PmoB is critically important for the enzymatic function of pMMO, which is consistent with the models of the functional mechanism of pMMO proposed so far.
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Affiliation(s)
- Akimitsu Miyaji
- Department of Environmental Chemistry and Engineering, Tokyo Institute of Technology, 4259-G1-14, Nagatsuta-cho, Midori-ku, Yokohama 226-8502, Japan.
| | - Keita Satou
- Department of Environmental Chemistry and Engineering, Tokyo Institute of Technology, 4259-G1-14, Nagatsuta-cho, Midori-ku, Yokohama 226-8502, Japan
| | - Toshihide Baba
- Department of Environmental Chemistry and Engineering, Tokyo Institute of Technology, 4259-G1-14, Nagatsuta-cho, Midori-ku, Yokohama 226-8502, Japan
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42
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Musiani F, Broll V, Evangelisti E, Ciurli S. The model structure of the copper-dependent ammonia monooxygenase. J Biol Inorg Chem 2020; 25:995-1007. [PMID: 32926231 PMCID: PMC7584546 DOI: 10.1007/s00775-020-01820-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 09/02/2020] [Indexed: 12/24/2022]
Abstract
Abstract Ammonia monooxygenase is a copper-dependent membrane-bound enzyme that catalyzes the first step of nitrification in ammonia-oxidizing bacteria to convert ammonia to hydroxylamine, through the reductive insertion of a dioxygen-derived O atom in an N–H bond. This reaction is analogous to that carried out by particulate methane monooxygenase, which catalyzes the conversion of methane to methanol. The enzymatic activity of ammonia monooxygenase must be modulated to reduce the release of nitrogen-based soil nutrients for crop production into the atmosphere or underground waters, a phenomenon known to significantly decrease the efficiency of primary production as well as increase air and water pollution. The structure of ammonia monooxygenase is not available, rendering the rational design of enzyme inhibitors impossible. This study describes a successful attempt to build a structural model of ammonia monooxygenase, and its accessory proteins AmoD and AmoE, from Nitrosomonas europaea, taking advantage of the high sequence similarity with particulate methane monooxygenase and the homologous PmoD protein, for which crystal structures are instead available. The results obtained not only provide the structural details of the proteins ternary and quaternary structures, but also suggest a location for the copper-containing active site for both ammonia and methane monooxygenases, as well as support a proposed structure of a CuA-analogue dinuclear copper site in AmoD and PmoD. Graphic abstract ![]()
Electronic supplementary material The online version of this article (10.1007/s00775-020-01820-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Francesco Musiani
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127, Bologna, Italy.
| | - Valquiria Broll
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127, Bologna, Italy
| | - Elisa Evangelisti
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127, Bologna, Italy
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127, Bologna, Italy.
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43
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Lerch M, Weitzer M, Stumpf TJ, Laurini L, Hoffmann A, Becker J, Miska A, Göttlich R, Herres‐Pawlis S, Schindler S. Kinetic Investigation of the Reaction of Dioxygen with the Copper(I) Complex [Cu(Pim
i
Pr2
)(CH
3
CN)]CF
3
SO
3
{Pim
i
Pr2
= Tris[2‐(1,4‐diisopropylimidazolyl)]phosphine}. Eur J Inorg Chem 2020. [DOI: 10.1002/ejic.202000462] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Markus Lerch
- Institut für Anorganische und Analytische Chemie Justus‐Liebig‐Universität Gießen Heinrich‐Buff‐Ring 17 35392 Gießen Germany
| | - Markus Weitzer
- Institut für Anorganische und Analytische Chemie Justus‐Liebig‐Universität Gießen Heinrich‐Buff‐Ring 17 35392 Gießen Germany
| | - Tim‐Daniel J. Stumpf
- Institut für Anorganische und Analytische Chemie Justus‐Liebig‐Universität Gießen Heinrich‐Buff‐Ring 17 35392 Gießen Germany
- Institut für Organische Chemie Justus‐Liebig‐Universität Gießen Heinrich‐Buff‐Ring 17 35392 Gießen Germany
| | - Larissa Laurini
- Institut für Anorganische Chemie RWTH Aachen University Landoltweg 1A 52074 Aachen Germany
| | - Alexander Hoffmann
- Institut für Anorganische Chemie RWTH Aachen University Landoltweg 1A 52074 Aachen Germany
| | - Jonathan Becker
- Institut für Anorganische und Analytische Chemie Justus‐Liebig‐Universität Gießen Heinrich‐Buff‐Ring 17 35392 Gießen Germany
| | - Andreas Miska
- Institut für Anorganische und Analytische Chemie Justus‐Liebig‐Universität Gießen Heinrich‐Buff‐Ring 17 35392 Gießen Germany
| | - Richard Göttlich
- Institut für Organische Chemie Justus‐Liebig‐Universität Gießen Heinrich‐Buff‐Ring 17 35392 Gießen Germany
| | - Sonja Herres‐Pawlis
- Institut für Anorganische Chemie RWTH Aachen University Landoltweg 1A 52074 Aachen Germany
| | - Siegfried Schindler
- Institut für Anorganische und Analytische Chemie Justus‐Liebig‐Universität Gießen Heinrich‐Buff‐Ring 17 35392 Gießen Germany
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Liang P, Cao Y, Dong Q, Wang D, Zhang D, Jin S, Yu Z, Ye J, Zou M. A balsam pear-shaped CuO SERS substrate with highly chemical enhancement for pesticide residue detection. Mikrochim Acta 2020; 187:335. [PMID: 32418132 DOI: 10.1007/s00604-020-04303-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 04/27/2020] [Indexed: 01/20/2023]
Abstract
Simple and traditional hydrothermal fabrication of a novel balsam pear-shaped CuO with high SERS enhancement is presented. XRD (X-ray diffraction), SEM (scanning electronic microscopy), TEM (transmission electron microscope), HRTEM (high-resolution transmission electron microscope), UV-Vis, and Raman are adopted to ensure that this balsam pear-shaped CuO with dense nanoparticle protuberance is successfully prepared. The LOD of this CuO SERS substrate is 4.79 μg L-1 with R6G as molecular probe. By using DFT (density functional theory) calculation and FDTD (finite difference time domainmethod) simulation, both EM (electromagnetic enhancement) and CM (chemical enhancement) mechanisms are investigated, and the results show that these two-enhancement mechanisms can coexist in this balsam pear-shaped CuO. Finally, the prepared substrate has been applied for the determination of trace levels of paraquat in solution , and results show that its LOD for paraquat is 275 μg L-1 (optimum Raman band: 1646 cm-1 Raman shift), which is better than the government standard in China. A dexterous and facile way for fabrication of CuO SERS-active substrates with low cost and high performance, quite promising in detection of chemically hazardous substances and pesticide residue is provided. Graphical abstract.
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Affiliation(s)
- Pei Liang
- College of Optical and Electronic Technology, China Jiliang University, Hangzhou, 310018, China.
| | - Yu Cao
- College of Optical and Electronic Technology, China Jiliang University, Hangzhou, 310018, China
| | - Qianmin Dong
- College of Optical and Electronic Technology, China Jiliang University, Hangzhou, 310018, China.
| | - Dan Wang
- College of Optical and Electronic Technology, China Jiliang University, Hangzhou, 310018, China
| | - De Zhang
- College of Horticulture & Forestry Sciences, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shangzhong Jin
- College of Optical and Electronic Technology, China Jiliang University, Hangzhou, 310018, China
| | - Zhi Yu
- College of Horticulture & Forestry Sciences, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jiaming Ye
- Analysis and Testing Center, Yangtze Delta Region Institute of Tsinghua University, Jiaxing, 314006, China
| | - Mingqiang Zou
- Chinese Academy of Inspection and Quarantine (CAIQ), No.A 3, Gaobeidian Road, Chaoyang District, Beijing, 100123, China.,China Inspection Laboratory Technologies Co. Ltd (CILT), No.A 3, Gaobeidian Road, Chaoyang District, Beijing, 100123, China
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Morris RH. Methane activation by a single copper center in particulate methane monooxygenase: A computational study. Inorganica Chim Acta 2020. [DOI: 10.1016/j.ica.2020.119441] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Fisher OS, Sendzik MR, Ross MO, Lawton TJ, Hoffman BM, Rosenzweig AC. PCu AC domains from methane-oxidizing bacteria use a histidine brace to bind copper. J Biol Chem 2019; 294:16351-16363. [PMID: 31527086 PMCID: PMC6827282 DOI: 10.1074/jbc.ra119.010093] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 09/09/2019] [Indexed: 01/07/2023] Open
Abstract
Copper is critically important for methanotrophic bacteria because their primary metabolic enzyme, particulate methane monooxygenase (pMMO), is copper-dependent. In addition to pMMO, many other copper proteins are encoded in the genomes of methanotrophs, including proteins that contain periplasmic copper-Achaperone (PCuAC) domains. Using bioinformatics analyses, we identified three distinct classes of PCuAC domain-containing proteins in methanotrophs, termed PmoF1, PmoF2, and PmoF3. PCuAC domains from other types of bacteria bind a single Cu(I) ion via an HXnMX21/22HXM motif, which is also present in PmoF3, but PmoF1 and PmoF2 lack this motif entirely. Instead, the PCuAC domains of PmoF1 and PmoF2 bind only Cu(II), and PmoF1 binds additional Cu(II) ions in a His-rich extension to its PCuAC domain. Crystal structures of the PmoF1 and PmoF2 PCuAC domains reveal that Cu(II) is coordinated by an N-terminal histidine brace HX10H motif. This binding site is distinct from those of previously characterized PCuAC domains but resembles copper centers in CopC proteins and lytic polysaccharide monooxygenase (LPMO) enzymes. Bioinformatics analysis of the entire PCuAC family reveals previously unappreciated diversity, including sequences that contain both the HXnMX21/22HXM and HX10H motifs, and sequences that lack either set of copper-binding ligands. These findings provide the first characterization of an additional class of copper proteins from methanotrophs, further expand the PCuAC family, and afford new insight into the biological significance of histidine brace-mediated copper coordination.
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Affiliation(s)
- Oriana S. Fisher
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208
| | - Madison R. Sendzik
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208
| | - Matthew O. Ross
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208
| | - Thomas J. Lawton
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208
| | - Brian M. Hoffman
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208
| | - Amy C. Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, To whom correspondence should be addressed:
Depts. of Molecular Biosciences and Chemistry, Northwestern University, Evanston, IL 60208. Tel.:
847-467-5301; Fax:
847-467-6489; E-mail:
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Zhang S, Zhao L. A merged copper(I/II) cluster isolated from Glaser coupling. Nat Commun 2019; 10:4848. [PMID: 31649254 PMCID: PMC6813345 DOI: 10.1038/s41467-019-12889-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 10/08/2019] [Indexed: 12/04/2022] Open
Abstract
Ubiquitous copper-oxygen species are pivotal in enabling multifarious oxidation reactions in biological and chemical transformations. We herein construct a macrocycle-protected mixed-valence cluster [(tBuC≡CCuI3)-(μ2-OH)-CuII] by merging a copper acetylide cluster with a copper-oxygen moiety formed in Glaser coupling. This merged Cu(I/II) cluster shows remarkably strong oxidation capacity, whose reduction potential is among the most positive for Cu(II) and even comparable with some Cu(III) species. Consequently, the cluster exhibits high hydrogen atom transfer (HAT) reactivity with inert hydrocarbons. In contrast, the degraded [CuII-(μ2-OH)-CuII] embedded in a small macrocyclic homologue shows no HAT reactivity. Theoretical calculations indicate that the strong oxidation ability of Cu(II) in [(tBuC≡CCuI3)-(μ2-OH)-CuII] is mainly ascribed to the uneven charge distribution of Cu(I) ions in the tBuC≡CCuI3 unit because of significant [dCu(I) → π*(C≡C)] back donation. The present study on in situ formed metal clusters opens a broad prospect for mechanistic studies of Cu-based catalytic reactions. Copper-oxygen species in organometallic complexes and enzymes are involved in many oxidation reactions. Here, the authors synthesize a macrocycle-protected mixed valence Cu(I/II) cluster with an unusually strong oxidation capacity and apply it to hydrogen atom transfer reactions with inert hydrocarbons.
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Affiliation(s)
- Siqi Zhang
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Liang Zhao
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing, 100084, China.
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Miyanishi M, Abe T, Hori Y, Shiota Y, Yoshizawa K. Role of Amino Acid Residues for Dioxygen Activation in the Second Coordination Sphere of the Dicopper Site of pMMO. Inorg Chem 2019; 58:12280-12288. [DOI: 10.1021/acs.inorgchem.9b01752] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Mayuko Miyanishi
- Institute for Materials Chemistry and Engineering and IRCCS, Kyushu University, Fukuoka 819-0395, Japan
| | - Tsukasa Abe
- Institute for Materials Chemistry and Engineering and IRCCS, Kyushu University, Fukuoka 819-0395, Japan
| | - Yuta Hori
- Institute for Materials Chemistry and Engineering and IRCCS, Kyushu University, Fukuoka 819-0395, Japan
| | - Yoshihito Shiota
- 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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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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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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