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Arora S, Rawal P, Gupta P. Orbital Analysis Captures the Existence of a Mixed-Valent Cu III -O-Cu II Active-Site and its Role in Water-Assisted Aliphatic Hydroxylation. Chemistry 2024; 30:e202303722. [PMID: 38168869 DOI: 10.1002/chem.202303722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/31/2023] [Accepted: 01/03/2024] [Indexed: 01/05/2024]
Abstract
The Cu-O-Cu core has been proposed as a potential site for methane oxidation in particulate methane monooxygenase. In this work, we used density functional theory (DFT) to design a mixed-valent CuIII -O-CuII species from an experimentally known peroxo-dicopper complex supported by N-donor ligands containing phenolic groups. We found that the transfer of two-protons and two-electrons from phenolic groups to peroxo-dicopper core takes place, which results to the formation of a bis-μ-hydroxo-dicopper core. The bis-μ-hydroxo-dicopper core converts to a mixed-valent CuIII -O-CuII core with the removal of a water molecule. The orbital and spin density analyses unravel the mixed-valent nature of CuIII -O-CuII . We further investigated the reactivity of this mixed-valent core for aliphatic C-H hydroxylation. Our study unveiled that mixed-valent CuIII -O-CuII core follows a hydrogen atom transfer mechanism for C-H activation. An in-situ generated water molecule plays an important role in C-H hydroxylation by acting as a proton transfer bridge between carbon and oxygen. Furthermore, to assess the relevance of a mixed-valent CuIII -O-CuII core, we investigated aliphatic C-H activation by a symmetrical CuII -O-CuII core. DFT results show that the mixed-valent CuIII -O-CuII core is more reactive toward the C-H bond than the symmetrical CuII -O-CuII core.
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Affiliation(s)
- Sumangla Arora
- Computational Catalysis Center, Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667
| | - Parveen Rawal
- Computational Catalysis Center, Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667
| | - Puneet Gupta
- Computational Catalysis Center, Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667
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2
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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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3
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Wendeborn S. Chemie, Biologie und Regulierung der Nitrifikation von Ammonium im Boden. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201903014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Sebastian Wendeborn
- Fachhochschule Nordwestschweiz FHNWHochschule für Life SciencesInstitut für Chemie und Bioanalytik Hofackerstrasse 30 CH-4132 Muttenz Schweiz
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Wendeborn S. The Chemistry, Biology, and Modulation of Ammonium Nitrification in Soil. Angew Chem Int Ed Engl 2019; 59:2182-2202. [PMID: 31116902 DOI: 10.1002/anie.201903014] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 05/15/2019] [Indexed: 11/11/2022]
Abstract
Approximately two percent of the world's energy is consumed in the production of ammonia from hydrogen and nitrogen gas. Ammonia is used as a fertilizer ingredient for agriculture and distributed in the environment on an enormous scale to promote crop growth in intensive farming. Only 30-50 % of the nitrogen applied is assimilated by crop plants; the remaining 50-70 % goes into biological processes such as nitrification by microbial metabolism in the soil. This leads to an imbalance in the global nitrogen cycle and higher nitrous oxide emissions (a potent and significant greenhouse gas) as well as contamination of ground and surface waters by nitrate from the nitrogen-fertilized farmland. This Review gives a critical overview of the current knowledge of soil microbes involved in the chemistry of ammonia nitrification, the structures and mechanisms of the enzymes involved, and phytochemicals capable of inhibiting ammonia nitrification.
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Affiliation(s)
- Sebastian Wendeborn
- University of Applied Sciences and Arts Northwestern Switzerland, School of Life Sciences, Institute for Chemistry and Bioanalytics, Hofackerstrasse 30, CH-4132, Muttenz, Switzerland
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5
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Borah BJ, Mahanta A, Mondal M, Gogoi H, Yamada Y, Bharali P. Cobalt-Copper Nanoparticles Catalyzed Selective Oxidation Reactions: Efficient Catalysis at Room Temperature. ChemistrySelect 2018. [DOI: 10.1002/slct.201801140] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Biraj Jyoti Borah
- Department of Chemical Sciences; Tezpur University, Napaam; Tezpur - 784 028 India (P. Bharali
| | - Abhijit Mahanta
- Department of Chemical Sciences; Tezpur University, Napaam; Tezpur - 784 028 India (P. Bharali
| | - Manoj Mondal
- Department of Chemical Sciences; Tezpur University, Napaam; Tezpur - 784 028 India (P. Bharali
| | - Hemen Gogoi
- Department of Chemical Sciences; Tezpur University, Napaam; Tezpur - 784 028 India (P. Bharali
| | - Yusuke Yamada
- Department of Applied Chemistry & Bioengineering; Graduate School of Engineering; Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku; Osaka 558-8585 Japan
| | - Pankaj Bharali
- Department of Chemical Sciences; Tezpur University, Napaam; Tezpur - 784 028 India (P. Bharali
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6
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Kochem A, Molloy JK, Gellon G, Leconte N, Philouze C, Berthiol F, Jarjayes O, Thomas F. A Structurally Characterized Cu III Complex Supported by a Bis(anilido) Ligand and Its Oxidative Catalytic Activity. Chemistry 2017; 23:13929-13940. [PMID: 28742929 DOI: 10.1002/chem.201702010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Indexed: 01/23/2023]
Abstract
Three copper(II) complexes of the (R,R)-N,N'-bis(3,5-di-tert-butyl-2-aminobenzylidene)-1,2-diaminocyclohexane ligand, namely [Cu(N L)], [Cu(N LH)]+ and [Cu(N LH2 )]2+ , were prepared and structurally characterized. In [Cu(N LH2 )]2+ the copper ion lies in an octahedral geometry with the aniline groups coordinated in equatorial positions. In [Cu(N L)] the anilines are deprotonated (anilido moieties) and coordinated to an almost square-planar metal ion. Complex [Cu(N L)] displays two oxidation waves at E1/2ox, 1 =-0.14 V and E1/2ox, 2 =0.36 V vs. Fc+ /Fc in CH2 Cl2 . Complex [Cu(N LH2 )]2+ displays an irreversible oxidation wave at high potential (1.21 V), but shows a readily accessible and reversible metal-centered reduction at E1/2red =-0.67 V (CuII /CuI redox couple). Oxidation of [Cu(N L)] by AgSbF6 produces [Cu(N L)](SbF6 ), which was isolated as single crystals. X-ray structure analysis discloses a contraction of the coordination sphere by 0.05 Å upon oxidation, supporting a metal-centered process. Complex [Cu(N L)](SbF6 ) displays an intense NIR band at 1260 nm corresponding to an anilido-to-copper(III) charge transfer transition. This compound slowly evolves in CH2 Cl2 solution towards [Cu(N LH)](SbF6 ), which is a copper(II) complex comprised of both anilido and aniline groups coordinated to the metal center. The copper(III) complex [Cu(N L)](SbF6 ) is an efficient catalyst for benzyl alcohol oxidation, with 236 TON in 24 h at 298 K, without additives other than oxygen and a base.
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Affiliation(s)
- Amélie Kochem
- Département de Chimie Moléculaire, UMR-5250, Université Grenoble Alpes, BP 53, 38041, Grenoble Cedex 9, France
| | - Jennifer K Molloy
- Département de Chimie Moléculaire, UMR-5250, Université Grenoble Alpes, BP 53, 38041, Grenoble Cedex 9, France
| | - Gisèle Gellon
- Département de Chimie Moléculaire, UMR-5250, Université Grenoble Alpes, BP 53, 38041, Grenoble Cedex 9, France
| | - Nicolas Leconte
- Département de Chimie Moléculaire, UMR-5250, Université Grenoble Alpes, BP 53, 38041, Grenoble Cedex 9, France
| | - Christian Philouze
- Département de Chimie Moléculaire, UMR-5250, Université Grenoble Alpes, BP 53, 38041, Grenoble Cedex 9, France
| | - Florian Berthiol
- Département de Chimie Moléculaire, UMR-5250, Université Grenoble Alpes, BP 53, 38041, Grenoble Cedex 9, France
| | - Olivier Jarjayes
- Département de Chimie Moléculaire, UMR-5250, Université Grenoble Alpes, BP 53, 38041, Grenoble Cedex 9, France
| | - Fabrice Thomas
- Département de Chimie Moléculaire, UMR-5250, Université Grenoble Alpes, BP 53, 38041, Grenoble Cedex 9, France
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Ghashghavi M, Jetten MSM, Lüke C. Survey of methanotrophic diversity in various ecosystems by degenerate methane monooxygenase gene primers. AMB Express 2017; 7:162. [PMID: 28831762 PMCID: PMC5567572 DOI: 10.1186/s13568-017-0466-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 08/17/2017] [Indexed: 01/07/2023] Open
Abstract
Methane is the second most important greenhouse gas contributing to about 20% of global warming. Its mitigation is conducted by methane oxidizing bacteria that act as a biofilter using methane as their energy and carbon source. Since their first discovery in 1906, methanotrophs have been studied using a complementary array of methods. One of the most used molecular methods involves PCR amplification of the functional gene marker for the diagnostic of copper and iron containing particulate methane monooxygenase. To investigate the diversity of methanotrophs and to extend their possible molecular detection, we designed a new set of degenerate methane monooxygenase primers to target an 850 nucleotide long sequence stretch from pmoC to pmoA. The primers were based on all available full genomic pmoCAB operons. The newly designed primers were tested on various pure cultures, enrichment cultures and environmental samples using PCR. The results demonstrated that this primer set has the ability to correctly amplify the about 850 nucleotide long pmoCA product from Alphaproteobacteria, Gammaproteobacteria, Verrucomicrobia and the NC10 phyla methanotrophs. The new primer set will thus be a valuable tool to screen ecosystems and can be applied in conjunction with previously used pmoA primers to extend the diversity of currently known methane-oxidizing bacteria.
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8
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Ross MO, Rosenzweig AC. A tale of two methane monooxygenases. J Biol Inorg Chem 2017; 22:307-319. [PMID: 27878395 PMCID: PMC5352483 DOI: 10.1007/s00775-016-1419-y] [Citation(s) in RCA: 148] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 11/15/2016] [Indexed: 11/24/2022]
Abstract
Methane monooxygenase (MMO) enzymes activate O2 for oxidation of methane. Two distinct MMOs exist in nature, a soluble form that uses a diiron active site (sMMO) and a membrane-bound form with a catalytic copper center (pMMO). Understanding the reaction mechanisms of these enzymes is of fundamental importance to biologists and chemists, and is also relevant to the development of new biocatalysts. The sMMO catalytic cycle has been elucidated in detail, including O2 activation intermediates and the nature of the methane-oxidizing species. By contrast, many aspects of pMMO catalysis remain unclear, most notably the nuclearity and molecular details of the copper active site. Here, we review the current state of knowledge for both enzymes, and consider pMMO O2 activation intermediates suggested by computational and synthetic studies in the context of existing biochemical data. Further work is needed on all fronts, with the ultimate goal of understanding how these two remarkable enzymes catalyze a reaction not readily achieved by any other metalloenzyme or biomimetic compound.
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Affiliation(s)
- Matthew O Ross
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL, 60208, USA
| | - Amy C Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL, 60208, USA.
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9
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Lawton TJ, Rosenzweig AC. Methane-Oxidizing Enzymes: An Upstream Problem in Biological Gas-to-Liquids Conversion. J Am Chem Soc 2016; 138:9327-40. [PMID: 27366961 PMCID: PMC5242187 DOI: 10.1021/jacs.6b04568] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Biological conversion of natural gas to liquids (Bio-GTL) represents an immense economic opportunity. In nature, aerobic methanotrophic bacteria and anaerobic archaea are able to selectively oxidize methane using methane monooxygenase (MMO) and methyl coenzyme M reductase (MCR) enzymes. Although significant progress has been made toward genetically manipulating these organisms for biotechnological applications, the enzymes themselves are slow, complex, and not recombinantly tractable in traditional industrial hosts. With turnover numbers of 0.16-13 s(-1), these enzymes pose a considerable upstream problem in the biological production of fuels or chemicals from methane. Methane oxidation enzymes will need to be engineered to be faster to enable high volumetric productivities; however, efforts to do so and to engineer simpler enzymes have been minimally successful. Moreover, known methane-oxidizing enzymes have different expression levels, carbon and energy efficiencies, require auxiliary systems for biosynthesis and function, and vary considerably in terms of complexity and reductant requirements. The pros and cons of using each methane-oxidizing enzyme for Bio-GTL are considered in detail. The future for these enzymes is bright, but a renewed focus on studying them will be critical to the successful development of biological processes that utilize methane as a feedstock.
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Affiliation(s)
- Thomas J Lawton
- Departments of Molecular Biosciences and of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Amy C Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
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10
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Tishchenko KI, Beloglazkina EK, Mazhuga AG, Zyk NV. Copper-containing enzymes: Site types and low-molecular-weight model compounds. ACTA ACUST UNITED AC 2016. [DOI: 10.1134/s2079978016010027] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Kafentzi MC, Orio M, Réglier M, Yao S, Kuhlmann U, Hildebrandt P, Driess M, Simaan AJ, Ray K. Changing the chemical and physical properties of high valent heterobimetallic bis-(μ-oxido) Cu–Ni complexes by ligand effects. Dalton Trans 2016; 45:15994-16000. [DOI: 10.1039/c6dt02391f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two new heterobimetallic [LNiO2Cu(RPY2)]+ (RPY2 = N-substituted bis 2-pyridyl(ethylamine) ligands with R = indane, 3a or R = Me, 3b) complexes have been spectroscopically trapped at low temperatures.
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Affiliation(s)
| | - Maylis Orio
- Aix Marseille Univ
- CNRS
- Centrale Marseille
- iSm2
- Marseille
| | | | - Shenglai Yao
- Department of Chemistry
- Technische Universität Berlin
- 10623 Berlin
- Germany
| | - Uwe Kuhlmann
- Department of Chemistry
- Technische Universität Berlin
- 10623 Berlin
- Germany
| | - Peter Hildebrandt
- Department of Chemistry
- Technische Universität Berlin
- 10623 Berlin
- Germany
| | - Matthias Driess
- Department of Chemistry
- Technische Universität Berlin
- 10623 Berlin
- Germany
| | | | - Kallol Ray
- Department of Chemistry
- Humboldt-Universität zu Berlin
- 12489 Berlin
- Germany
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12
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Gilman A, Laurens LM, Puri AW, Chu F, Pienkos PT, Lidstrom ME. Bioreactor performance parameters for an industrially-promising methanotroph Methylomicrobium buryatense 5GB1. Microb Cell Fact 2015; 14:182. [PMID: 26572866 PMCID: PMC4647623 DOI: 10.1186/s12934-015-0372-8] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 10/29/2015] [Indexed: 11/22/2022] Open
Abstract
Background Methane is a feedstock of interest for the future, both from natural gas and from renewable biogas sources. Methanotrophic bacteria have the potential to enable commercial methane bioconversion to value-added products such as fuels and chemicals. A strain of interest for such applications is Methylomicrobium buryatense 5GB1, due to its robust growth characteristics. However, to take advantage of the potential of this methanotroph, it is important to generate comprehensive bioreactor-based datasets for different growth conditions to compare bioprocess parameters. Results Datasets of growth parameters, gas utilization rates, and products (total biomass, extracted fatty acids, glycogen, excreted acids) were obtained for cultures of M. buryatense 5GB1 grown in continuous culture under methane limitation and O2 limitation conditions. Additionally, experiments were performed involving unrestricted batch growth conditions with both methane and methanol as substrate. All four growth conditions show significant differences. The most notable changes are the high glycogen content and high formate excretion for cells grown on methanol (batch), and high O2:CH4 utilization ratio for cells grown under methane limitation. Conclusions The results presented here represent the most comprehensive published bioreactor datasets for a gamma-proteobacterial methanotroph. This information shows that metabolism by M. buryatense 5GB1 differs significantly for each of the four conditions tested. O2 limitation resulted in the lowest relative O2 demand and fed-batch growth on methane the highest. Future studies are needed to understand the metabolic basis of these differences. However, these results suggest that both batch and continuous culture conditions have specific advantages, depending on the product of interest. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0372-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexey Gilman
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, USA.
| | - Lieve M Laurens
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, USA.
| | - Aaron W Puri
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, USA.
| | - Frances Chu
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, USA.
| | - Philip T Pienkos
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, USA.
| | - Mary E Lidstrom
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, USA. .,Department of Microbiology, University of Washington, Seattle, WA, 98195, USA.
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Sutradhar M, Martins LMDRS, Guedes da Silva MFC, Mahmudov KT, Liu CM, Pombeiro AJL. Trinuclear CuIIStructural Isomers: Coordination, Magnetism, Electrochemistry and Catalytic Activity towards the Oxidation of Alkanes. Eur J Inorg Chem 2015. [DOI: 10.1002/ejic.201500440] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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14
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Beeson WT, Vu VV, Span EA, Phillips CM, Marletta MA. Cellulose degradation by polysaccharide monooxygenases. Annu Rev Biochem 2015; 84:923-46. [PMID: 25784051 DOI: 10.1146/annurev-biochem-060614-034439] [Citation(s) in RCA: 198] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Polysaccharide monooxygenases (PMOs), also known as lytic PMOs (LPMOs), enhance the depolymerization of recalcitrant polysaccharides by hydrolytic enzymes and are found in the majority of cellulolytic fungi and actinomycete bacteria. For more than a decade, PMOs were incorrectly annotated as family 61 glycoside hydrolases (GH61s) or family 33 carbohydrate-binding modules (CBM33s). PMOs have an unusual surface-exposed active site with a tightly bound Cu(II) ion that catalyzes the regioselective hydroxylation of crystalline cellulose, leading to glycosidic bond cleavage. The genomes of some cellulolytic fungi contain more than 20 genes encoding cellulose-active PMOs, suggesting a diversity of biological activities. PMOs show great promise in reducing the cost of conversion of lignocellulosic biomass to fermentable sugars; however, many questions remain about their reaction mechanism and biological function. This review addresses, in depth, the structural and mechanistic aspects of oxidative depolymerization of cellulose by PMOs and considers their biological function and phylogenetic diversity.
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Affiliation(s)
- William T Beeson
- Department of Chemistry, University of California, Berkeley, California 94720
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15
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Chidambarampadmavathy K, Obulisamy P. K, Heimann K. Role of copper and iron in methane oxidation and bacterial biopolymer accumulation. Eng Life Sci 2015. [DOI: 10.1002/elsc.201400127] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Karthigeyan Chidambarampadmavathy
- Collegeof Marine and Environmental ScienceJames Cook University Townsville Queensland Australia
- Centre for Sustainable Fisheries and AquacultureJames Cook University Townsville Queensland Australia
| | - Karthikeyan Obulisamy P.
- Collegeof Marine and Environmental ScienceJames Cook University Townsville Queensland Australia
- Centre for Sustainable Fisheries and AquacultureJames Cook University Townsville Queensland Australia
| | - Kirsten Heimann
- Collegeof Marine and Environmental ScienceJames Cook University Townsville Queensland Australia
- Centre for Sustainable Fisheries and AquacultureJames Cook University Townsville Queensland Australia
- Centre for Biodiscovery and Molecular Development of TherapeuticsJames Cook University Townsville Queensland Australia
- Comparative Genomics CentreJames Cook University Townsville Queensland Australia
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16
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Sazinsky MH, Lippard SJ. Methane Monooxygenase: Functionalizing Methane at Iron and Copper. Met Ions Life Sci 2015; 15:205-56. [DOI: 10.1007/978-3-319-12415-5_6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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17
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Abstract
Particulate methane monooxygenase (pMMO) is an integral membrane metalloenzyme that oxidizes methane to methanol in methanotrophic bacteria, organisms that live on methane gas as their sole carbon source. Understanding pMMO function has important implications for bioremediation applications and for the development of new, environmentally friendly catalysts for the direct conversion of methane to methanol. Crystal structures of pMMOs from three different methanotrophs reveal a trimeric architecture, consisting of three copies each of the pmoB, pmoA, and pmoC subunits. There are three distinct metal centers in each protomer of the trimer, mononuclear and dinuclear copper sites in the periplasmic regions of pmoB and a mononuclear site within the membrane that can be occupied by copper or zinc. Various models for the pMMO active site have been proposed within these structural constraints, including dicopper, tricopper, and diiron centers. Biochemical and spectroscopic data on pMMO and recombinant soluble fragments, denoted spmoB proteins, indicate that the active site involves copper and is located at the site of the dicopper center in the pmoB subunit. Initial spectroscopic evidence for O(2) binding at this site has been obtained. Despite these findings, questions remain about the active site identity and nuclearity and will be the focus of future studies.
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Affiliation(s)
- Megen A. Culpepper
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Amy C. Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL 60208, USA
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18
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The divergent AmoC3 subunit of ammonia monooxygenase functions as part of a stress response system in Nitrosomonas europaea. J Bacteriol 2012; 194:3448-56. [PMID: 22544266 DOI: 10.1128/jb.00133-12] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ammonia monooxygenase of chemolithotrophic ammonia-oxidizing bacteria (AOB) catalyzes the first step in ammonia oxidation by converting ammonia to hydroxylamine. The monooxygenase of Nitrosomonas europaea is encoded by two nearly identical operon copies (amoCAB(1,2)). Several AOB, including N. europaea, also possess a divergent monocistronic copy of amoC (amoC(3)) of unknown function. Previous work suggested a possible functional role for amoC(3) as part of the σ(E) stress response regulon during the recovery of N. europaea from extended ammonia starvation, thus indicating its importance during the exit of cells from starvation. We here used global transcription analysis to show that expression of amoC(3) is part of a general poststarvation cellular response system in N. europaea. We also found that amoC(3) is required for an efficient response to some stress conditions, as deleting this gene impaired growth at elevated temperatures and recovery following starvation under high oxygen tensions. Deletion of the σ(32) global stress response regulator demonstrated that the heat shock regulon plays a significant role in mediating the recovery of N. europaea from starvation. These findings provide the first described phenotype associated with the divergent AmoC(3) subunit which appears to function as a stress-responsive subunit capable of maintaining ammonia oxidation activity under stress conditions. While this study was limited to starvation and heat shock, it is possible that the AmoC(3) subunit may be responsive to other membrane stressors (e.g., solvent or osmotic shocks) that are prevalent in the environments of AOB.
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A three-dimensional metal–organic framework based on hexanuclear copper units with unsaturated CuII centers. INORG CHEM COMMUN 2012. [DOI: 10.1016/j.inoche.2011.11.040] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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20
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Kenney GE, Rosenzweig AC. Chemistry and biology of the copper chelator methanobactin. ACS Chem Biol 2012; 7:260-8. [PMID: 22126187 DOI: 10.1021/cb2003913] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Methanotrophic bacteria, organisms that oxidize methane, produce a small copper chelating molecule called methanobactin (Mb). Mb binds Cu(I) with high affinity and is hypothesized to mediate copper acquisition from the environment. Recent advances in Mb characterization include revision of the chemical structure of Mb from Methylosinus trichosporium OB3b and further investigation of its biophysical properties. In addition, Mb production by several other methanotroph strains has been investigated, and preliminary characterization suggests diversity in chemical composition. Initial clues into Mb biosynthesis have been obtained by identification of a putative precursor gene in the M. trichosporium OB3b genome. Finally, direct uptake of intact Mb into the cytoplasm of M. trichosporium OB3b cells has been demonstrated, and studies of the transport mechanism have been initiated. Taken together, these advances represent significant progress and set the stage for exciting new research directions.
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Affiliation(s)
- Grace E. Kenney
- 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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21
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Smith SM, Rawat S, Telser J, Hoffman BM, Stemmler TL, Rosenzweig AC. Crystal structure and characterization of particulate methane monooxygenase from Methylocystis species strain M. Biochemistry 2011; 50:10231-40. [PMID: 22013879 PMCID: PMC3364217 DOI: 10.1021/bi200801z] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Particulate methane monooxygenase (pMMO) is an integral membrane metalloenzyme that oxidizes methane to methanol in methanotrophic bacteria. Previous biochemical and structural studies of pMMO have focused on preparations from Methylococcus capsulatus (Bath) and Methylosinus trichosporium OB3b. A pMMO from a third organism, Methylocystis species strain M, has been isolated and characterized. Both membrane-bound and solubilized Methylocystis sp. strain M pMMO contain ~2 copper ions per 100 kDa protomer and exhibit copper-dependent propylene epoxidation activity. Spectroscopic data indicate that Methylocystis sp. strain M pMMO contains a mixture of Cu(I) and Cu(II), of which the latter exhibits two distinct type 2 Cu(II) electron paramagnetic resonance (EPR) signals. Extended X-ray absorption fine structure (EXAFS) data are best fit with a mixture of Cu-O/N and Cu-Cu ligand environments with a Cu-Cu interaction at 2.52-2.64 Å. The crystal structure of Methylocystis sp. strain M pMMO was determined to 2.68 Å resolution and is the best quality pMMO structure obtained to date. It provides a revised model for the pmoA and pmoC subunits and has led to an improved model of M. capsulatus (Bath) pMMO. In these new structures, the intramembrane zinc/copper binding site has a different coordination environment from that in previous models.
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Affiliation(s)
- Stephen M. Smith
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Swati Rawat
- Department of Biochemistry and Molecular Biology, Wayne State University, School of Medicine, Detroit, Michigan 48201, United States
| | - Joshua Telser
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Brian M. Hoffman
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Timothy L. Stemmler
- Department of Biochemistry and Molecular Biology, Wayne State University, School of Medicine, Detroit, Michigan 48201, United States
| | - Amy C. Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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22
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Tumanova LV, Tukhvatullin IA, Burbaev DS, Gvozdev RI, Andersson KK. The binuclear iron site of membrane-bound methane hydroxylase from Methylococcus capsulatus (Strain M). RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2011; 34:194-203. [DOI: 10.1134/s1068162008020064] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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Xuereb DJ, Raja R. Design strategies for engineering selectivity in bio-inspired heterogeneous catalysts. Catal Sci Technol 2011. [DOI: 10.1039/c0cy00088d] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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24
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Himes RA, Karlin KD. Copper-dioxygen complex mediated C-H bond oxygenation: relevance for particulate methane monooxygenase (pMMO). Curr Opin Chem Biol 2009; 13:119-31. [PMID: 19286415 DOI: 10.1016/j.cbpa.2009.02.025] [Citation(s) in RCA: 176] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2009] [Revised: 02/11/2009] [Accepted: 02/23/2009] [Indexed: 10/21/2022]
Abstract
Particulate methane monooxygenase (pMMO), an integral membrane protein found in methanotrophic bacteria, catalyzes the oxidation of methane to methanol. Expression and greater activity of the enzyme in the presence of copper ion suggest that pMMO is a cuprous metalloenzyme. Recent advances - especially the first crystal structures of pMMO - have energized the field, but the nature of the active site(s) and the mechanism of methane oxidation remain poorly understood-yet hotly contested. Herein the authors briefly review the current understanding of the pMMO metal sites and discuss advances in small molecule Cu-O(2) chemistry that may contribute to an understanding of copper-ion mediated hydrocarbon oxidation chemistry.
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Affiliation(s)
- Richard A Himes
- Department of Chemistry, The Johns Hopkins University, Baltimore, MD 21218, United States.
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26
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Junier P, Kim OS, Junier T, Ahn TS, Imhoff JF, Witzel KP. Community analysis of betaproteobacterial ammonia-oxidizing bacteria using the amoCAB operon. Appl Microbiol Biotechnol 2009; 83:175-88. [PMID: 19274459 PMCID: PMC2845890 DOI: 10.1007/s00253-009-1923-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2008] [Revised: 02/17/2009] [Accepted: 02/17/2009] [Indexed: 01/03/2023]
Abstract
The genes and intergenic regions of the amoCAB operon were analyzed to establish their potential as molecular markers for analyzing ammonia-oxidizing betaproteobacterial (beta-AOB) communities. Initially, sequence similarity for related taxa, evolutionary rates from linear regressions, and the presence of conserved and variable regions were analyzed for all available sequences of the complete amoCAB operon. The gene amoB showed the highest sequence variability of the three amo genes, suggesting that it might be a better molecular marker than the most frequently used amoA to resolve closely related AOB species. To test the suitability of using the amoCAB genes for community studies, a strategy involving nested PCR was employed. Primers to amplify the whole amoCAB operon and each individual gene were tested. The specificity of the products generated was analyzed by denaturing gradient gel electrophoresis, cloning, and sequencing. The fragments obtained showed different grades of sequence identity to amoCAB sequences in the GenBank database. The nested PCR approach provides a possibility to increase the sensitivity of detection of amo genes in samples with low abundance of AOB. It also allows the amplification of the almost complete amoA gene, with about 300 bp more sequence information than the previous approaches. The coupled study of all three amo genes and the intergenic spacer regions that are under different selection pressure might allow a more detailed analysis of the evolutionary processes, which are responsible for the differentiation of AOB communities in different habitats.
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Affiliation(s)
- Pilar Junier
- Ecole Polytechnique Fédérale de Lausanne (EPFL ENAC ISTE EML), CE 1 644 (Centre Est), Station 6, 1015 Lausanne, Switzerland.
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27
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Gilch S, Vogel M, Lorenz MW, Meyer O, Schmidt I. Interaction of the mechanism-based inactivator acetylene with ammonia monooxygenase of Nitrosomonas europaea. MICROBIOLOGY-SGM 2009; 155:279-284. [PMID: 19118368 DOI: 10.1099/mic.0.023721-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The ammonia monooxygenase (AMO) of Nitrosomonas europaea is a metalloenzyme that catalyses the oxidation of ammonia to hydroxylamine. We have identified histidine 191 of AmoA as the binding site for the oxidized mechanism-based inactivator acetylene. Binding of acetylene changed the molecular mass of His-191 from 155.15 to 197.2 Da (+42.05), providing evidence that acetylene was oxidized to ketene (CH2CO; 42.04 Da) which binds specifically to His-191. It must be assumed that His-191 is part of the acetylene-activating site in AMO or at least directly neighbours this site.
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Affiliation(s)
- Stefan Gilch
- Department of Microbiology, University of Bayreuth, 95447 Bayreuth, Germany
| | - Manja Vogel
- Department of Microbiology, University of Bayreuth, 95447 Bayreuth, Germany
| | - Matthias W Lorenz
- Department of Animal Ecology, University of Bayreuth, 95447 Bayreuth, Germany
| | - Ortwin Meyer
- Department of Microbiology, University of Bayreuth, 95447 Bayreuth, Germany
| | - Ingo Schmidt
- Department of Microbiology, University of Bayreuth, 95447 Bayreuth, Germany
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28
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Abstract
pMMO (particulate methane mono-oxygenase) is an integral membrane metalloenzyme that catalyses the oxidation of methane to methanol. The pMMO metal active site has not been identified, precluding detailed investigation of the reaction mechanism. Models for the metal centres proposed by various research groups have evolved as crystallographic and spectroscopic data have become available. The present review traces the evolution of these active-site models before and after the 2005 Methylococcus capsulatus (Bath) pMMO crystal structure determination.
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29
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Hakemian AS, Kondapalli KC, Telser J, Hoffman BM, Stemmler TL, Rosenzweig AC. The metal centers of particulate methane monooxygenase from Methylosinus trichosporium OB3b. Biochemistry 2008; 47:6793-801. [PMID: 18540635 PMCID: PMC2664655 DOI: 10.1021/bi800598h] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Particulate methane monooxygenase (pMMO) is a membrane-bound metalloenzyme that oxidizes methane to methanol in methanotrophic bacteria. The nature of the pMMO active site and the overall metal content are controversial, with spectroscopic and crystallographic data suggesting the presence of a mononuclear copper center, a dinuclear copper center, a trinuclear center, and a diiron center or combinations thereof. Most studies have focused on pMMO from Methylococcus capsulatus (Bath). pMMO from a second organism, Methylosinus trichosporium OB3b, has been purified and characterized by spectroscopic and crystallographic methods. Purified M. trichosporium OB3b pMMO contains approximately 2 copper ions per 100 kDa protomer. Electron paramagnetic resonance (EPR) spectroscopic parameters indicate that type 2 Cu(II) is present as two distinct species. Extended X-ray absorption fine structure (EXAFS) data are best fit with oxygen/nitrogen ligands and reveal a Cu-Cu interaction at 2.52 A. Correspondingly, X-ray crystallography of M. trichosporium OB3b pMMO shows a dinuclear copper center, similar to that observed previously in the crystal structure of M. capsulatus (Bath) pMMO. There are, however, significant differences between the pMMO structures from the two organisms. A mononuclear copper center present in M. capsulatus (Bath) pMMO is absent in M. trichosporium OB3b pMMO, whereas a metal center occupied by zinc in the M. capsulatus (Bath) pMMO structure is occupied by copper in M. trichosporium OB3b pMMO. These findings extend previous work on pMMO from M. capsulatus (Bath) and provide new insight into the functional importance of the different metal centers.
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Affiliation(s)
| | | | | | | | - Timothy L. Stemmler
- To whom correspondence may be addressed. A.C.R.: tel, 847-467-5301; fax, 847-467-6489; e-mail, . T.L.S.: tel, 313-577-5712; fax, 313-577-2765; e-mail,
| | - Amy C. Rosenzweig
- To whom correspondence may be addressed. A.C.R.: tel, 847-467-5301; fax, 847-467-6489; e-mail, . T.L.S.: tel, 313-577-5712; fax, 313-577-2765; e-mail,
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30
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Junier P, Kim OS, Molina V, Limburg P, Junier T, Imhoff JF, Witzel KP. Comparative in silico analysis of PCR primers suited for diagnostics and cloning of ammonia monooxygenase genes from ammonia-oxidizing bacteria. FEMS Microbiol Ecol 2008; 64:141-52. [PMID: 18248438 DOI: 10.1111/j.1574-6941.2007.00437.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Over recent years, several PCR primers have been described to amplify genes encoding the structural subunits of ammonia monooxygenase (AMO) from ammonia-oxidizing bacteria (AOB). Most of them target amoA, while amoB and amoC have been neglected so far. This study compared the nucleotide sequence of 33 primers that have been used to amplify different regions of the amoCAB operon with alignments of all available sequences in public databases. The advantages and disadvantages of these primers are discussed based on the original description and the spectrum of matching sequences obtained. Additionally, new primers to amplify the almost complete amoCAB operon of AOB belonging to Betaproteobacteria (betaproteobacterial AOB), a primer pair for DGGE analysis of amoA and specific primers for gammaproteobacterial AOB, are also described. The specificity of these new primers was also evaluated using the databases of the sequences created during this study.
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Affiliation(s)
- Pilar Junier
- Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland.
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31
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Abstract
Methanotrophic bacteria oxidize methane to methanol in the first step of their metabolic pathway. Two forms of methane monooxygenase (MMO) enzymes catalyze this reaction: soluble MMO (sMMO) and membrane-bound or particulate MMO (pMMO). pMMO is expressed when copper is available, and its active site is believed to contain copper. Whereas sMMO is well characterized, most aspects of pMMO biochemistry remain unknown and somewhat controversial. This review emphasizes advances in the past two to three years related to pMMO and to copper uptake and copper-dependent regulation in methanotrophs. The pMMO metal centers have been characterized spectroscopically, and the first pMMO crystal structure has been determined. Significant effort has been devoted to improving in vitro pMMO activity. Proteins involved in sMMO regulation and additional copper-regulated proteins have been identified, and the Methylococcus capsulatus (Bath) genome has been sequenced. Finally, methanobactin (mb), a small copper chelator proposed to facilitate copper uptake, has been characterized.
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Affiliation(s)
- Amanda S Hakemian
- Department of Biochemistry, Northwestern University, Evanston, Illinois 60208, USA.
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32
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Balasubramanian R, Rosenzweig AC. Structural and mechanistic insights into methane oxidation by particulate methane monooxygenase. Acc Chem Res 2007; 40:573-80. [PMID: 17444606 DOI: 10.1021/ar700004s] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Particulate methane monooxygense (pMMO) is an integral membrane copper-containing enzyme that converts methane to methanol. Knowledge of how pMMO selectively oxidizes methane under ambient conditions could impact the development of new catalysts. The crystal structure of Methylococcus capsulatus (Bath) pMMO reveals the composition and location of three metal centers. Spectroscopic data provide insight into the coordination environments and oxidation states of these metal centers. These results, combined with computational studies and comparisons to relevant systems, are discussed in the context of identifying the most likely site for O 2 activation.
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33
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York JT, Llobet A, Cramer CJ, Tolman WB. Heterobimetallic dioxygen activation: synthesis and reactivity of mixed Cu-Pd and Cu-Pt bis(mu-oxo) complexes. J Am Chem Soc 2007; 129:7990-9. [PMID: 17550254 PMCID: PMC2625287 DOI: 10.1021/ja071744g] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Heterobimetallic CuPd and CuPt bis(mu-oxo) complexes have been prepared by the reaction of (PPh3)2MO2 (M=Pd, Pt) with LCu(I) precursors (L=beta-diketiminate and di- and triamine ligands) and characterized by low-temperature UV-vis, resonance Raman, and 1H and 31P[1H] NMR spectroscopy in conjunction with DFT calculations. The complexes decompose upon warming to yield OPPh3, and in one case this was shown to occur by an intramolecular process through crossover experiments using double-labeling (oxo and phosphine). The reactivity of one of the complexes, LMe2Cu(mu-O)2Pt(PPh3)2 (LMe2 = beta-diketiminate), with a variety of reagents including CO2, 2,4-di-tert-butylphenol, 2,4-di-tert-butylphenolate, [NH4][PF6], and dihydroanthracene, was compared to that of homometallic Pt2 and Cu2 counterparts. Unlike typical [Cu2(mu-O)2]2+ cores which have electrophilic oxo groups, the oxo groups in the [Cu(mu-O)2Pt]+ core behave as bases and nucleophiles, similar to previously described Pt2 compounds. In addition, however, the [Cu(mu-O)2Pt]+ core is capable of oxidatively coupling 2,4-di-tert-butylphenol and 2,4-di-tert-butylphenolate. Theoretical evaluation of the electron affinities, basicities, and H-atom transfer kinetics and thermodynamics of the Cu2 and CuM (M=Pd, Pt) cores showed that the latter are more basic and form stronger O-H bonds.
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Affiliation(s)
- John T York
- Department of Chemistry, Center for Metals in Biocatalysis, and Supercomputer Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, USA
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34
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Berube PM, Samudrala R, Stahl DA. Transcription of all amoC copies is associated with recovery of Nitrosomonas europaea from ammonia starvation. J Bacteriol 2007; 189:3935-44. [PMID: 17384196 PMCID: PMC1913382 DOI: 10.1128/jb.01861-06] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2006] [Accepted: 03/14/2007] [Indexed: 11/20/2022] Open
Abstract
The chemolithotrophic ammonia-oxidizing bacterium Nitrosomonas europaea is known to be highly resistant to starvation conditions. The transcriptional response of N. europaea to ammonia addition following short- and long-term starvation was examined by primer extension and S1 nuclease protection analyses of genes encoding enzymes for ammonia oxidation (amoCAB operons) and CO(2) fixation (cbbLS), a third, lone copy of amoC (amoC(3)), and two representative housekeeping genes (glyA and rpsJ). Primer extension analysis of RNA isolated from growing, starved, and recovering cells revealed two differentially regulated promoters upstream of the two amoCAB operons. The distal sigma(70) type amoCAB promoter was constitutively active in the presence of ammonia, but the proximal promoter was only active when cells were recovering from ammonia starvation. The lone, divergent copy of amoC (amoC(3)) was expressed only during recovery. Both the proximal amoC(1,2) promoter and the amoC(3) promoter are similar to gram-negative sigma(E) promoters, thus implicating sigma(E) in the regulation of the recovery response. Although modeling of subunit interactions suggested that a nonconservative proline substitution in AmoC(3) may modify the activity of the holoenzyme, characterization of a DeltaamoC(3) strain showed no significant difference in starvation recovery under conditions evaluated. In contrast to the amo transcripts, a delayed appearance of transcripts for a gene required for CO(2) fixation (cbbL) suggested that its transcription is retarded until sufficient energy is available. Overall, these data revealed a programmed exit from starvation likely involving regulation by sigma(E) and the coordinated regulation of catabolic and anabolic genes.
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Affiliation(s)
- Paul M Berube
- Department of Microbiology, University of Washington, Seattle, WA 98195-2700, USA
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35
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Chan S, Wang VC, Lai JH, Yu SF, Chen PY, Chen KC, Chen CL, Chan M. Redox Potentiometry Studies of Particulate Methane Monooxygenase: Support for a Trinuclear Copper Cluster Active Site. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200604647] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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36
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Chan SI, Wang VCC, Lai JCH, Yu SSF, Chen PPY, Chen KHC, Chen CL, Chan MK. Redox Potentiometry Studies of Particulate Methane Monooxygenase: Support for a Trinuclear Copper Cluster Active Site. Angew Chem Int Ed Engl 2007; 46:1992-4. [PMID: 17274089 DOI: 10.1002/anie.200604647] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Sunney I Chan
- Institute of Chemistry, Academia Sinica, Nankang, Taipei, Taiwan 11529, Republic of China.
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37
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Rosenzweig AC, Sazinsky MH. Structural insights into dioxygen-activating copper enzymes. Curr Opin Struct Biol 2006; 16:729-35. [PMID: 17011183 DOI: 10.1016/j.sbi.2006.09.005] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2006] [Revised: 08/10/2006] [Accepted: 09/19/2006] [Indexed: 10/24/2022]
Abstract
Copper-containing enzymes that react with O(2) play a key role in many biological processes. Mononuclear, dinuclear and trinuclear copper centers function in O(2) binding, activation and subsequent substrate oxidation. Recent advances in the structural biology of O(2)-activating copper enzymes range from the identification of novel copper centers, such as that of particulate methane monooxygenase, to the elucidation of the details of O(2) binding and reactivity in peptidylglycine alpha-hydroxylating monooxygenase. Structures of phenoxazinone synthase and Fet3 contribute to our understanding of multicopper oxidases. Additionally, details of the tyrosinase structure provide new insight into how dicopper sites confer substrate specificity. A common theme for each of these enzymes is that the protein scaffold plays a major role in dictating the overall function.
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Affiliation(s)
- Amy C Rosenzweig
- Department of Biochemistry, Northwestern University, Evanston, IL 60208, USA.
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38
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Nesterov DS, Kokozay VN, Dyakonenko VV, Shishkin OV, Jezierska J, Ozarowski A, Kirillov AM, Kopylovich MN, Pombeiro AJL. An unprecedented heterotrimetallic Fe/Cu/Co core for mild and highly efficient catalytic oxidation of cycloalkanes by hydrogen peroxide. Chem Commun (Camb) 2006:4605-7. [PMID: 17082857 DOI: 10.1039/b608790f] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An unprecedented hexanuclear heterotrimetallic Fe/Cu/Co complex bearing two Cu(mu-O)2Co(mu-O)2Fe cores is easily prepared by self-assembly and acts as a remarkable catalyst for the peroxidative oxidation of cycloalkanes under mild conditions.
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Affiliation(s)
- Dmytro S Nesterov
- Depart. Inorg. Chemistry, National Taras Shevchenko Univ., Volodymyrska str. 64, Kyiv, 01033, Ukraine
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39
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Aboelella NW, Gherman BF, Hill LMR, York JT, Holm N, Young VG, Cramer CJ, Tolman WB. Effects of thioether substituents on the O2 reactivity of beta-diketiminate-Cu(I) complexes: probing the role of the methionine ligand in copper monooxygenases. J Am Chem Soc 2006; 128:3445-58. [PMID: 16522125 PMCID: PMC2593856 DOI: 10.1021/ja057745v] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The activation of dioxygen by dopamine beta-monooxygenase (DbetaM) and peptidylglycine alpha-hydroxylating monooxygenase (PHM) is postulated to occur at a copper site ligated by two histidine imidazoles and a methionine thioether, which is unusual because such thioether ligation is not present in other O2-activating copper proteins. To assess the possible role of the thioether ligand in O2 activation by DbetaM and PHM, two new ligands comprising beta-diketiminates with thioether substituents were synthesized and Cu(I) and Cu(II) complexes were isolated. The Cu(II) compounds are monomeric and exhibit intramolecular thioether coordination. While the Cu(I) complexes exhibit a multinuclear topology in the solid state, variable-temperature 1H NMR studies implicate equilibria in solution, possibly including monomers with intramolecular thioether coordination that are structurally defined by DFT calculations. Low-temperature oxygenation of solutions of the Cu(I) complexes generates stable 1:1 Cu/O2 adducts, which on the basis of combined experimental and theoretical studies adopt side-on "eta(2)" structures with negligible Cu-thioether bonding and significant peroxo-Cu(III) character. In contrast to previously reported findings with related ligands lacking the thioether group, however (cf., Aboelella; et al. J. Am. Chem. Soc. 2004, 126, 16896), purging the solutions of the thioether-containing adducts with argon results in conversion to bis(mu-oxo)dicopper(III) species. A role for the thioether in promoting loss of O2 from the 1:1 Cu/O2 adduct and facilitating trapping of the resulting Cu(I) complex to yield the bis(mu-oxo) species is proposed, and the possible relevance of this role to that of the methionine in the active sites of DbetaM and PHM is discussed.
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Affiliation(s)
- Nermeen W Aboelella
- Department of Chemistry, Center for Metals in Biocatalysis, and Minnesota Supercomputer Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, USA
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40
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Hakemian AS, Tinberg CE, Kondapalli KC, Telser J, Hoffman BM, Stemmler TL, Rosenzweig AC. The copper chelator methanobactin from Methylosinus trichosporium OB3b binds copper(I). J Am Chem Soc 2006; 127:17142-3. [PMID: 16332035 PMCID: PMC2864604 DOI: 10.1021/ja0558140] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The oxidation state of copper bound to methanobactin, a small siderophore-like molecule from the methanotroph Methylosinus trichosporium OB3b, was investigated. Purified methanobactin loaded with Cu(II) exhibits a weak EPR signal probably due to adventitious Cu(II). The EPR signal intensity increases significantly upon addition of the strong oxidant nitric acid. Features of the X-ray absorption near edge spectrum, including a 1s --> 4p transition at 8985 eV, further indicate the presence of Cu(I). EXAFS data were best fit using a multiple scattering model generated from previously reported crystallographic parameters. These results establish definitively that M. trichosporium OB3b methanobactin binds Cu(I) and suggest that methanobactin itself reduces Cu(II) to Cu(I).
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Tolman WB. Using synthetic chemistry to understand copper protein active sites: a personal perspective. J Biol Inorg Chem 2006; 11:261-71. [PMID: 16447049 DOI: 10.1007/s00775-006-0078-9] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2005] [Accepted: 01/03/2006] [Indexed: 10/25/2022]
Abstract
The results of studies performed in the author's laboratory are surveyed, with particular emphasis on demonstrating the value of a multidisciplinary synthetic modeling approach for discovering new and unusual chemistry helpful for understanding the properties of the active sites of copper proteins or assessing the feasibility of mechanistic pathways they might follow during catalysis. The discussion focuses on the progress made to date toward comprehending the nitrite reductase catalytic site and mechanism, the electronic structures of copper thiolate electron transfer centers, the sulfido-bridged "CuZ" site in nitrous oxide reductase, and the processes of dioxygen binding and activation by mono- and dicopper centers in oxidases and oxygenases.
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Affiliation(s)
- William B Tolman
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455, USA.
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Garner D, McMaster J, Raven E, Walton P. Dalton Discussion No. 8. Metals: centres of biological activity. Dalton Trans 2005:3372-4. [PMID: 16234913 DOI: 10.1039/b513314a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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