151
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Suzuki S, Toda T, Kuwata S. A diazene-bridged diruthenium complex with structural restraint defined by single meta-diphosphinobenzene. Dalton Trans 2021; 50:4789-4795. [PMID: 33625422 DOI: 10.1039/d0dt04398b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Creation of confined coordination spaces with controlled flexibility is of importance in mimicking enzymatic reactions. We found that a simple, non-chelating 1,3-bis(diphenylphosphino)benzene (DPPBz) assembled two Cp*Ru units to give a dinuclear complex, wherein only one DPPBz supports an open framework without metal-metal bonding. Subsequent treatment with an excess of hydrazine resulted in formal 2e-/2H+ transfer from hydrazine to afford a diazene-bridged complex featuring intramolecular NHCl hydrogen bonds. In constrast, a monophosphine failed to stabilize the diazene-bridged dinuclear structure due to the lack of the enforcement of the conformation.
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Affiliation(s)
- Satoshi Suzuki
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 2-12-1 E4-1 O-okayama, Meguro-ku, Tokyo 152-8552, Japan.
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152
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Yang ZY, Jimenez-Vicente E, Kallas H, Lukoyanov DA, Yang H, Martin Del Campo JS, Dean DR, Hoffman BM, Seefeldt LC. The electronic structure of FeV-cofactor in vanadium-dependent nitrogenase. Chem Sci 2021; 12:6913-6922. [PMID: 34123320 PMCID: PMC8153082 DOI: 10.1039/d0sc06561g] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/26/2021] [Indexed: 01/01/2023] Open
Abstract
The electronic structure of the active-site metal cofactor (FeV-cofactor) of resting-state V-dependent nitrogenase has been an open question, with earlier studies indicating that it exhibits a broad S = 3/2 EPR signal (Kramers state) having g values of ∼4.3 and 3.8, along with suggestions that it contains metal-ions with valencies [1V3+, 3Fe3+, 4Fe2+]. In the present work, genetic, biochemical, and spectroscopic approaches were combined to reveal that the EPR signals previously assigned to FeV-cofactor do not correlate with active VFe-protein, and thus cannot arise from the resting-state of catalytically relevant FeV-cofactor. It, instead, appears resting-state FeV-cofactor is either diamagnetic, S = 0, or non-Kramers, integer-spin (S = 1, 2 etc.). When VFe-protein is freeze-trapped during high-flux turnover with its natural electron-donating partner Fe protein, conditions which populate reduced states of the FeV-cofactor, a new rhombic S = 1/2 EPR signal from such a reduced state is observed, with g = [2.18, 2.12, 2.09] and showing well-defined 51V (I = 7/2) hyperfine splitting, a iso = 110 MHz. These findings indicate a different assignment for the electronic structure of the resting state of FeV-cofactor: S = 0 (or integer-spin non-Kramers state) with metal-ion valencies, [1V3+, 4Fe3+, 3Fe2+]. Our findings suggest that the V3+ does not change valency throughout the catalytic cycle.
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Affiliation(s)
- Zhi-Yong Yang
- Department of Chemistry and Biochemistry, Utah State University Logan UT 84322 USA +1-435-797-3964
| | | | - Hayden Kallas
- Department of Chemistry and Biochemistry, Utah State University Logan UT 84322 USA +1-435-797-3964
| | - Dmitriy A Lukoyanov
- Department of Chemistry, Northwestern University Evanston IL 60208 USA +1-847-491-3104
| | - Hao Yang
- Department of Chemistry, Northwestern University Evanston IL 60208 USA +1-847-491-3104
| | | | - Dennis R Dean
- Department of Biochemistry, Virginia Tech Blacksburg VA 24061 USA +1-540-231-5895
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University Evanston IL 60208 USA +1-847-491-3104
| | - Lance C Seefeldt
- Department of Chemistry and Biochemistry, Utah State University Logan UT 84322 USA +1-435-797-3964
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153
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Abstract
In this Viewpoint, we address some of the limitations within our current understanding of the complex chemistry of the enzymes used in the Nitrogen Cycle. Further understanding of these chemical processes will play a large role in limiting the anthropogenic effects on our environment.
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Affiliation(s)
- Nicolai Lehnert
- Department of Chemistry and Department of Biophysics, The University of Michigan, Ann Arbor, MI 48109-1055, USA.
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154
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Bergmann J, Oksanen E, Ryde U. Quantum-refinement studies of the bidentate ligand of V‑nitrogenase and the protonation state of CO-inhibited Mo‑nitrogenase. J Inorg Biochem 2021; 219:111426. [PMID: 33756394 DOI: 10.1016/j.jinorgbio.2021.111426] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/19/2021] [Accepted: 03/10/2021] [Indexed: 10/21/2022]
Abstract
Nitrogenase is the only enzyme that can cleave the triple bond in N2, making nitrogen available to plants (although the enzyme itself is strictly microbial). It has been studied extensively with both experimental and computational methods, but many details of the reaction mechanism are still unclear. X-ray crystallography is the main source of structural information for biomacromolecules, but it has problems to discern hydrogen atoms or to distinguish between elements with the same number of electrons. These problems can sometimes be alleviated by introducing quantum chemical calculations in the refinement, providing information about the ideal structure (in the same way as the empirical restraints used in standard crystallographic refinement) and comparing different interpretations of the structure with normal crystallographic and quantum mechanical quality measures. We have performed such quantum-refinement calculations to address two important issues for nitrogenase. First, we show that the bidentate ligand of the active-site FeV cluster in V‑nitrogenase is carbonate, rather than bicarbonate or nitrate. Second, we study the CO-inhibited structure of Mo‑nitrogenase. CO binds to a reduced and protonated state of the enzyme by replacing one of the sulfide ions (S2B) in the active-site FeMo cluster. We examined if it is possible to deduce from the crystal structure the location of the protons. Our results indicates that the crystal structure is best modelled as fully deprotonated.
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Affiliation(s)
- Justin Bergmann
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Esko Oksanen
- European Spallation Source ESS ERIC, Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden.
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155
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Buscagan TM, Perez KA, Maggiolo AO, Rees DC, Spatzal T. Structural Characterization of Two CO Molecules Bound to the Nitrogenase Active Site. Angew Chem Int Ed Engl 2021; 60:5704-5707. [PMID: 33320413 PMCID: PMC7920927 DOI: 10.1002/anie.202015751] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Indexed: 12/31/2022]
Abstract
As an approach towards unraveling the nitrogenase mechanism, we have studied the binding of CO to the active-site FeMo-cofactor. CO is not only an inhibitor of nitrogenase, but it is also a substrate, undergoing reduction to hydrocarbons (Fischer-Tropsch-type chemistry). The C-C bond forming capabilities of nitrogenase suggest that multiple CO or CO-derived ligands bind to the active site. Herein, we report a crystal structure with two CO ligands coordinated to the FeMo-cofactor of the molybdenum nitrogenase at 1.33 Å resolution. In addition to the previously observed bridging CO ligand between Fe2 and Fe6 of the FeMo-cofactor, a new ligand binding mode is revealed through a second CO ligand coordinated terminally to Fe6. While the relevance of this state to nitrogenase-catalyzed reactions remains to be established, it highlights the privileged roles for Fe2 and Fe6 in ligand binding, with multiple coordination modes available depending on the ligand and reaction conditions.
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Affiliation(s)
- Trixia M. Buscagan
- Division of Chemistry and Chemical EngineeringCalifornia Institute of Technology1200 E. California Blvd.PasadenaCA91125USA
- Howard Hughes Medical InstituteCalifornia Institute of Technology1200 E. California Blvd.PasadenaCA91125USA
| | - Kathryn A. Perez
- Division of Chemistry and Chemical EngineeringCalifornia Institute of Technology1200 E. California Blvd.PasadenaCA91125USA
- Present address: European Molecular Biology LaboratoryMeyerhofstrasse 169117HeidelbergGermany
| | - Ailiena O. Maggiolo
- Division of Chemistry and Chemical EngineeringCalifornia Institute of Technology1200 E. California Blvd.PasadenaCA91125USA
| | - Douglas C. Rees
- Division of Chemistry and Chemical EngineeringCalifornia Institute of Technology1200 E. California Blvd.PasadenaCA91125USA
- Howard Hughes Medical InstituteCalifornia Institute of Technology1200 E. California Blvd.PasadenaCA91125USA
| | - Thomas Spatzal
- Division of Chemistry and Chemical EngineeringCalifornia Institute of Technology1200 E. California Blvd.PasadenaCA91125USA
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156
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Kuriyama S, Nishibayashi Y. Development of catalytic nitrogen fixation using transition metal complexes not relevant to nitrogenases. Tetrahedron 2021. [DOI: 10.1016/j.tet.2021.131986] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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157
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Peters JW, Einsle O, Dean DR, DeBeer S, Hoffman BM, Holland PL, Seefeldt LC. Comment on "Structural evidence for a dynamic metallocofactor during N 2 reduction by Mo-nitrogenase". Science 2021; 371:eabe5481. [PMID: 33574183 PMCID: PMC7931246 DOI: 10.1126/science.abe5481] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 12/18/2020] [Indexed: 01/08/2023]
Abstract
Kang et al (Reports, 19 June 2020, p. 1381) report a structure of the nitrogenase MoFe protein that is interpreted to indicate binding of N2 or an N2-derived species to the active-site FeMo cofactor. Independent refinement of the structure and consideration of biochemical evidence do not support this claim.
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Affiliation(s)
- John W Peters
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA.
| | - Oliver Einsle
- Institute of Biochemistry, Albert-Ludwigs Universität, Freiburg, Germany.
| | - Dennis R Dean
- Biochemistry Department, Virginia Tech, Blacksburg, VA 24061, USA
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion, D-45470 Mülheim an der Ruhr, Germany
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | | | - Lance C Seefeldt
- Chemistry and Biochemistry, Utah State University, Logan, UT 84322, USA
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158
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Abstract
[FeFe] hydrogenases, which are considered the most active naturally occurring catalysts for hydrogen oxidation and proton reduction, are extensively studied as models to learn the important features for efficient H2 conversion catalysis. Using infrared spectroscopy as a selective probe, the redox behaviour of the active site H-cluster is routinely modelled with thermodynamic schemes based on the Nernst equation for determining thermodynamic parameters, such as redox midpoint potentials and pKa values. Here, the thermodynamic models usually applied to [FeFe] hydrogenases are introduced and discussed in a pedagogic fashion and their applicability to additional metalloenzymes and molecular catalysts is also addressed.
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159
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Ashida Y, Nishibayashi Y. Catalytic conversion of nitrogen molecule into ammonia using molybdenum complexes under ambient reaction conditions. Chem Commun (Camb) 2021; 57:1176-1189. [PMID: 33443504 DOI: 10.1039/d0cc07146c] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nitrogen fixation using homogeneous transition metal complexes under mild reaction conditions is a challenging topic in the field of chemistry. Several successful examples of the catalytic conversion of nitrogen molecule into ammonia using various transition metal complexes in the presence of reductants and proton sources have been reported so far, together with detailed investigations on the reaction mechanism. Among these, only molybdenum complexes have been shown to serve as effective catalysts under ambient reaction conditions, in stark contrast with other transition metal-catalysed reactions that proceed at low reaction temperature such as -78 °C. In this feature article, we classify the molybdenum-catalysed reactions into four types: reactions via the Schrock cycle, reactions via dinuclear reaction systems, reactions via direct cleavage of the nitrogen-nitrogen triple bond of dinitrogen, and reactions via the Chatt-type cycle. We describe these catalytic systems focusing on the catalytic activity and mechanistic investigations. We hope that the present feature article provides useful information to develop more efficient nitrogen fixation systems under mild reaction conditions.
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Affiliation(s)
- Yuya Ashida
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
| | - Yoshiaki Nishibayashi
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
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160
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Van Stappen C, Decamps L, DeBeer S. Preparation and spectroscopic characterization of lyophilized Mo nitrogenase. J Biol Inorg Chem 2021; 26:81-91. [PMID: 33381859 PMCID: PMC8038959 DOI: 10.1007/s00775-020-01838-4] [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: 08/27/2020] [Accepted: 11/22/2020] [Indexed: 11/30/2022]
Abstract
Mo nitrogenase is the primary source of biologically fixed nitrogen, making this system highly interesting for developing new, energy efficient ways of ammonia production. Although heavily investigated, studies of the active site of this enzyme have generally been limited to spectroscopic methods that are compatible with the presence of water and relatively low protein concentrations. One method of overcoming this limitation is through lyophilization, which allows for measurements to be performed on solvent free, high concentration samples. This method also has the potential for allowing efficient protein storage and solvent exchange. To investigate the viability of this preparatory method with Mo nitrogenase, we employ a combination of electron paramagnetic resonance, Mo and Fe K-edge X-ray absorption spectroscopy, and acetylene reduction assays. Our results show that while some small distortions in the metallocofactors occur, oxidation and spin states are maintained through the lyophilization process and that reconstitution of either lyophilized protein component into buffer restores acetylene reducing activity.
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Affiliation(s)
- Casey Van Stappen
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany.
| | - Laure Decamps
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany
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161
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Speelman AL, Skubi KL, Mercado BQ, Holland PL. Synthesis and Reactivity of Iron Complexes with a Biomimetic SCS Pincer Ligand. Inorg Chem 2021; 60:1965-1974. [PMID: 33443404 DOI: 10.1021/acs.inorgchem.0c03427] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recent experimental evidence suggests that the FeMoco of nitrogenase undergoes structural rearrangement during N2 reduction, which may result in the generation of coordinatively unsaturated iron sites with two sulfur donors and a carbon donor. In an effort to synthesize and study small-molecule model complexes with a one-carbon/two-sulfur coordination environment, we have designed two new SCS pincer ligands containing a central NHC donor accompanied by thioether- or thiolate-functionalized aryl groups. Metalation of the thioether ligand with Fe(OTf)2 gives 6-coordinate complexes in which the SCS ligand binds meridionally. In contrast, metalation of the thiolate ligand with Fe(HMDS)2 gives a four-coordinate pseudotetrahedral amide complex in which the ligand binds facially, illustrating the potential structural flexibility of these ligands. Reaction of the amide complex with a bulky monothiol gives a four-coordinate complex with a one-carbon/three-sulfur coordination environment that resembles the resting state of nitrogenase. Reaction of the amide complex with phenylhydrazine gives a product with a rare κ1-bound phenylhydrazido group which undergoes N-N cleavage to give a phenylamido complex.
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Affiliation(s)
- Amy L Speelman
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
| | - Kazimer L Skubi
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
| | - Brandon Q Mercado
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
| | - Patrick L Holland
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
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162
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Ghosh AC, Duboc C, Gennari M. Synergy between metals for small molecule activation: Enzymes and bio-inspired complexes. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2020.213606] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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163
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Buscagan TM, Perez KA, Maggiolo AO, Rees DC, Spatzal T. Structural Characterization of Two CO Molecules Bound to the Nitrogenase Active Site. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202015751] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Trixia M. Buscagan
- Division of Chemistry and Chemical Engineering California Institute of Technology 1200 E. California Blvd. Pasadena CA 91125 USA
- Howard Hughes Medical Institute California Institute of Technology 1200 E. California Blvd. Pasadena CA 91125 USA
| | - Kathryn A. Perez
- Division of Chemistry and Chemical Engineering California Institute of Technology 1200 E. California Blvd. Pasadena CA 91125 USA
- Present address: European Molecular Biology Laboratory Meyerhofstrasse 1 69117 Heidelberg Germany
| | - Ailiena O. Maggiolo
- Division of Chemistry and Chemical Engineering California Institute of Technology 1200 E. California Blvd. Pasadena CA 91125 USA
| | - Douglas C. Rees
- Division of Chemistry and Chemical Engineering California Institute of Technology 1200 E. California Blvd. Pasadena CA 91125 USA
- Howard Hughes Medical Institute California Institute of Technology 1200 E. California Blvd. Pasadena CA 91125 USA
| | - Thomas Spatzal
- Division of Chemistry and Chemical Engineering California Institute of Technology 1200 E. California Blvd. Pasadena CA 91125 USA
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164
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Jiang X, Payá-Tormo L, Coroian D, García-Rubio I, Castellanos-Rueda R, Eseverri Á, López-Torrejón G, Burén S, Rubio LM. Exploiting genetic diversity and gene synthesis to identify superior nitrogenase NifH protein variants to engineer N 2-fixation in plants. Commun Biol 2021; 4:4. [PMID: 33398015 PMCID: PMC7782807 DOI: 10.1038/s42003-020-01536-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 11/25/2020] [Indexed: 01/01/2023] Open
Abstract
Engineering nitrogen fixation in eukaryotes requires high expression of functional nitrogenase structural proteins, a goal that has not yet been achieved. Here we build a knowledge-based library containing 32 nitrogenase nifH sequences from prokaryotes of diverse ecological niches and metabolic features and combine with rapid screening in tobacco to identify superior NifH variants for plant mitochondria expression. Three NifH variants outperform in tobacco mitochondria and are further tested in yeast. Hydrogenobacter thermophilus (Aquificae) NifH is isolated in large quantities from yeast mitochondria and fulfills NifH protein requirements for efficient N2 fixation, including electron transfer for substrate reduction, P-cluster maturation, and FeMo-co biosynthesis. H. thermophilus NifH expressed in tobacco leaves shows lower nitrogenase activity than that from yeast. However, transfer of [Fe4S4] clusters from NifU to NifH in vitro increases 10-fold the activity of the tobacco-isolated NifH, revealing that plant mitochondria [Fe-S] cluster availability constitutes a bottleneck to engineer plant nitrogenases.
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Affiliation(s)
- Xi Jiang
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón, 28223, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid, 28040, Madrid, Spain
| | - Lucía Payá-Tormo
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón, 28223, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid, 28040, Madrid, Spain
| | - Diana Coroian
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - Inés García-Rubio
- Centro Universitario de la Defensa, Ctra. de Huesca s/n, 50090, Zaragoza, Spain
| | - Rocío Castellanos-Rueda
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón, 28223, Madrid, Spain
- Department of Biosystems Science and Engineering, ETH Zürich, 4058, Basel, Switzerland
| | - Álvaro Eseverri
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón, 28223, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid, 28040, Madrid, Spain
| | - Gema López-Torrejón
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón, 28223, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid, 28040, Madrid, Spain
| | - Stefan Burén
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón, 28223, Madrid, Spain.
| | - Luis Manuel Rubio
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón, 28223, Madrid, Spain.
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid, 28040, Madrid, Spain.
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165
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Xiao L, Chen P, Yang W, Zhao X, Dong F. Photocatalytic reaction mechanisms at the gas–solid interface for environmental and energy applications. Catal Sci Technol 2021. [DOI: 10.1039/d1cy01776d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Five gas–solid photocatalytic reactions including the oxidation of NOx, VOCs and NH3, and reduction of CO2 and N2 are summarized. Besides, basic properties of gas molecules, their adsorption and activation, and various reaction pathways are analyzed.
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Affiliation(s)
- Lei Xiao
- Research Center for Environmental and Energy Catalysis, Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 611731, China
- Yangtze Delta Region Institute (Huzhou), University of Electronic Science and Technology of China, Huzhou 313000, China
| | - Peng Chen
- The Center of New Energy Materials and Technology, School of New Energy and Materials, Southwest Petroleum University, Chengdu 610500, China
| | - Weiping Yang
- Research Center for Environmental and Energy Catalysis, Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 611731, China
- Yangtze Delta Region Institute (Huzhou), University of Electronic Science and Technology of China, Huzhou 313000, China
| | - Xiaoli Zhao
- Research Center for Environmental and Energy Catalysis, Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Fan Dong
- Research Center for Environmental and Energy Catalysis, Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 611731, China
- Yangtze Delta Region Institute (Huzhou), University of Electronic Science and Technology of China, Huzhou 313000, China
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166
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Abstract
An overview of the available methods to functionalize dinitrogen with boron reagents using transition metal complexes is given.
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167
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Mallamace D, Papanikolaou G, Perathoner S, Centi G, Lanzafame P. Comparing Molecular Mechanisms in Solar NH 3 Production and Relations with CO 2 Reduction. Int J Mol Sci 2020; 22:E139. [PMID: 33375617 PMCID: PMC7795446 DOI: 10.3390/ijms22010139] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 12/20/2020] [Accepted: 12/22/2020] [Indexed: 11/16/2022] Open
Abstract
Molecular mechanisms for N2 fixation (solar NH3) and CO2 conversion to C2+ products in enzymatic conversion (nitrogenase), electrocatalysis, metal complexes and plasma catalysis are analyzed and compared. It is evidenced that differently from what is present in thermal and plasma catalysis, the electrocatalytic path requires not only the direct coordination and hydrogenation of undissociated N2 molecules, but it is necessary to realize features present in the nitrogenase mechanism. There is the need for (i) a multi-electron and -proton simultaneous transfer, not as sequential steps, (ii) forming bridging metal hydride species, (iii) generating intermediates stabilized by bridging multiple metal atoms and (iv) the capability of the same sites to be effective both in N2 fixation and in COx reduction to C2+ products. Only iron oxide/hydroxide stabilized at defective sites of nanocarbons was found to have these features. This comparison of the molecular mechanisms in solar NH3 production and CO2 reduction is proposed to be a source of inspiration to develop the next generation electrocatalysts to address the challenging transition to future sustainable energy and chemistry beyond fossil fuels.
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Affiliation(s)
| | | | | | - Gabriele Centi
- Departments ChiBioFarAm and MIFT, University of Messina, ERIC aisbl, INSTM/CASPE, V. le F. Stagno D’Alcontres 31, 98166 Messina, Italy; (D.M.); (G.P.); (S.P.)
| | - Paola Lanzafame
- Departments ChiBioFarAm and MIFT, University of Messina, ERIC aisbl, INSTM/CASPE, V. le F. Stagno D’Alcontres 31, 98166 Messina, Italy; (D.M.); (G.P.); (S.P.)
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168
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Lukoyanov DA, Yang ZY, Dean DR, Seefeldt LC, Raugei S, Hoffman BM. Electron Redistribution within the Nitrogenase Active Site FeMo-Cofactor During Reductive Elimination of H 2 to Achieve N≡N Triple-Bond Activation. J Am Chem Soc 2020; 142:21679-21690. [PMID: 33326225 DOI: 10.1021/jacs.0c07914] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nitrogen fixation by nitrogenase begins with the accumulation of four reducing equivalents at the active-site FeMo-cofactor (FeMo-co), generating a state (denoted E4(4H)) with two [Fe-H-Fe] bridging hydrides. Recently, photolytic reductive elimination (re) of the E4(4H) hydrides showed that enzymatic re of E4(4H) hydride yields an H2-bound complex (E4(H2,2H)), in a process corresponding to a formal 2-electron reduction of the metal-ion core of FeMo-co. The resulting electron-density redistribution from Fe-H bonds to the metal ions themselves enables N2 to bind with concomitant H2 release, a process illuminated here by QM/MM molecular dynamics simulations. What is the nature of this redistribution? Although E4(H2,2H) has not been trapped, cryogenic photolysis of E4(4H) provides a means to address this question. Photolysis of E4(4H) causes hydride-re with release of H2, generating doubly reduced FeMo-co (denoted E4(2H)*), the extreme limit of the electron-density redistribution upon formation of E4(H2,2H). Here we examine the doubly reduced FeMo-co core of the E4(2H)* limiting-state by 1H, 57Fe, and 95Mo ENDOR to illuminate the partial electron-density redistribution upon E4(H2,2H) formation during catalysis, complementing these results with corresponding DFT computations. Inferences from the E4(2H)* ENDOR results as extended by DFT computations include (i) the Mo-site participates negligibly, and overall it is unlikely that Mo changes valency throughout the catalytic cycle; and (ii) two distinctive E4(4H) 57Fe signals are suggested as associated with structurally identified "anchors" of one bridging hydride, two others with identified anchors of the second, with NBO-analysis further identifying one anchor of each hydride as a major recipient of electrons released upon breaking Fe-H bonds.
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Affiliation(s)
- Dmitriy A Lukoyanov
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Zhi-Yong Yang
- Department of Chemistry and Biocemistry, Utah State University, Logan, Utah 84322, United States
| | - Dennis R Dean
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Lance C Seefeldt
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Simone Raugei
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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169
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Sun T, Xu S, Yang D, Su L, Wang B, Qu J. Catalytic Disproportionation of Hydrazine Promoted by Biomimetic Diiron Complexes with Benzene‐1,2‐Dithiolate Bridge Modified by Different Substituents. Eur J Inorg Chem 2020. [DOI: 10.1002/ejic.202000851] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Tie Sun
- State Key Laboratory of Fine Chemicals Dalian University of Technology 116024 Dalian P. R. China
| | - Sunlin Xu
- State Key Laboratory of Fine Chemicals Dalian University of Technology 116024 Dalian P. R. China
| | - Dawei Yang
- State Key Laboratory of Fine Chemicals Dalian University of Technology 116024 Dalian P. R. China
| | - Linan Su
- State Key Laboratory of Fine Chemicals Dalian University of Technology 116024 Dalian P. R. China
| | - Baomin Wang
- State Key Laboratory of Fine Chemicals Dalian University of Technology 116024 Dalian P. R. China
| | - Jingping Qu
- State Key Laboratory of Fine Chemicals Dalian University of Technology 116024 Dalian P. R. China
- Key Laboratory for Advanced Materials East China University of Science and Technology 200237 Shanghai P. R. China
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170
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Harris DF, Jimenez-Vicente E, Yang ZY, Hoffman BM, Dean DR, Seefeldt LC. CO as a substrate and inhibitor of H+ reduction for the Mo-, V-, and Fe-nitrogenase isozymes. J Inorg Biochem 2020; 213:111278. [DOI: 10.1016/j.jinorgbio.2020.111278] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 09/29/2020] [Accepted: 10/03/2020] [Indexed: 10/23/2022]
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171
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Kang W, Rettberg LA, Stiebritz MT, Jasniewski AJ, Tanifuji K, Lee CC, Ribbe MW, Hu Y. X‐Ray Crystallographic Analysis of NifB with a Full Complement of Clusters: Structural Insights into the Radical SAM‐Dependent Carbide Insertion During Nitrogenase Cofactor Assembly. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202011367] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Wonchull Kang
- Department of Molecular Biology & Biochemistry University of California, Irvine Irvine CA 92697-3900 USA
| | - Lee A. Rettberg
- Department of Molecular Biology & Biochemistry University of California, Irvine Irvine CA 92697-3900 USA
| | - Martin T. Stiebritz
- Department of Molecular Biology & Biochemistry University of California, Irvine Irvine CA 92697-3900 USA
| | - Andrew J. Jasniewski
- Department of Molecular Biology & Biochemistry University of California, Irvine Irvine CA 92697-3900 USA
| | - Kazuki Tanifuji
- Department of Molecular Biology & Biochemistry University of California, Irvine Irvine CA 92697-3900 USA
| | - Chi Chung Lee
- Department of Molecular Biology & Biochemistry University of California, Irvine Irvine CA 92697-3900 USA
| | - Markus W. Ribbe
- Department of Molecular Biology & Biochemistry University of California, Irvine Irvine CA 92697-3900 USA
- Department of Chemistry University of California, Irvine Irvine CA 92697-2025 USA
| | - Yilin Hu
- Department of Molecular Biology & Biochemistry University of California, Irvine Irvine CA 92697-3900 USA
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172
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Kang W, Rettberg LA, Stiebritz MT, Jasniewski AJ, Tanifuji K, Lee CC, Ribbe MW, Hu Y. X-Ray Crystallographic Analysis of NifB with a Full Complement of Clusters: Structural Insights into the Radical SAM-Dependent Carbide Insertion During Nitrogenase Cofactor Assembly. Angew Chem Int Ed Engl 2020; 60:2364-2370. [PMID: 33035363 DOI: 10.1002/anie.202011367] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/27/2020] [Indexed: 12/13/2022]
Abstract
NifB is an essential radical SAM enzyme required for the assembly of an 8Fe core of the nitrogenase cofactor. Herein, we report the X-ray crystal structures of Methanobacterium thermoautotrophicum NifB without (apo MtNifB) and with (holo MtNifB) a full complement of three [Fe4 S4 ] clusters. Both apo and holo MtNifB contain a partial TIM barrel core, but unlike apo MtNifB, holo MtNifB is fully assembled and competent in cofactor biosynthesis. The radical SAM (RS)-cluster is coordinated by three Cys, and the adjacent K1- and K2-clusters, representing the precursor to an 8Fe cofactor core, are each coordinated by one His and two Cys. Prediction of substrate channels, combined with in silico docking of SAM in holo MtNifB, suggests the binding of SAM between the RS- and K2-clusters and putative paths for entry of SAM and exit of products of SAM cleavage, thereby providing important mechanistic insights into the radical SAM-dependent carbide insertion concomitant with cofactor core formation.
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Affiliation(s)
- Wonchull Kang
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
| | - Lee A Rettberg
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
| | - Martin T Stiebritz
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
| | - Andrew J Jasniewski
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
| | - Kazuki Tanifuji
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
| | - Chi Chung Lee
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
| | - Markus W Ribbe
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA.,Department of Chemistry, University of California, Irvine, Irvine, CA, 92697-2025, USA
| | - Yilin Hu
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
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173
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Yang K, Koepf M, Artero V. Revisiting amorphous molybdenum sulfide's activity for the electro-driven reduction of dinitrogen and N-containing substrates. Chem Commun (Camb) 2020; 56:13975-13978. [PMID: 33084630 DOI: 10.1039/d0cc05078d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Ammonia (NH3) is a major feedstock of the chemical industry. The imperious need to decarbonize its production has stimulated a quest for efficient catalysts able to drive the direct electro-reduction of dinitrogen (N2) into NH3. A large number of materials have now been proposed for this reaction, including bioinspired molybdenum sulfide derivatives. Here, we revisit the potential of amorphous molybdenum sulfide to drive the electrocatalytic reduction of N2 and other substrates of nitrogenase. We find that this material exhibits negligible activity towards N2 but achieves efficient reduction of inorganic azides.
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Affiliation(s)
- Kun Yang
- Univ. Grenoble Alpes, CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, Grenoble 38000, France.
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174
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Inomura K, Deutsch C, Masuda T, Prášil O, Follows MJ. Quantitative models of nitrogen-fixing organisms. Comput Struct Biotechnol J 2020; 18:3905-3924. [PMID: 33335688 PMCID: PMC7733014 DOI: 10.1016/j.csbj.2020.11.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 11/11/2020] [Accepted: 11/13/2020] [Indexed: 10/26/2022] Open
Abstract
Nitrogen-fixing organisms are of importance to the environment, providing bioavailable nitrogen to the biosphere. Quantitative models have been used to complement the laboratory experiments and in situ measurements, where such evaluations are difficult or costly. Here, we review the current state of the quantitative modeling of nitrogen-fixing organisms and ways to enhance the bridge between theoretical and empirical studies.
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Affiliation(s)
- Keisuke Inomura
- School of Oceanography, University of Washington, Seattle, WA, USA
| | - Curtis Deutsch
- School of Oceanography, University of Washington, Seattle, WA, USA
| | - Takako Masuda
- Institute of Microbiology, The Czech Academy of Sciences, Opatovický mlýn, Třeboň, Czech Republic
| | - Ondřej Prášil
- Institute of Microbiology, The Czech Academy of Sciences, Opatovický mlýn, Třeboň, Czech Republic
| | - Michael J. Follows
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
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175
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Liedtke J, Lee CC, Tanifuji K, Jasniewski AJ, Ribbe MW, Hu Y. Characterization of a Mo-Nitrogenase Variant Containing a Citrate-Substituted Cofactor. Chembiochem 2020; 22:151-155. [PMID: 32918851 DOI: 10.1002/cbic.202000598] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/04/2020] [Indexed: 11/10/2022]
Abstract
Nitrogenase converts N2 to NH3 , and CO to hydrocarbons, at its cofactor site. Herein, we report a biochemical and spectroscopic characterization of a Mo-nitrogenase variant expressed in an Azotobacter vinelandii strain containing a deletion of nifV, the gene encoding the homocitrate synthase. Designated NifDKCit , the catalytic component of this Mo-nitrogenase variant contains a citrate-substituted cofactor analogue. Activity analysis of NifDKCit reveals a shift of CO reduction from H2 evolution toward hydrocarbon formation and an opposite shift of N2 reduction from NH3 formation toward H2 evolution. Consistent with a shift in the Mo K-edge energy of NifDKCit relative to that of its wild-type counterpart, EPR analysis demonstrates a broadening of the line-shape and a decrease in the intensity of the cofactor-originated S=3/2 signal, suggesting a change in the spin properties of the cofactor upon citrate substitution. These observations point to a crucial role of homocitrate in substrate reduction by nitrogenase and the possibility to tune product profiles of nitrogenase reactions via organic ligand substitution.
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Affiliation(s)
- Jasper Liedtke
- Department of Molecular Biology & Biochemistry, University of California, Irvine, 2236 McGaugh Hall, Irvine, CA 92697-3900, USA
| | - Chi Chung Lee
- Department of Molecular Biology & Biochemistry, University of California, Irvine, 2236 McGaugh Hall, Irvine, CA 92697-3900, USA
| | - Kazuki Tanifuji
- Department of Molecular Biology & Biochemistry, University of California, Irvine, 2236 McGaugh Hall, Irvine, CA 92697-3900, USA
| | - Andrew J Jasniewski
- Department of Molecular Biology & Biochemistry, University of California, Irvine, 2236 McGaugh Hall, Irvine, CA 92697-3900, USA
| | - Markus W Ribbe
- Department of Molecular Biology & Biochemistry, University of California, Irvine, 2236 McGaugh Hall, Irvine, CA 92697-3900, USA.,Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, USA
| | - Yilin Hu
- Department of Molecular Biology & Biochemistry, University of California, Irvine, 2236 McGaugh Hall, Irvine, CA 92697-3900, USA
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176
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Luxem KE, Leavitt WD, Zhang X. Large Hydrogen Isotope Fractionation Distinguishes Nitrogenase-Derived Methane from Other Methane Sources. Appl Environ Microbiol 2020; 86:e00849-20. [PMID: 32709722 PMCID: PMC7499036 DOI: 10.1128/aem.00849-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 07/16/2020] [Indexed: 02/01/2023] Open
Abstract
Biological nitrogen fixation is catalyzed by the enzyme nitrogenase. Two forms of this metalloenzyme, the vanadium (V)- and iron (Fe)-only nitrogenases, were recently found to reduce small amounts of carbon dioxide (CO2) into the potent greenhouse gas methane (CH4). Here, we report carbon (13C/12C) and hydrogen (2H/1H) stable isotopic compositions and fractionations of methane generated by V- and Fe-only nitrogenases in the metabolically versatile nitrogen fixer Rhodopseudomonas palustris The stable carbon isotope fractionation imparted by both forms of alternative nitrogenase are within the range observed for hydrogenotrophic methanogenesis (13αCO2/CH4 = 1.051 ± 0.002 for V-nitrogenase and 1.055 ± 0.001 for Fe-only nitrogenase; values are means ± standard errors). In contrast, the hydrogen isotope fractionations (2αH2O/CH4 = 2.071 ± 0.014 for V-nitrogenase and 2.078 ± 0.018 for Fe-only nitrogenase) are the largest of any known biogenic or geogenic pathway. The large 2αH2O/CH4 shows that the reaction pathway nitrogenases use to form methane strongly discriminates against 2H, and that 2αH2O/CH4 distinguishes nitrogenase-derived methane from all other known biotic and abiotic sources. These findings on nitrogenase-derived methane will help constrain carbon and nitrogen flows in microbial communities and the role of the alternative nitrogenases in global biogeochemical cycles.IMPORTANCE All forms of life require nitrogen for growth. Many different kinds of microbes living in diverse environments make inert nitrogen gas from the atmosphere bioavailable using a special enzyme, nitrogenase. Nitrogenase has a wide substrate range, and, in addition to producing bioavailable nitrogen, some forms of nitrogenase also produce small amounts of the greenhouse gas methane. This is different from other microbes that produce methane to generate energy. Until now, there was no good way to determine when microbes with nitrogenases are making methane in nature. Here, we present an isotopic fingerprint that allows scientists to distinguish methane from microbes making it for energy versus those making it as a by-product of nitrogen acquisition. With this new fingerprint, it will be possible to improve our understanding of the relationship between methane production and nitrogen acquisition in nature.
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Affiliation(s)
- Katja E Luxem
- Department of Geosciences, Princeton University, Princeton, New Jersey, USA
- Princeton Environmental Institute, Princeton University, Princeton, New Jersey, USA
| | - William D Leavitt
- Department of Earth Sciences, Dartmouth College, Hanover, New Hampshire, USA
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire, USA
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, USA
| | - Xinning Zhang
- Department of Geosciences, Princeton University, Princeton, New Jersey, USA
- Princeton Environmental Institute, Princeton University, Princeton, New Jersey, USA
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177
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Benediktsson B, Bjornsson R. Quantum Mechanics/Molecular Mechanics Study of Resting-State Vanadium Nitrogenase: Molecular and Electronic Structure of the Iron-Vanadium Cofactor. Inorg Chem 2020; 59:11514-11527. [PMID: 32799489 PMCID: PMC7458435 DOI: 10.1021/acs.inorgchem.0c01320] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Indexed: 12/18/2022]
Abstract
The nitrogenase enzymes are responsible for all biological nitrogen reduction. How this is accomplished at the atomic level, however, has still not been established. The molybdenum-dependent nitrogenase has been extensively studied and is the most active catalyst for dinitrogen reduction of the nitrogenase enzymes. The vanadium-dependent form, on the other hand, displays different reactivity, being capable of CO and CO2 reduction to hydrocarbons. Only recently did a crystal structure of the VFe protein of vanadium nitrogenase become available, paving the way for detailed theoretical studies of the iron-vanadium cofactor (FeVco) within the protein matrix. The crystal structure revealed a bridging 4-atom ligand between two Fe atoms, proposed to be either a CO32- or NO3- ligand. Using a quantum mechanics/molecular mechanics model of the VFe protein, starting from the 1.35 Å crystal structure, we have systematically explored multiple computational models for FeVco, considering either a CO32- or NO3- ligand, three different redox states, and multiple broken-symmetry states. We find that only a [VFe7S8C(CO3)]2- model for FeVco reproduces the crystal structure of FeVco well, as seen in a comparison of the Fe-Fe and V-Fe distances in the computed models. Furthermore, a broken-symmetry solution with Fe2, Fe3, and Fe5 spin-down (BS7-235) is energetically preferred. The electronic structure of the [VFe7S8C(CO3)]2- BS7-235 model is compared to our [MoFe7S9C]- BS7-235 model of FeMoco via localized orbital analysis and is discussed in terms of local oxidation states and different degrees of delocalization. As previously found from Fe X-ray absorption spectroscopy studies, the Fe part of FeVco is reduced compared to FeMoco, and the calculations reveal Fe5 as locally ferrous. This suggests resting-state FeVco to be analogous to an unprotonated E1 state of FeMoco. Furthermore, V-Fe interactions in FeVco are not as strong compared to Mo-Fe interactions in FeMoco. These clear differences in the electronic structures of otherwise similar cofactors suggest an explanation for distinct differences in reactivity.
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Affiliation(s)
- Bardi Benediktsson
- Science Institute, University of Iceland, Dunhagi 3, 107 Reykjavik, Iceland
| | - Ragnar Bjornsson
- Science Institute, University of Iceland, Dunhagi 3, 107 Reykjavik, Iceland
- Max-Planck Institute
for Chemical Energy Conversion, Stiftstrasse 34−36, 45470 Mülheim an der Ruhr, Germany
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