1
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Barchenko M, Malcomson T, de Visser SP, O’Malley PJ. Computational Study on the Influence of Mo/V Centers on the Electronic Structure and Hydrazine Reduction Capability of [MFe 3S 4] 3+/2+ Complexes. Inorg Chem 2023; 62:16401-16411. [PMID: 37756478 PMCID: PMC10565805 DOI: 10.1021/acs.inorgchem.3c02072] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Indexed: 09/29/2023]
Abstract
[MFe3S4] cubanes have for some time been of interest for their ability to mimic the electronic and geometric structure of the active site of nitrogenase, the enzyme responsible for fixing N2 to NH3. Nitrogenase naturally occurs in three forms, with the major difference being that the metal ion present in the cofactor active site is either molybdenum (FeMoco), vanadium (FeVco), or iron. The molybdenum and vanadium versions of these cofactors are more closely studied, owing to their larger abundance and rate of catalysis. In this study, we compare free energy profiles and electronic properties of the Mo/V cubanes at various stages during the reduction of N2H4 to NH3. Our findings highlight the differences in how the complexes facilitate the reaction, in particular, vanadium's comparatively weaker ability to interact with the Fe/S network and stabilize reducing electrons prior to N-N bond cleavage, which may have implications when considering the lower efficiency of the vanadium-dependent nitrogenase.
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Affiliation(s)
- Maxim Barchenko
- Department
of Chemistry, School of Natural Sciences, The University of Manchester, Manchester M13 9PL, U.K.
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess
Street, Manchester M1 7DN, U.K.
| | - Thomas Malcomson
- Department
of Chemistry, School of Natural Sciences, The University of Manchester, Manchester M13 9PL, U.K.
| | - Sam P. de Visser
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess
Street, Manchester M1 7DN, U.K.
- Department
of Chemical Engineering, The University
of Manchester, Oxford
Road, Manchester M13 9PL, U.K.
| | - Patrick J. O’Malley
- Department
of Chemistry, School of Natural Sciences, The University of Manchester, Manchester M13 9PL, U.K.
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2
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Threatt SD, Rees DC. Biological nitrogen fixation in theory, practice, and reality: a perspective on the molybdenum nitrogenase system. FEBS Lett 2023; 597:45-58. [PMID: 36344435 PMCID: PMC10100503 DOI: 10.1002/1873-3468.14534] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/30/2022] [Accepted: 10/31/2022] [Indexed: 11/09/2022]
Abstract
Nitrogenase is the sole enzyme responsible for the ATP-dependent conversion of atmospheric dinitrogen into the bioavailable form of ammonia (NH3 ), making this protein essential for the maintenance of the nitrogen cycle and thus life itself. Despite the widespread use of the Haber-Bosch process to industrially produce NH3 , biological nitrogen fixation still accounts for half of the bioavailable nitrogen on Earth. An important feature of nitrogenase is that it operates under physiological conditions, where the equilibrium strongly favours ammonia production. This biological, multielectron reduction is a complex catalytic reaction that has perplexed scientists for decades. In this review, we explore the current understanding of the molybdenum nitrogenase system based on experimental and computational research, as well as the limitations of the crystallographic, spectroscopic, and computational techniques employed. Finally, essential outstanding questions regarding the nitrogenase system will be highlighted alongside suggestions for future experimental and computational work to elucidate this essential yet elusive process.
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Affiliation(s)
- Stephanie D Threatt
- Division of Chemistry and Chemical Engineering, Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA
| | - Douglas C Rees
- Division of Chemistry and Chemical Engineering, Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA
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3
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Kim J. Metal complexes containing
silicon‐based
pincer ligands: Reactivity and application in small molecule activation. B KOREAN CHEM SOC 2022. [DOI: 10.1002/bkcs.12491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jin Kim
- Department of Chemistry Sunchon National University Suncheon Jeollanam‐do Republic of Korea
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4
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Spiller N, Bjornsson R, DeBeer S, Neese F. Carbon Monoxide Binding to the Iron-Molybdenum Cofactor of Nitrogenase: a Detailed Quantum Mechanics/Molecular Mechanics Investigation. Inorg Chem 2021; 60:18031-18047. [PMID: 34767349 PMCID: PMC8653219 DOI: 10.1021/acs.inorgchem.1c02649] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Carbon monoxide (CO) is a well-known inhibitor of nitrogenase activity. Under turnover conditions, CO binds to FeMoco, the active site of Mo nitrogenase. Time-resolved IR measurements suggest an initial terminal CO at 1904 cm-1 that converts to a bridging CO at 1715 cm-1, and an X-ray structure shows that CO can displace one of the bridging belt sulfides of FeMoco. However, the CO-binding redox state(s) of FeMoco (En) and the role of the protein environment in stabilizing specific CO-bound intermediates remain elusive. In this work, we carry out an in-depth analysis of the CO-FeMoco interaction based on quantum chemical calculations addressing different aspects of the electronic structure. (1) The local electronic structure of the Fe-CO bond is studied through diamagnetically substituted FeMoco. (2) A cluster model of FeMoco within a polarizable continuum illustrates how CO binding may affect the spin-coupling between the metal centers. (3) A QM/MM model incorporates the explicit influence of the amino acid residues surrounding FeMoco in the MoFe protein. The QM/MM model predicts both a terminal and a bridging CO in the E1 redox state. The scaled calculated CO frequencies (1922 and 1716 cm-1, respectively) are in good agreement with the experimentally observed IR bands supporting CO binding to the E1 state. Alternatively, an E2 state QM/MM model, which has the same atomic structure as the CO-bound X-ray structure, features a semi-bridging CO with a scaled calculated frequency (1718 cm-1) similar to the bridging CO in the E1 model.
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Affiliation(s)
- Nico Spiller
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Ragnar Bjornsson
- Max Planck Institute for Chemical Energy Conversion, Stiftstr 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion, Stiftstr 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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5
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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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6
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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: 41] [Impact Index Per Article: 13.7] [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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7
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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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8
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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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9
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Van Stappen C, Decamps L, Cutsail GE, Bjornsson R, Henthorn JT, Birrell JA, DeBeer S. The Spectroscopy of Nitrogenases. Chem Rev 2020; 120:5005-5081. [PMID: 32237739 PMCID: PMC7318057 DOI: 10.1021/acs.chemrev.9b00650] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Indexed: 01/08/2023]
Abstract
Nitrogenases are responsible for biological nitrogen fixation, a crucial step in the biogeochemical nitrogen cycle. These enzymes utilize a two-component protein system and a series of iron-sulfur clusters to perform this reaction, culminating at the FeMco active site (M = Mo, V, Fe), which is capable of binding and reducing N2 to 2NH3. In this review, we summarize how different spectroscopic approaches have shed light on various aspects of these enzymes, including their structure, mechanism, alternative reactivity, and maturation. Synthetic model chemistry and theory have also played significant roles in developing our present understanding of these systems and are discussed in the context of their contributions to interpreting the nature of nitrogenases. Despite years of significant progress, there is still much to be learned from these enzymes through spectroscopic means, and we highlight where further spectroscopic investigations are needed.
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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
| | - George E. Cutsail
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Ragnar Bjornsson
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Justin T. Henthorn
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - James A. Birrell
- 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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10
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Affiliation(s)
- Oliver Einsle
- Institute for Biochemistry, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Douglas C. Rees
- Division of Chemistry and Chemical Engineering, Howard Hughes Medical Institute, California Institute of Technology, Pasadena California 91125, United States
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11
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Tanifuji K, Ohki Y. Metal–Sulfur Compounds in N2 Reduction and Nitrogenase-Related Chemistry. Chem Rev 2020; 120:5194-5251. [DOI: 10.1021/acs.chemrev.9b00544] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Kazuki Tanifuji
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California 92697-3900, United States
| | - Yasuhiro Ohki
- Department of Chemsitry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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12
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Jin WT, Yang M, Zhu SS, Zhou ZH. Bond-valence analyses of the crystal structures of FeMo/V cofactors in FeMo/V proteins. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2020; 76:428-437. [PMID: 32355039 DOI: 10.1107/s2059798320003952] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 03/18/2020] [Indexed: 12/15/2022]
Abstract
The bond-valence method has been used for valence calculations of FeMo/V cofactors in FeMo/V proteins using 51 crystallographic data sets of FeMo/V proteins from the Protein Data Bank. The calculations show molybdenum(III) to be present in MoFe7S9C(Cys)(HHis)[R-(H)homocit] (where H4homocit is homocitric acid, HCys is cysteine and HHis is histidine) in FeMo cofactors, while vanadium(III) with a more reduced iron complement is obtained for FeV cofactors. Using an error analysis of the calculated valences, it was found that in FeMo cofactors Fe1, Fe6 and Fe7 can be unambiguously assigned as iron(III), while Fe2, Fe3, Fe4 and Fe5 show different degrees of mixed valences for the individual Fe atoms. For the FeV cofactors in PDB entry 5n6y, Fe4, Fe5 and Fe6 correspond to iron(II), iron(II) and iron(III), respectively, while Fe1, Fe2, Fe3 and Fe7 exhibit strongly mixed valences. Special situations such as CO-bound and selenium-substituted FeMo cofactors and O(N)H-bridged FeV cofactors are also discussed and suggest rearrangement of the electron configuration on the substitution of the bridging S atoms.
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Affiliation(s)
- Wan Ting Jin
- State Key Laboratory for Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People's Republic of China
| | - Min Yang
- State Key Laboratory for Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People's Republic of China
| | - Shuang Shuang Zhu
- State Key Laboratory for Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People's Republic of China
| | - Zhao Hui Zhou
- State Key Laboratory for Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People's Republic of China
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13
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Seefeldt LC, Yang ZY, Lukoyanov DA, Harris DF, Dean DR, Raugei S, Hoffman BM. Reduction of Substrates by Nitrogenases. Chem Rev 2020; 120:5082-5106. [PMID: 32176472 DOI: 10.1021/acs.chemrev.9b00556] [Citation(s) in RCA: 184] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Nitrogenase is the enzyme that catalyzes biological N2 reduction to NH3. This enzyme achieves an impressive rate enhancement over the uncatalyzed reaction. Given the high demand for N2 fixation to support food and chemical production and the heavy reliance of the industrial Haber-Bosch nitrogen fixation reaction on fossil fuels, there is a strong need to elucidate how nitrogenase achieves this difficult reaction under benign conditions as a means of informing the design of next generation synthetic catalysts. This Review summarizes recent progress in addressing how nitrogenase catalyzes the reduction of an array of substrates. New insights into the mechanism of N2 and proton reduction are first considered. This is followed by a summary of recent gains in understanding the reduction of a number of other nitrogenous compounds not considered to be physiological substrates. Progress in understanding the reduction of a wide range of C-based substrates, including CO and CO2, is also discussed, and remaining challenges in understanding nitrogenase substrate reduction are considered.
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Affiliation(s)
- Lance C Seefeldt
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Zhi-Yong Yang
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Dmitriy A Lukoyanov
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Derek F Harris
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Dennis R Dean
- Biochemistry Department, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Simone Raugei
- Physical and Computational Sciences Directorate, 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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14
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Buscagan TM, Rees DC. Rethinking the Nitrogenase Mechanism: Activating the Active Site. JOULE 2019; 3:2662-2678. [PMID: 32864580 PMCID: PMC7451245 DOI: 10.1016/j.joule.2019.09.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Metalloenzymes called nitrogenases (N2ases) harness the reactivity of transition metals to reduce N2 to NH3. Specifically, N2ases feature a multimetallic active site, called a cofactor, which binds and reduces N2. The seven Fe centers and one additional metal center (Mo, V, or Fe) that make up the cofactor are all potential substrate binding sites. Unraveling the mechanism by which the cofactor binds N2 and reduces N2 to NH3 represents a multifaceted challenge because cofactor activation is required for N2 binding and functionalization to NH3. Despite decades of fascinating contributions, the nature of N2 binding to the active site and the structure of the activated cofactor remain unknown. Herein, we discuss the challenges associated with N2 reduction and how transition metal complexes facilitate N2 functionalization by coordinating N2. We also review the activation and/or reaction mechanisms reported for small molecule catalysts and the Haber-Bosch catalyst and discuss their potential relevance to biological N2 fixation. Finally, we survey what is known about the mechanism of N2ase and highlight recent X-ray crystallographic studies supporting Fe-S bond cleavage at the active site to generate reactive Fe centers as a potential, underexplored route for cofactor activation. We propose that structural rearrangements, beyond electron and proton transfers, are key in generating the catalytically active state(s) of the cofactor. Understanding the mechanism of activation will be key to understanding N2 binding and reduction.
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Affiliation(s)
- Trixia M. Buscagan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125 USA
| | - Douglas C. Rees
- to whom correspondence concerning the manuscript may be addressed, , telephone: 1-626-395-8393
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15
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Zanello P. Structure and electrochemistry of proteins harboring iron-sulfur clusters of different nuclearities. Part V. Nitrogenases. Coord Chem Rev 2019. [DOI: 10.1016/j.ccr.2019.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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16
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Speelman AL, Čorić I, Van Stappen C, DeBeer S, Mercado BQ, Holland PL. Nitrogenase-Relevant Reactivity of a Synthetic Iron-Sulfur-Carbon Site. J Am Chem Soc 2019; 141:13148-13157. [PMID: 31403298 DOI: 10.1021/jacs.9b05353] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Simple synthetic compounds with only S and C donors offer a ligation environment similar to the active site of nitrogenase (FeMoco) and thus demonstrate reasonable mechanisms and geometries for N2 binding and reduction in nature. We recently reported the first example of N2 binding at a mononuclear iron site supported by only S and C donors. In this work, we report experiments that examine the mechanism of N2 binding in this system. The reduction of an iron(II) tris(thiolate) complex with 1 equiv of KC8 leads to a thermally unstable intermediate, and a combination of Mössbauer, EPR, and X-ray absorption spectroscopies identifies it as a high-spin (S = 3/2) iron(I) species that maintains coordination of all three sulfur atoms. DFT calculations suggest that this iron(I) intermediate has a pseudotetrahedral geometry that resembles the S3C iron coordination environment of the belt iron sites in the resting state of the FeMoco. Further reduction to the iron(0) oxidation level under argon causes the dissociation of one of the thiolate donors and gives an η6-arene species which reacts with N2. Thus, in this system the loss of thiolate and binding of N2 require reduction beyond the iron(I) level to the iron(0) level. Further reduction of the iron(0)-N2 complex gives a reactive, formally iron(-I) species. Treatment of the putative iron(-I) complex with weak acids gives low yields of ammonia and hydrazine, demonstrating that these nitrogenase products can be generated from N2 at a synthetic Fe-S-C site. Catalytic N2 reduction is not observed, which is attributed to protonation of the supporting ligand and degradation of the complex via ligand dissociation. Identification of the challenges in this system gives insight into the design features needed for functional biomimetic complexes.
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Affiliation(s)
- Amy L Speelman
- Department of Chemistry , Yale University , 225 Prospect Street , New Haven , Connecticut 06520 , United States
| | - Ilija Čorić
- Department of Chemistry , Yale University , 225 Prospect Street , New Haven , Connecticut 06520 , United States
| | - Casey Van Stappen
- Max Planck Institute for Chemical Energy Conversion , Stiftstraße 34-36 , D-45470 Mülheim an der Ruhr , Germany
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion , Stiftstraße 34-36 , D-45470 Mülheim an der Ruhr , Germany
| | - 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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17
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Kowalska JK, Henthorn JT, Van Stappen C, Trncik C, Einsle O, Keavney D, DeBeer S. X-ray Magnetic Circular Dichroism Spectroscopy Applied to Nitrogenase and Related Models: Experimental Evidence for a Spin-Coupled Molybdenum(III) Center. Angew Chem Int Ed Engl 2019; 58:9373-9377. [PMID: 31119827 PMCID: PMC6772009 DOI: 10.1002/anie.201901899] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 04/17/2019] [Indexed: 11/23/2022]
Abstract
Nitrogenase enzymes catalyze the reduction of atmospheric dinitrogen to ammonia utilizing a Mo‐7Fe‐9S‐C active site, the so‐called FeMoco cluster. FeMoco and an analogous small‐molecule (Et4N)[(Tp)MoFe3S4Cl3] cubane have both been proposed to contain unusual spin‐coupled MoIII sites with an S(Mo)=1/2 non‐Hund configuration at the Mo atom. Herein, we present Fe and Mo L3‐edge X‐ray magnetic circular dichroism (XMCD) spectroscopy of the (Et4N)[(Tp)MoFe3S4Cl3] cubane and Fe L2,3‐edge XMCD spectroscopy of the MoFe protein (containing both FeMoco and the 8Fe‐7S P‐cluster active sites). As the P‐clusters of MoFe protein have an S=0 total spin, these are effectively XMCD‐silent at low temperature and high magnetic field, allowing for FeMoco to be selectively probed by Fe L2,3‐edge XMCD within the intact MoFe protein. Further, Mo L3‐edge XMCD spectroscopy of the cubane model has provided experimental support for a local S(Mo)=1/2 configuration, demonstrating the power and selectivity of XMCD.
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Affiliation(s)
- Joanna K Kowalska
- Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany
| | - Justin T Henthorn
- Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany
| | - Casey Van Stappen
- Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany
| | - Christian Trncik
- Institute for Biochemistry and BIOSS Centre for Biological Signalling Studies, Albert Ludwigs University of Freiburg, Albertstrasse 21, 79104, Freiburg, Germany
| | - Oliver Einsle
- Institute for Biochemistry and BIOSS Centre for Biological Signalling Studies, Albert Ludwigs University of Freiburg, Albertstrasse 21, 79104, Freiburg, Germany
| | - David Keavney
- Argonne National Laboratory, 9700 S. Cass Ave, Argonne, IL, 60439, USA
| | - Serena DeBeer
- Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany
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Kowalska JK, Henthorn JT, Van Stappen C, Trncik C, Einsle O, Keavney D, DeBeer S. X‐ray Magnetic Circular Dichroism Spectroscopy Applied to Nitrogenase and Related Models: Experimental Evidence for a Spin‐Coupled Molybdenum(III) Center. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201901899] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Joanna K. Kowalska
- Inorganic Spectroscopy Max Planck Institute for Chemical Energy Conversion Stiftstrasse 34–36 45470 Mülheim an der Ruhr Germany
| | - Justin T. Henthorn
- Inorganic Spectroscopy Max Planck Institute for Chemical Energy Conversion Stiftstrasse 34–36 45470 Mülheim an der Ruhr Germany
| | - Casey Van Stappen
- Inorganic Spectroscopy Max Planck Institute for Chemical Energy Conversion Stiftstrasse 34–36 45470 Mülheim an der Ruhr Germany
| | - Christian Trncik
- Institute for Biochemistry and BIOSS Centre for Biological Signalling Studies Albert Ludwigs University of Freiburg Albertstrasse 21 79104 Freiburg Germany
| | - Oliver Einsle
- Institute for Biochemistry and BIOSS Centre for Biological Signalling Studies Albert Ludwigs University of Freiburg Albertstrasse 21 79104 Freiburg Germany
| | - David Keavney
- Argonne National Laboratory 9700 S. Cass Ave Argonne IL 60439 USA
| | - Serena DeBeer
- Inorganic Spectroscopy Max Planck Institute for Chemical Energy Conversion Stiftstrasse 34–36 45470 Mülheim an der Ruhr Germany
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Jin WT, Wang H, Wang SY, Dapper CH, Li X, Newton WE, Zhou ZH, Cramer SP. Preliminary Assignment of Protonated and Deprotonated Homocitrates in Extracted FeMo-Cofactors by Comparisons with Molybdenum(IV) Lactates and Oxidovanadium Glycolates. Inorg Chem 2019; 58:2523-2532. [PMID: 30726074 DOI: 10.1021/acs.inorgchem.8b03108] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A similar pair of protonated and deprotonated mononuclear oxidovanadium glycolates [VO(Hglyc)(phen)(H2O)]Cl·2H2O (1) and [VO(glyc)(bpy)(H2O)] (2) and a mixed-(de)protonated oxidovanadium triglycolate (NH4)2[VO(Hglyc)2(glyc)]·H2O (3) were isolated and examined. The ≡C-O(H) (≡C-OH or ≡C-O) groups coordinated to vanadium were spectroscopically and structurally identified. The glycolate in 1 features a bidentate chelation through protonated α-hydroxy and α-carboxy groups, whereas the glycolate in 2 coordinates through deprotonated α-alkoxy and α-carboxy groups. The glycolates in 3 coordinate to vanadium through α-alkoxy or α-hydroxy and α-carboxy groups and thus have both protonated ≡C-OH and deprotonated ≡C-O bonds simultaneously. Structural investigations revealed that the longer protonated V-Oα-hydroxy bonds [2.234(2) Å and 2.244(2) Å] in 1 and 3 are close to those of FeV-cofactor (FeV-co) 2.17 Å1 (FeMo-co 2.17 Å2), while deprotonated V-Oα-alkoxy bonds [2, 1.930(2); 3, 1.927(2) Å] were obviously shorter. This shows a similar elongated trend as the Mo-O distances in the previously reported deprotonated vs protonated molybdenum lactates (Wang, S. Y. et al. Dalton Trans. 2018, 47, 7412-7421) and these vanadium and molybdenum complexes have the same local V/Mo-homocitrate structures as those of FeV/Mo-cos of nitrogenases. The IR spectra of these oxidovanadium and the previously synthesized molybdenum complexes including different substituted ≡C-O(H) model compounds show red-shifts for ≡C-OH vs ≡C-O alternation, which further assign the two IR bands of extracted FeMo-co at 1084 and 1031 cm-1 to ≡C-O and ≡C-OH vibrations, respectively. Although the structural data or IR spectra for some of the previously synthesized Mo/V complexes and extracted FeMo-co were measured earlier, this is the first time that the ≡C-O(H) coordinated peaks are assigned. The overall structural and IR results well suggest the coexistence of homocitrates coordinated with α-alkoxy (deprotonated) and α-hydroxy (protonated) groups in the extracted FeMo-co.
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Affiliation(s)
- Wan-Ting Jin
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 361005 , China
| | - Hongxin Wang
- Department of Chemistry , University of California , Davis , California 95616 , United States.,Physical Biosciences Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Si-Yuan Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 361005 , China
| | - Christie H Dapper
- Department of Biochemistry , Virginia Polytechnic Institute and State University , Blacksburg , Virginia 24061 , United States
| | - Xing Li
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 361005 , China
| | - William E Newton
- Department of Biochemistry , Virginia Polytechnic Institute and State University , Blacksburg , Virginia 24061 , United States
| | - Zhao-Hui Zhou
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 361005 , China
| | - Stephen P Cramer
- Department of Chemistry , University of California , Davis , California 95616 , United States.,Physical Biosciences Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
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Montgomery JM, Mazziotti DA. Strong Electron Correlation in Nitrogenase Cofactor, FeMoco. J Phys Chem A 2018; 122:4988-4996. [DOI: 10.1021/acs.jpca.8b00941] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Jason M. Montgomery
- Department of Chemistry, Biochemistry, and Physics, Florida Southern College, Lakeland, Florida 33801, United States
| | - David A. Mazziotti
- Department of Chemistry and The James Franck Institute, University of Chicago, Chicago, Illinois 60637, United States
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Benediktsson B, Bjornsson R. QM/MM Study of the Nitrogenase MoFe Protein Resting State: Broken-Symmetry States, Protonation States, and QM Region Convergence in the FeMoco Active Site. Inorg Chem 2017; 56:13417-13429. [DOI: 10.1021/acs.inorgchem.7b02158] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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
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Anderton KJ, Knight BJ, Rheingold AL, Abboud KA, García-Serres R, Murray LJ. Reactivity of hydride bridges in a high-spin [Fe 3(μ-H) 3] 3+ cluster: reversible H 2/CO exchange and Fe-H/B-F bond metathesis. Chem Sci 2017; 8:4123-4129. [PMID: 28603601 PMCID: PMC5443887 DOI: 10.1039/c6sc05583d] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 03/27/2017] [Indexed: 01/08/2023] Open
Abstract
The triiron trihydride complex Fe3H3L (1) [where L3– is a tris(β-diketiminate)cyclophanate] reacts with CO and with BF3·OEt2 to afford (FeICO)2FeII(μ3-H)L (2) and Fe3F3L (3), respectively.
The triiron trihydride complex Fe3H3L (1) [where L3– is a tris(β-diketiminate)cyclophanate] reacts with CO and with BF3·OEt2 to afford (FeICO)2FeII(μ3-H)L (2) and Fe3F3L (3), respectively. Variable-temperature and applied-field Mössbauer spectroscopy support the assignment of two high-spin (HS) iron(i) centers and one HS iron(ii) ion in 2. Preliminary studies support a CO-induced reductive elimination of H2 from 1, rather than CO trapping a species from an equilibrium mixture. This complex reacts with H2 to regenerate 1 under a dihydrogen atmosphere, which represents a rare example of reversible CO/H2 exchange and the first to occur at high-spin metal centers, as well as the first example of a reversible multielectron redox reaction at a designed high-spin metal cluster. The formation of 3 proceeds through a previously unreported net fluoride-for-hydride substitution, and 3 is surprisingly chemically inert to Si–H bonds and points to an unexpectedly large difference between the Fe–F and Fe–H bonds in this high-spin system.
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Affiliation(s)
- Kevin J Anderton
- Center for Catalysis , University of Florida , 214 Leigh Hall P.O. Box 117200 , Gainesville , FL 32611 , USA .
| | - Brian J Knight
- Center for Catalysis , University of Florida , 214 Leigh Hall P.O. Box 117200 , Gainesville , FL 32611 , USA .
| | - Arnold L Rheingold
- Department of Chemistry and Biochemistry , University of California San Diego , 9500 Gilman Drive, MC 0358 , La Jolla , CA 92093-0358 , USA
| | - Khalil A Abboud
- Department of Chemistry , University of Florida , 214 Leigh Hall P.O. Box 117200 , Gainesville , FL 32611 , USA
| | - Ricardo García-Serres
- Laboratoire de Chimie de Biologie des Métaux , UMR 5249 , Université Joseph Fourier , Grenoble-1, CNRS-CEA 17 Rue des Martyrs , 38054 Grenoble Cedex 9 , France
| | - Leslie J Murray
- Center for Catalysis , University of Florida , 214 Leigh Hall P.O. Box 117200 , Gainesville , FL 32611 , USA .
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Bjornsson R, Neese F, DeBeer S. Revisiting the Mössbauer Isomer Shifts of the FeMoco Cluster of Nitrogenase and the Cofactor Charge. Inorg Chem 2017; 56:1470-1477. [DOI: 10.1021/acs.inorgchem.6b02540] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Ragnar Bjornsson
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
- Science Institute, University of Iceland, Dunhagi 3, 107 Reykjavik, Iceland
| | - Frank Neese
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
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Affiliation(s)
- Yilin Hu
- Department of Molecular Biology and Biochemistry and
| | - Markus W. Ribbe
- Department of Molecular Biology and Biochemistry and
- Department of Chemistry, University of California, Irvine, California 92697-2025; ,
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25
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Nitrogenase FeMoco investigated by spatially resolved anomalous dispersion refinement. Nat Commun 2016; 7:10902. [PMID: 26973151 PMCID: PMC4793075 DOI: 10.1038/ncomms10902] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 01/31/2016] [Indexed: 02/06/2023] Open
Abstract
The [Mo:7Fe:9S:C] iron-molybdenum cofactor (FeMoco) of nitrogenase is the largest known metal cluster and catalyses the 6-electron reduction of dinitrogen to ammonium in biological nitrogen fixation. Only recently its atomic structure was clarified, while its reactivity and electronic structure remain under debate. Here we show that for its resting S=3/2 state the common iron oxidation state assignments must be reconsidered. By a spatially resolved refinement of the anomalous scattering contributions of the 7 Fe atoms of FeMoco, we conclude that three irons (Fe1/3/7) are more reduced than the other four (Fe2/4/5/6). Our data are in agreement with the recently revised oxidation state assignment for the molybdenum ion, providing the first spatially resolved picture of the resting-state electron distribution within FeMoco. This might provide the long-sought experimental basis for a generally accepted theoretical description of the cluster that is in line with available spectroscopic and functional data. The [Mo:7Fe:9S:C] iron-molybdenum cofactor (FeMoco) of nitrogenase is a large metal cluster with an important role in biological nitrogen fixation. Here, the authors use spatially resolved refinement of the anomalous scattering contributions of the iron atoms to determine the resting-state electron distribution of FeMoco.
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Cutsail GE, Telser J, Hoffman BM. Advanced paramagnetic resonance spectroscopies of iron-sulfur proteins: Electron nuclear double resonance (ENDOR) and electron spin echo envelope modulation (ESEEM). BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:1370-94. [PMID: 25686535 DOI: 10.1016/j.bbamcr.2015.01.025] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 01/29/2015] [Accepted: 01/29/2015] [Indexed: 12/20/2022]
Abstract
The advanced electron paramagnetic resonance (EPR) techniques, electron nuclear double resonance (ENDOR) and electron spin echo envelope modulation (ESEEM) spectroscopies, provide unique insights into the structure, coordination chemistry, and biochemical mechanism of nature's widely distributed iron-sulfur cluster (FeS) proteins. This review describes the ENDOR and ESEEM techniques and then provides a series of case studies on their application to a wide variety of FeS proteins including ferredoxins, nitrogenase, and radical SAM enzymes. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.
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Affiliation(s)
- George E Cutsail
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Joshua Telser
- Department of Biological, Chemical and Physical Sciences, Roosevelt University, Chicago, IL 60605, USA
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.
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Bjornsson R, Neese F, Schrock RR, Einsle O, DeBeer S. The discovery of Mo(III) in FeMoco: reuniting enzyme and model chemistry. J Biol Inorg Chem 2014; 20:447-60. [PMID: 25549604 PMCID: PMC4334110 DOI: 10.1007/s00775-014-1230-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Accepted: 12/11/2014] [Indexed: 12/02/2022]
Abstract
Biological nitrogen fixation is enabled by molybdenum-dependent nitrogenase enzymes, which effect the reduction of dinitrogen to ammonia using an Fe7MoS9C active site, referred to as the iron molybdenum cofactor or FeMoco. In this mini-review, we summarize the current understanding of the molecular and electronic structure of FeMoco. The advances in our understanding of the active site structure are placed in context with the parallel evolution of synthetic model studies. The recent discovery of Mo(III) in the FeMoco active site is highlighted with an emphasis placed on the important role that model studies have played in this finding. In addition, the reactivities of synthetic models are discussed in terms of their relevance to the enzymatic system.
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Affiliation(s)
- Ragnar Bjornsson
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstr. 34-36, 45470, Mülheim and Der Ruhr, Germany,
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Hu Y, Ribbe MW. Nitrogenase and homologs. J Biol Inorg Chem 2014; 20:435-45. [PMID: 25491285 DOI: 10.1007/s00775-014-1225-3] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 11/24/2014] [Indexed: 11/24/2022]
Abstract
Nitrogenase catalyzes biological nitrogen fixation, a key step in the global nitrogen cycle. Three homologous nitrogenases have been identified to date, along with several structural and/or functional homologs of this enzyme that are involved in nitrogenase assembly, bacteriochlorophyll biosynthesis and methanogenic process, respectively. In this article, we provide an overview of the structures and functions of nitrogenase and its homologs, which highlights the similarity and disparity of this uniquely versatile group of enzymes.
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Affiliation(s)
- Yilin Hu
- Department of Molecular Biology and Biochemistry, 2230 McGaugh Hall, University of California, Irvine, CA, 92697-3900, USA,
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Bjornsson R, Lima FA, Spatzal T, Weyhermüller T, Glatzel P, Bill E, Einsle O, Neese F, DeBeer S. Identification of a spin-coupled Mo(iii) in the nitrogenase iron–molybdenum cofactor. Chem Sci 2014. [DOI: 10.1039/c4sc00337c] [Citation(s) in RCA: 133] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The molybdenum atom in FeMoco is imperative to the high activity of the enzyme and has been proposed to be Mo(iv). We demonstrate that only Mo(iii) fits Mo HERFD XAS data, the first example of Mo(iii) in biology. Theoretical calculations further reveal an unusual spin-coupled Mo(iii).
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Affiliation(s)
- Ragnar Bjornsson
- Max-Planck-Institut für Chemische Energiekonversion
- 45470 Mülheim an der Ruhr, Germany
| | - Frederico A. Lima
- Max-Planck-Institut für Chemische Energiekonversion
- 45470 Mülheim an der Ruhr, Germany
| | - Thomas Spatzal
- Institute for Biochemistry
- Albert-Ludwigs-Universität Freiburg
- 79104 Freiburg, Germany
| | - Thomas Weyhermüller
- Max-Planck-Institut für Chemische Energiekonversion
- 45470 Mülheim an der Ruhr, Germany
| | - Pieter Glatzel
- European Synchrotron Radiation Facility
- 38043 Grenoble Cedex, France
| | - Eckhard Bill
- Max-Planck-Institut für Chemische Energiekonversion
- 45470 Mülheim an der Ruhr, Germany
| | - Oliver Einsle
- Institute for Biochemistry
- Albert-Ludwigs-Universität Freiburg
- 79104 Freiburg, Germany
| | - Frank Neese
- Max-Planck-Institut für Chemische Energiekonversion
- 45470 Mülheim an der Ruhr, Germany
| | - Serena DeBeer
- Max-Planck-Institut für Chemische Energiekonversion
- 45470 Mülheim an der Ruhr, Germany
- Department of Chemistry and Chemical Biology
- Cornell University
- Ithaca, USA
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Cleaving the n,n triple bond: the transformation of dinitrogen to ammonia by nitrogenases. Met Ions Life Sci 2014; 14:147-76. [PMID: 25416394 DOI: 10.1007/978-94-017-9269-1_7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Biological nitrogen fixation is a natural process that converts atmospheric nitrogen (N2) to bioavailable ammonia (NH3). This reaction not only plays a key role in supplying bio-accessible nitrogen to all life forms on Earth, but also embodies the powerful chemistry of cleaving the inert N,N triple bond under ambient conditions. The group of enzymes that carry out this reaction are called nitrogenases and typically consist of two redox active protein components, each containing metal cluster(s) that are crucial for catalysis. In the past decade, a number of crystal structures, including several at high resolutions, have been solved. However, the catalytic mechanism of nitrogenase, namely, how the N,N triple bond is cleaved by this enzyme under ambient conditions, has remained elusive. Nevertheless, recent biochemical and spectroscopic studies have led to a better understanding of the potential intermediates of N2 reduction by the molybdenum (Mo)-nitrogenase. In addition, it has been demonstrated that carbon monoxide (CO), which was thought to be an inhibitor of N2 reduction, could also be reduced by the vanadium (V)-nitrogenase to small alkanes and alkenes. This chapter will begin with an introduction to biological nitrogen fixation and Mo-nitrogenase, continue with a discussion of the catalytic mechanism of N2 reduction by Mo-nitrogenase, and conclude with a survey of the current knowledge of N2- and CO-reduction by V-nitrogenase and how V-nitrogenase compares to its Mo-counterpart in these catalytic activities.
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Ribbe MW, Hu Y, Hodgson KO, Hedman B. Biosynthesis of nitrogenase metalloclusters. Chem Rev 2013; 114:4063-80. [PMID: 24328215 DOI: 10.1021/cr400463x] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Markus W Ribbe
- Department of Molecular Biology and Biochemistry, University of California , Irvine, California 92697-3900, United States
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Spatzal T, Einsle O, Andrade SLA. Analysis of the Magnetic Properties of Nitrogenase FeMo Cofactor by Single-Crystal EPR Spectroscopy. Angew Chem Int Ed Engl 2013; 52:10116-9. [DOI: 10.1002/anie.201303000] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 06/11/2013] [Indexed: 11/09/2022]
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Spatzal T, Einsle O, Andrade SLA. Analyse der magnetischen Eigenschaften des FeMo-Cofaktors der Nitrogenase mittels Einkristall-EPR-Spektroskopie. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201303000] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Seefeldt LC, Yang ZY, Duval S, Dean DR. Nitrogenase reduction of carbon-containing compounds. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:1102-11. [PMID: 23597875 DOI: 10.1016/j.bbabio.2013.04.003] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 04/03/2013] [Accepted: 04/08/2013] [Indexed: 10/27/2022]
Abstract
Nitrogenase is an enzyme found in many bacteria and archaea that catalyzes biological dinitrogen fixation, the reduction of N2 to NH3, accounting for the major input of fixed nitrogen into the biogeochemical N cycle. In addition to reducing N2 and protons, nitrogenase can reduce a number of small, non-physiological substrates. Among these alternative substrates are included a wide array of carbon-containing compounds. These compounds have provided unique insights into aspects of the nitrogenase mechanism. Recently, it was shown that carbon monoxide (CO) and carbon dioxide (CO2) can also be reduced by nitrogenase to yield hydrocarbons, opening new insights into the mechanism of small molecule activation and reduction by this complex enzyme as well as providing clues for the design of novel molecular catalysts. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.
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Affiliation(s)
- Lance C Seefeldt
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322, USA.
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Yan L, Pelmenschikov V, Dapper CH, Scott AD, Newton WE, Cramer SP. IR-monitored photolysis of CO-inhibited nitrogenase: a major EPR-silent species with coupled terminal CO ligands. Chemistry 2012; 18:16349-57. [PMID: 23136072 PMCID: PMC4497518 DOI: 10.1002/chem.201202072] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Revised: 08/22/2012] [Indexed: 11/07/2022]
Abstract
Fourier transform infrared spectroscopy (FTIR) was used to observe the photolysis and recombination of a new EPR-silent CO-inhibited form of α-H195Q nitrogenase from Azotobacter vinelandii. Photolysis at 4 K reveals a strong negative IR difference band at nu = 1938 cm(-1), along with a weaker negative feature at 1911 cm(-1). These bands and the associated chemical species have both been assigned the label "Hi-3". A positive band at nu = 1921 cm(-1) was assigned to the "Lo-3" photoproduct. By using an isotopic mixture of (12)C (16)O and (13)C (18)O, we show that the Hi-3 bands arise from coupling of two similar CO oscillators with one uncoupled frequency at approximately nu = 1917 cm(-1). Although in previous studies Lo-3 was not observed to recombine, by extending the observation range to 200-240 K, we found that recombination to Hi-3 does indeed occur, with an activation energy of approximately 6.5 kJ mol(-1). The frequencies of the Hi-3 bands suggest terminal CO ligation. This hypothesis was tested with DFT calculations on models with terminal CO ligands on Fe2 and Fe6 of the FeMo-cofactor. An S = 0 model with both CO ligands in exo positions predicts symmetric and asymmetric stretches at nu = 1938 and 1909 cm(-1), respectively, with relative band intensities of about 3.5:1, which is in good agreement with experiment. From the observed IR intensities, Hi-3 was found to be present at a concentration about equal to that of the EPR-active Hi-1 species. The relevance of Hi-3 to the nitrogenase catalytic mechanism and its recently discovered Fischer-Tropsch chemistry is discussed.
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Affiliation(s)
- Lifen Yan
- Department of Chemistry, University of California, Davis, CA 95616
| | | | - Christie H. Dapper
- Department of Biochemistry, Virginia Polytechnic Institute, Blacksburg, VA 24061, USA
| | - Aubrey D. Scott
- Department of Chemistry, University of California, Davis, CA 95616
| | - William E. Newton
- Department of Biochemistry, Virginia Polytechnic Institute, Blacksburg, VA 24061, USA
| | - Stephen P. Cramer
- Department of Chemistry, University of California, Davis, CA 95616
- Physical Biosciences Division, Lawrence Berkeley National Lab, Berkeley, CA 94720
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Hu Y, Ribbe MW. Nitrogenase assembly. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1827:1112-22. [PMID: 23232096 DOI: 10.1016/j.bbabio.2012.12.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 12/02/2012] [Accepted: 12/03/2012] [Indexed: 11/18/2022]
Abstract
Nitrogenase contains two unique metalloclusters: the P-cluster and the M-cluster. The assembly processes of P- and M-clusters are arguably the most complicated processes in bioinorganic chemistry. There is considerable interest in decoding the biosynthetic mechanisms of the P- and M-clusters, because these clusters are not only biologically important, but also chemically unprecedented. Understanding the assembly mechanisms of these unique metalloclusters is crucial for understanding the structure-function relationship of nitrogenase. Here, we review the recent advances in this research area, with an emphasis on our work that provide important insights into the biosynthetic pathways of these high-nuclearity metal centers. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.
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Affiliation(s)
- Yilin Hu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92687-3900, USA.
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39
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Asatryan R, Bozzelli JW, Ruckenstein E. Dihydrogen Catalysis: A Degradation Mechanism for N2-Fixation Intermediates. J Phys Chem A 2012; 116:11618-42. [DOI: 10.1021/jp303692v] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Rubik Asatryan
- Department of Chemical and Biological
Engineering, State University of New York, Buffalo, New York 14260, United States
- Department of Chemistry and
Environmental Science, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Joseph W. Bozzelli
- Department of Chemistry and
Environmental Science, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Eli Ruckenstein
- Department of Chemical and Biological
Engineering, State University of New York, Buffalo, New York 14260, United States
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Abstract
Nitrogenase catalyzes a key step in the global nitrogen cycle, the nucleotide-dependent reduction of atmospheric dinitrogen to bioavailable ammonia. There is a substantial amount of interest in elucidating the biosynthetic mechanisms of the FeMoco and the P-cluster of nitrogenase, because these clusters are not only biologically important but also chemically unprecedented. In this review, we summarize the recent advances in this research area, with an emphasis on our work that aims at providing structural and spectroscopic insights into the assembly of these complex metalloclusters.
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41
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Seefeldt LC, Hoffman BM, Dean DR. Electron transfer in nitrogenase catalysis. Curr Opin Chem Biol 2012; 16:19-25. [PMID: 22397885 DOI: 10.1016/j.cbpa.2012.02.012] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Revised: 02/11/2012] [Accepted: 02/13/2012] [Indexed: 11/30/2022]
Abstract
Nitrogenase is a two-component enzyme that catalyzes the nucleotide-dependent reduction of N2 to 2NH3. This process involves three redox-active metal-containing cofactors including a [4Fe-4S] cluster, an eight-iron P cluster and a seven-iron plus molybdenum FeMo-cofactor, the site of substrate reduction. A deficit-spending model for electron transfer has recently been proposed that incorporates protein conformational gating that favors uni-directional electron transfer among the metalloclusters for the activation of the substrate-binding site. Also reviewed is a proposal that each of the metal clusters cycles through only two redox states of the metal-sulfur core as the system accumulates the multiple electrons required for substrate binding and reduction. In particular, it was suggested that as FeMo-cofactor acquires the four electrons necessary for optimal binding of N2, each successive pair of electrons is stored as an Fe-H--Fe bridging hydride, with the FeMo-cofactor metal-ion core retaining its resting redox state. We here broaden the discussion of stable intermediates that might form when FeMo-cofactor receives an odd number of electrons.
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Affiliation(s)
- Lance C Seefeldt
- Department of Chemistry and Biochemistry, Utah State University, 0300 Old Main Hill, Logan, UT 84322, USA.
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42
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Ruiz E. Theoretical Study of the Exchange Coupling in Large Polynuclear Transition Metal Complexes Using DFT Methods. STRUCTURE AND BONDING 2012. [DOI: 10.1007/b97942] [Citation(s) in RCA: 159] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Lancaster KM, Roemelt M, Ettenhuber P, Hu Y, Ribbe MW, Neese F, Bergmann U, DeBeer S. X-ray emission spectroscopy evidences a central carbon in the nitrogenase iron-molybdenum cofactor. Science 2011; 334:974-7. [PMID: 22096198 PMCID: PMC3800678 DOI: 10.1126/science.1206445] [Citation(s) in RCA: 613] [Impact Index Per Article: 47.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Nitrogenase is a complex enzyme that catalyzes the reduction of dinitrogen to ammonia. Despite insight from structural and biochemical studies, its structure and mechanism await full characterization. An iron-molybdenum cofactor (FeMoco) is thought to be the site of dinitrogen reduction, but the identity of a central atom in this cofactor remains unknown. Fe Kβ x-ray emission spectroscopy (XES) of intact nitrogenase MoFe protein, isolated FeMoco, and the FeMoco-deficient nifB protein indicates that among the candidate atoms oxygen, nitrogen, and carbon, it is carbon that best fits the XES data. The experimental XES is supported by computational efforts, which show that oxidation and spin states do not affect the assignment of the central atom to C(4-). Identification of the central atom will drive further studies on its role in catalysis.
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Affiliation(s)
- Kyle M. Lancaster
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Michael Roemelt
- Institut für Physikalische und Theoretische Chemie, Universität Bonn, D-53115 Bonn, Germany
| | - Patrick Ettenhuber
- Institut für Physikalische und Theoretische Chemie, Universität Bonn, D-53115 Bonn, Germany
| | - Yilin Hu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
| | - Markus W. Ribbe
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
| | - Frank Neese
- Institut für Physikalische und Theoretische Chemie, Universität Bonn, D-53115 Bonn, Germany
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Uwe Bergmann
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Serena DeBeer
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
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44
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Doan PE, Telser J, Barney BM, Igarashi RY, Dean DR, Seefeldt LC, Hoffman BM. 57Fe ENDOR spectroscopy and 'electron inventory' analysis of the nitrogenase E4 intermediate suggest the metal-ion core of FeMo-cofactor cycles through only one redox couple. J Am Chem Soc 2011; 133:17329-40. [PMID: 21980917 DOI: 10.1021/ja205304t] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
N(2) binds to the active-site metal cluster in the nitrogenase MoFe protein, the FeMo-cofactor ([7Fe-9S-Mo-homocitrate-X]; FeMo-co) only after the MoFe protein has accumulated three or four electrons/protons (E(3) or E(4) states), with the E(4) state being optimally activated. Here we study the FeMo-co (57)Fe atoms of E(4) trapped with the α-70(Val→Ile) MoFe protein variant through use of advanced ENDOR methods: 'random-hop' Davies pulsed 35 GHz ENDOR; difference triple resonance; the recently developed Pulse-Endor-SaTuration and REcovery (PESTRE) protocol for determining hyperfine-coupling signs; and Raw-DATA (RD)-PESTRE, a PESTRE variant that gives a continuous sign readout over a selected radiofrequency range. These methods have allowed experimental determination of the signed isotropic (57)Fe hyperfine couplings for five of the seven iron sites of the reductively activated E(4) FeMo-co, and given the magnitude of the coupling for a sixth. When supplemented by the use of sum-rules developed to describe electron-spin coupling in FeS proteins, these (57)Fe measurements yield both the magnitude and signs of the isotropic couplings for the complete set of seven Fe sites of FeMo-co in E(4). In light of the previous findings that FeMo-co of E(4) binds two hydrides in the form of (Fe-(μ-H(-))-Fe) fragments, and that molybdenum has not become reduced, an 'electron inventory' analysis assigns the formal redox level of FeMo-co metal ions in E(4) to that of the resting state (M(N)), with the four accumulated electrons residing on the two Fe-bound hydrides. Comparisons with earlier (57)Fe ENDOR studies and electron inventory analyses of the bio-organometallic intermediate formed during the reduction of alkynes and the CO-inhibited forms of nitrogenase (hi-CO and lo-CO) inspire the conjecture that throughout the eight-electron reduction of N(2) plus 2H(+) to two NH(3) plus H(2), the inorganic core of FeMo-co cycles through only a single redox couple connecting two formal redox levels: those associated with the resting state, M(N), and with the one-electron reduced state, M(R). We further note that this conjecture might apply to other complex FeS enzymes.
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Affiliation(s)
- Peter E Doan
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, USA
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45
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Harris TV, Szilagyi RK. Comparative assessment of the composition and charge state of nitrogenase FeMo-cofactor. Inorg Chem 2011; 50:4811-24. [PMID: 21545160 DOI: 10.1021/ic102446n] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A significant limitation in our understanding of the molecular mechanism of biological nitrogen fixation is the uncertain composition of the FeMo-cofactor (FeMo-co) of nitrogenase. In this study we present a systematic, density functional theory-based evaluation of spin-coupling schemes, iron oxidation states, ligand protonation states, and interstitial ligand composition using a wide range of experimental criteria. The employed functionals and basis sets were validated with molecular orbital information from X-ray absorption spectroscopic data of relevant iron-sulfur clusters. Independently from the employed level of theory, the electronic structure with the greatest number of antiferromagnetic interactions corresponds to the lowest energy state for a given charge and oxidation state distribution of the iron ions. The relative spin state energies of resting and oxidized FeMo-co already allowed exclusion of certain iron oxidation state distributions and interstitial ligand compositions. Geometry-optimized FeMo-co structures of several models further eliminated additional states and compositions, while reduction potentials indicated a strong preference for the most likely charge state of FeMo-co. Mössbauer and ENDOR parameter calculations were found to be remarkably dependent on the employed training set, density functional, and basis set. Overall, we found that a more oxidized [Mo(IV)-2Fe(II)-5Fe(III)-9S(2-)-C(4-)] composition with a hydroxyl-protonated homocitrate ligand satisfies all of the available experimental criteria and is thus favored over the currently preferred composition of [Mo(IV)-4Fe(II)-3Fe(III)-9S(2-)-N(3-)] from the literature.
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Affiliation(s)
- Travis V Harris
- NAI Astrobiology Biogeocatalysis Research Center, Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, USA
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46
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Roth LE, Nguyen JC, Tezcan FA. ATP- and iron-protein-independent activation of nitrogenase catalysis by light. J Am Chem Soc 2011; 132:13672-4. [PMID: 20843032 DOI: 10.1021/ja1071866] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We report here the light-driven activation of the molybdenum-iron-protein (MoFeP) of nitrogenase for substrate reduction independent of ATP hydrolysis and the iron-protein (FeP), which have been believed to be essential for catalytic turnover. A MoFeP variant labeled on its surface with a Ru-photosensitizer is shown to photocatalytically reduce protons and acetylene, most likely at its active site, FeMoco. The uncoupling of nitrogenase catalysis from ATP hydrolysis should enable the study of redox dynamics within MoFeP and the population of discrete reaction intermediates for structural investigations.
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Affiliation(s)
- Lauren E Roth
- University of California, San Diego, Department of Chemistry and Biochemistry, La Jolla, California 92093-0356, USA
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47
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Sandala GM, Noodleman L. Modeling the MoFe nitrogenase system with broken symmetry density functional theory. Methods Mol Biol 2011; 766:293-312. [PMID: 21833875 DOI: 10.1007/978-1-61779-194-9_19] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Density functional theory (DFT) represents a unified framework for gaining molecular level insight into molybdenum-iron (MoFe) nitrogenase. However, accurately describing the electronic structure of the spin-polarized and spin-coupled iron-molybdenum cofactor (FeMo-co) where N(2) reduction occurs within MoFe nitrogenase is challenging. Therefore, the enhancement of DFT to include broken symmetry (BS-DFT) plus approximate spin projection has proven valuable because it provides a procedure to compute reliable geometries, energies, redox potentials, and quantities relevant to Mössbauer and ENDOR spectroscopies. After describing the theoretical tools necessary to obtain this information, we show by way of examples how BS-DFT is a very powerful partner to experiment. We expect that quantitative quantum chemical theory of this type will play an ever-increasing role in helping to decipher complex bioinorganic systems like those found in MoFe nitrogenase.
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Affiliation(s)
- Gregory M Sandala
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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48
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Harris TV, Szilagyi RK. Nitrogenase structure and function relationships by density functional theory. Methods Mol Biol 2011; 766:267-291. [PMID: 21833874 DOI: 10.1007/978-1-61779-194-9_18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Modern density functional theory has tremendous potential with matching popularity in metalloenzymology to reveal the unseen atomic and molecular details of structural data, spectroscopic measurements, and biochemical experiments by providing insights into unobservable structures and states, while also offering theoretical justifications for observed trends and differences. An often untapped potential of this theoretical approach is to bring together diverse experimental structural and reactivity information and allow for these to be critically evaluated at the same level. This is particularly applicable for the tantalizingly complex problem of the structure and molecular mechanism of biological nitrogen fixation. In this chapter we provide a review with extensive practical details of the compilation and evaluation of experimental data for an unbiased and systematic density functional theory analysis that can lead to remarkable new insights about the structure-function relationships of the iron-sulfur clusters of nitrogenase.
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Affiliation(s)
- Travis V Harris
- Department of Chemistry and Biochemistry, Astrobiology Biogeochemistry Research Center, Montana State University, Bozeman, MT 59717, USA.
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49
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Abstract
Nitrogenase is the enzyme responsible for biological reduction of dinitrogen (N(2)) to ammonia, a form usable for life. Playing a central role in the global biogeochemical nitrogen cycle, this enzyme has been the focus of intensive research for over 60 years. This chapter provides an overview of the features of nitrogenase as a background to the subsequent chapters of this volume that detail the many methods that have been applied in an attempt to gain a deeper understanding of this complex enzyme.
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Affiliation(s)
- Zhi-Yong Yang
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322, USA.
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50
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Hernandez JA, George SJ, Rubio LM. Molybdenum trafficking for nitrogen fixation. Biochemistry 2009; 48:9711-21. [PMID: 19772354 DOI: 10.1021/bi901217p] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The molybdenum nitrogenase is responsible for most biological nitrogen fixation, a prokaryotic metabolic process that determines the global biogeochemical cycles of nitrogen and carbon. Here we describe the trafficking of molybdenum for nitrogen fixation in the model diazotrophic bacterium Azotobacter vinelandii. The genes and proteins involved in molybdenum uptake, homeostasis, storage, regulation, and nitrogenase cofactor biosynthesis are reviewed. Molybdenum biochemistry in A. vinelandii reveals unexpected mechanisms and a new role for iron-sulfur clusters in the sequestration and delivery of molybdenum.
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Affiliation(s)
- Jose A Hernandez
- Department of Biochemistry, Midwestern University, Glendale, Arizona 85308, USA
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