1
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Einsle O. On the Shoulders of Giants-Reaching for Nitrogenase. Molecules 2023; 28:7959. [PMID: 38138449 PMCID: PMC10745432 DOI: 10.3390/molecules28247959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 11/14/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
Only a single enzyme system-nitrogenase-carries out the conversion of atmospheric N2 into bioavailable ammonium, an essential prerequisite for all organismic life. The reduction of this inert substrate at ambient conditions poses unique catalytic challenges that strain our mechanistic understanding even after decades of intense research. Structural biology has added its part to this greater tapestry, and in this review, I provide a personal (and highly biased) summary of the parts of the story to which I had the privilege to contribute. It focuses on the crystallographic analysis of the three isoforms of nitrogenases at high resolution and the binding of ligands and inhibitors to the active-site cofactors of the enzyme. In conjunction with the wealth of available biochemical, biophysical, and spectroscopic data on the protein, this has led us to a mechanistic hypothesis based on an elementary mechanism of repetitive hydride formation and insertion.
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Affiliation(s)
- Oliver Einsle
- Institute of Biochemistry, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104 Freiburg im Breisgau, Germany
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2
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Einsle O. Catalysis and structure of nitrogenases. Curr Opin Struct Biol 2023; 83:102719. [PMID: 37802004 DOI: 10.1016/j.sbi.2023.102719] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/03/2023] [Accepted: 09/06/2023] [Indexed: 10/08/2023]
Abstract
In providing bioavailable nitrogen as building blocks for all classes of biomacromolecules, biological nitrogen fixation is an essential process for all organismic life. Only a single enzyme, nitrogenase, performs this task at ambient conditions and with ATP as an energy source. The assembly of the complex iron-sulfur enzyme nitrogenase and its catalytic mechanism remains a matter of intense study. Recent progress in the structural analysis of the three known isoforms of nitrogenase-differentiated primarily by the heterometal in their active site cofactor-has revealed a degree of structural plasticity of these clusters that suggest two distinct binding sites for substrates and reaction intermediates. A mechanistic proposal based on this finding integrates most of the available experimental data. Furthermore, the first applications of high-resolution cryo-electron microscopy have highlighted further dynamic conformational changes. Structures obtained under turnover conditions support the proposed alternating half-site reactivity in the C2-symmetric nitrogenase complex.
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Affiliation(s)
- Oliver Einsle
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104 Freiburg im Breisgau, Germany.
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3
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Lukoyanov DA, Yang ZY, Pérez-González A, Raugei S, Dean DR, Seefeldt LC, Hoffman BM. 13C ENDOR Characterization of the Central Carbon within the Nitrogenase Catalytic Cofactor Indicates That the CFe 6 Core Is a Stabilizing "Heart of Steel". J Am Chem Soc 2022; 144:18315-18328. [PMID: 36166637 DOI: 10.1021/jacs.2c06149] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Substrates and inhibitors of Mo-dependent nitrogenase bind and react at Fe ions of the active-site FeMo-cofactor [7Fe-9S-C-Mo-homocitrate] contained within the MoFe protein α-subunit. The cofactor contains a CFe6 core, a carbon centered within a trigonal prism of six Fe, whose role in catalysis is unknown. Targeted 13C labeling of the carbon enables electron-nuclear double resonance (ENDOR) spectroscopy to sensitively monitor the electronic properties of the Fe-C bonds and the spin-coupling scheme adopted by the FeMo-cofactor metal ions. This report compares 13CFe6 ENDOR measurements for (i) the wild-type protein resting state (E0; α-Val70) to those of (ii) α-Ile70, (iii) α-Ala70-substituted proteins; (iv) crystallographically characterized CO-inhibited "hi-CO" state; (v) E4(4H) Janus intermediate, activated for N2 binding/reduction by accumulation of 4[e-/H+]; (vi) E4(2H)* state containing a doubly reduced FeMo-cofactor without Fe-bound substrates; and (vii) propargyl alcohol reduction intermediate having allyl alcohol bound as a ferracycle to FeMo-cofactor Fe6. All states examined, both S = 1/2 and 3/2 exhibited near-zero 13C isotropic hyperfine coupling constants, Ca = [-1.3 ↔ +2.7] MHz. Density functional theory computations and natural bond orbital analysis of the Fe-C bonds show that this occurs because a (3 spin-up/3 spin-down) spin-exchange configuration of CFe6 Fe-ion spins produces cancellation of large spin-transfers to carbon in each Fe-C bond. Previous X-ray diffraction and DFT both indicate that trigonal-prismatic geometry around carbon is maintained with high precision in all these states. The persistent structure and Fe-C bonding of the CFe6 core indicate that it does not provide a functionally dynamic (hemilabile) "beating heart"─instead it acts as "a heart of steel", stabilizing the structure of the FeMo-cofactor-active site during nitrogenase catalysis.
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Affiliation(s)
- Dmitriy A Lukoyanov
- Departments of Chemistry and Molecular Biosciences, Northwestern University, Evanston, Illinois60208, United States
| | - Zhi-Yong Yang
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah84322, United States
| | - Ana Pérez-González
- Biochemistry Department, Virginia Tech, Blacksburg, Virginia24061, United States
| | - Simone Raugei
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington99352, United States
| | - Dennis R Dean
- Biochemistry Department, Virginia Tech, Blacksburg, Virginia24061, United States
| | - Lance C Seefeldt
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah84322, United States
| | - Brian M Hoffman
- Departments of Chemistry and Molecular Biosciences, Northwestern University, Evanston, Illinois60208, United States
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4
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Biz C, Fianchini M, Gracia J. Strongly Correlated Electrons in Catalysis: Focus on Quantum Exchange. ACS Catal 2021. [DOI: 10.1021/acscatal.1c03135] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Chiara Biz
- MagnetoCat SL, General Polavieja 9 3I, 03012 Alicante, Spain
- Universitat Jaume I, Av. Vicente Sos Baynat s/n, E-12071 Castellón de la Plana, Spain
| | - Mauro Fianchini
- MagnetoCat SL, General Polavieja 9 3I, 03012 Alicante, Spain
| | - Jose Gracia
- MagnetoCat SL, General Polavieja 9 3I, 03012 Alicante, Spain
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5
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Pérez-González A, Yang ZY, Lukoyanov DA, Dean DR, Seefeldt LC, Hoffman BM. Exploring the Role of the Central Carbide of the Nitrogenase Active-Site FeMo-cofactor through Targeted 13C Labeling and ENDOR Spectroscopy. J Am Chem Soc 2021; 143:9183-9190. [PMID: 34110795 DOI: 10.1021/jacs.1c04152] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Mo-dependent nitrogenase is a major contributor to global biological N2 reduction, which sustains life on Earth. Its multi-metallic active-site FeMo-cofactor (Fe7MoS9C-homocitrate) contains a carbide (C4-) centered within a trigonal prismatic CFe6 core resembling the structural motif of the iron carbide, cementite. The role of the carbide in FeMo-cofactor binding and activation of substrates and inhibitors is unknown. To explore this role, the carbide has been in effect selectively enriched with 13C, which enables its detailed examination by ENDOR/ESEEM spectroscopies. 13C-carbide ENDOR of the S = 3/2 resting state (E0) is remarkable, with an extremely small isotropic hyperfine coupling constant, Ca = +0.86 MHz. Turnover under high CO partial pressure generates the S = 1/2 hi-CO state, with two CO molecules bound to FeMo-cofactor. This conversion surprisingly leaves the small magnitude of the 13C carbide isotropic hyperfine-coupling constant essentially unchanged, Ca = -1.30 MHz. This indicates that both the E0 and hi-CO states exhibit an exchange-coupling scheme with nearly cancelling contributions to Ca from three spin-up and three spin-down carbide-bound Fe ions. In contrast, the anisotropic hyperfine coupling constant undergoes a symmetry change upon conversion of E0 to hi-CO that may be associated with bonding and coordination changes at Fe ions. In combination with the negligible difference between CFe6 core structures of E0 and hi-CO, these results suggest that in CO-inhibited hi-CO the dominant role of the FeMo-cofactor carbide is to maintain the core structure, rather than to facilitate inhibitor binding through changes in Fe-carbide covalency or stretching/breaking of carbide-Fe bonds.
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Affiliation(s)
- Ana Pérez-González
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, 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
| | - Dennis R Dean
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Lance C Seefeldt
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Brian M Hoffman
- Department of Chemistry Northwestern University, Evanston, Illinois 60208, United States
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6
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Chica B, Ruzicka J, Kallas H, Mulder DW, Brown KA, Peters JW, Seefeldt LC, Dukovic G, King PW. Defining Intermediates of Nitrogenase MoFe Protein during N 2 Reduction under Photochemical Electron Delivery from CdS Quantum Dots. J Am Chem Soc 2020; 142:14324-14330. [PMID: 32787260 DOI: 10.1021/jacs.0c06343] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Coupling the nitrogenase MoFe protein to light-harvesting semiconductor nanomaterials replaces the natural electron transfer complex of Fe protein and ATP and provides low-potential photoexcited electrons for photocatalytic N2 reduction. A central question is how direct photochemical electron delivery from nanocrystals to MoFe protein is able to support the multielectron ammonia production reaction. In this study, low photon flux conditions were used to identify the initial reaction intermediates of CdS quantum dot (QD):MoFe protein nitrogenase complexes under photochemical activation using EPR. Illumination of CdS QD:MoFe protein complexes led to redox changes in the MoFe protein active site FeMo-co observed as the gradual decline in the E0 resting state intensity that was accompanied by an increase in the intensity of a new "geff = 4.5" EPR signal. The magnetic properties of the geff = 4.5 signal support assignment as a reduced S = 3/2 state, and reaction modeling was used to define it as a two-electron-reduced "E2" intermediate. Use of a MoFe protein variant, β-188Cys, which poises the P cluster in the oxidized P+ state, demonstrated that the P cluster can function as a site of photoexcited electron delivery from CdS to MoFe protein. Overall, the results establish the initial steps for how photoexcited CdS delivers electrons into the MoFe protein during reduction of N2 to ammonia and the role of electron flux in the photochemical reaction cycle.
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Affiliation(s)
- Bryant Chica
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Jesse Ruzicka
- Department of Chemistry, University of Colorado-Boulder, Boulder, Colorado 80309, United States
| | - Hayden Kallas
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - David W Mulder
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Katherine A Brown
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - John W Peters
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99163, United States
| | - Lance C Seefeldt
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Gordana Dukovic
- Department of Chemistry, University of Colorado-Boulder, Boulder, Colorado 80309, United States
| | - Paul W King
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
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7
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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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8
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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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9
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Göb CR, Ehnbom A, Sturm L, Tobe Y, Oppel IM. Supramolecular Metallacycles and Their Binding of Fullerenes. Chemistry 2020; 26:3609-3613. [PMID: 31833098 PMCID: PMC7155124 DOI: 10.1002/chem.201905390] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Indexed: 12/22/2022]
Abstract
The synthesis of a new triaminoguanidinium-based ligand with three tris-chelating [NNO]-binding pockets and C3 symmetry is described. The reaction of tris-(2-pyridinylene-N-oxide)triaminoguanidinium salts with zinc(II) formate leads to the formation of cyclic supramolecular coordination compounds which in solution bind fullerenes in their spherical cavities. The rapid encapsulation of C60 can be observed by NMR spectroscopy and single-crystal X-ray diffraction and is verified using computation.
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Affiliation(s)
- Christian R. Göb
- Institute of Inorganic ChemistryRWTH Aachen UniversityLandoltweg 152074AachenGermany
| | - Andreas Ehnbom
- Department of ChemistryTexas A&M UniversityP.O. Box 30012College StationTX77843-3012USA
| | - Lisa Sturm
- Institute of Inorganic ChemistryRWTH Aachen UniversityLandoltweg 152074AachenGermany
| | - Yoshito Tobe
- Division of Frontier Materials ScienceGraduate School of Engineering ScienceOsaka UniversityToyonakaOsaka560-8531Japan
| | - Iris M. Oppel
- Institute of Inorganic ChemistryRWTH Aachen UniversityLandoltweg 152074AachenGermany
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10
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Chen X, Li JY, Tang ZR, Xu YJ. Surface-defect-engineered photocatalyst for nitrogen fixation into value-added chemical feedstocks. Catal Sci Technol 2020. [DOI: 10.1039/d0cy01227k] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Surface-defect-engineered photocatalyst for nitrogen fixation.
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Affiliation(s)
- Xue Chen
- State Key Laboratory of Photocatalysis on Energy and Environment
- College of Chemistry
- Fuzhou University
- Fuzhou
- China
| | - Jing-Yu Li
- State Key Laboratory of Photocatalysis on Energy and Environment
- College of Chemistry
- Fuzhou University
- Fuzhou
- China
| | - Zi-Rong Tang
- College of Chemistry
- New Campus, Fuzhou University
- Fuzhou
- China
| | - Yi-Jun Xu
- State Key Laboratory of Photocatalysis on Energy and Environment
- College of Chemistry
- Fuzhou University
- Fuzhou
- China
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11
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Arnett CH, Kaiser JT, Agapie T. Remote Ligand Modifications Tune Electronic Distribution and Reactivity in Site-Differentiated, High-Spin Iron Clusters: Flipping Scaling Relationships. Inorg Chem 2019; 58:15971-15982. [PMID: 31738534 DOI: 10.1021/acs.inorgchem.9b02470] [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
We report the synthesis, characterization, and reactivity of [LFe3O(RArIm)3Fe][OTf]2, the first Hammett series of a site-differentiated cluster. The cluster reduction potentials and CO stretching frequencies shift as expected on the basis of the electronic properties of the ligand: electron-donating substituents result in more reducing clusters and weaker C-O bonds. However, unusual trends in the energetics of their two sequential CO binding events with the substituent σp parameters are observed. Specifically, introduction of electron-donating substituents suppresses the first CO binding event (ΔΔH by as much as 7.9 kcal mol-1) but enhances the second (ΔΔH by as much as 1.9 kcal mol-1). X-ray crystallography, including multiple-wavelength anomalous diffraction, Mössbauer spectroscopy, and SQUID magnetometry, reveal that these substituent effects result from changes in the energetic penalty associated with electronic redistribution within the cluster, which occurs during the CO binding event.
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Affiliation(s)
- Charles H Arnett
- Division of Chemistry and Chemical Engineering , California Institute of Technology , Pasadena , California 91125 , United States
| | - Jens T Kaiser
- Division of Chemistry and Chemical Engineering , California Institute of Technology , Pasadena , California 91125 , United States
| | - Theodor Agapie
- Division of Chemistry and Chemical Engineering , California Institute of Technology , Pasadena , California 91125 , United States
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12
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Henthorn J, Arias RJ, Koroidov S, Kroll T, Sokaras D, Bergmann U, Rees DC, DeBeer S. Localized Electronic Structure of Nitrogenase FeMoco Revealed by Selenium K-Edge High Resolution X-ray Absorption Spectroscopy. J Am Chem Soc 2019; 141:13676-13688. [PMID: 31356071 PMCID: PMC6716209 DOI: 10.1021/jacs.9b06988] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Indexed: 11/28/2022]
Abstract
The size and complexity of Mo-dependent nitrogenase, a multicomponent enzyme capable of reducing dinitrogen to ammonia, have made a detailed understanding of the FeMo cofactor (FeMoco) active site electronic structure an ongoing challenge. Selective substitution of sulfur by selenium in FeMoco affords a unique probe wherein local Fe-Se interactions can be directly interrogated via high-energy resolution fluorescence detected X-ray absorption spectroscopic (HERFD XAS) and extended X-ray absorption fine structure (EXAFS) studies. These studies reveal a significant asymmetry in the electronic distribution of the FeMoco, suggesting a more localized electronic structure picture than is typically assumed for iron-sulfur clusters. Supported by experimental small molecule model data in combination with time dependent density functional theory (TDDFT) calculations, the HERFD XAS data is consistent with an assignment of Fe2/Fe6 as an antiferromagnetically coupled diferric pair. HERFD XAS and EXAFS have also been applied to Se-substituted CO-inhibited MoFe protein, demonstrating the ability of these methods to reveal electronic and structural changes that occur upon substrate binding. These results emphasize the utility of Se HERFD XAS and EXAFS for selectively probing the local electronic and geometric structure of FeMoco.
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Affiliation(s)
- Justin
T. Henthorn
- Max
Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, D-45470 Mülheim an der
Ruhr, Germany
| | - Renee J. Arias
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Sergey Koroidov
- PULSE
Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Thomas Kroll
- Stanford
Synchrotron Radiation Lightsource, SLAC
National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Dimosthenis Sokaras
- Stanford
Synchrotron Radiation Lightsource, SLAC
National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Uwe Bergmann
- PULSE
Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Douglas C. Rees
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
- Howard
Hughes Medical Institute, California Institute
of Technology, Pasadena, California 91125, United States
| | - Serena DeBeer
- Max
Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, D-45470 Mülheim an der
Ruhr, Germany
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13
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Morrison CN, Spatzal T, Rees DC. Reversible Protonated Resting State of the Nitrogenase Active Site. J Am Chem Soc 2017; 139:10856-10862. [PMID: 28692802 PMCID: PMC5553094 DOI: 10.1021/jacs.7b05695] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Protonated states of the nitrogenase
active site are mechanistically
significant since substrate reduction is invariably accompanied by
proton uptake. We report the low pH characterization by X-ray crystallography
and EPR spectroscopy of the nitrogenase molybdenum iron (MoFe) proteins
from two phylogenetically distinct nitrogenases (Azotobacter
vinelandii, Av, and Clostridium pasteurianum, Cp) at pHs between 4.5 and 8. X-ray data at pHs of 4.5–6
reveal the repositioning of side chains along one side of the FeMo-cofactor,
and the corresponding EPR data shows a new S = 3/2
spin system with spectral features similar to a state previously observed
during catalytic turnover. The structural changes suggest that FeMo-cofactor
belt sulfurs S3A or S5A are potential protonation sites. Notably,
the observed structural and electronic low pH changes are correlated
and reversible. The detailed structural rearrangements differ between
the two MoFe proteins, which may reflect differences in potential
protonation sites at the active site among nitrogenase species. These
observations emphasize the benefits of investigating multiple nitrogenase
species. Our experimental data suggest that reversible protonation
of the resting state is likely occurring, and we term this state “E0H+”, following the Lowe–Thorneley
naming scheme.
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Affiliation(s)
- Christine N Morrison
- Division of Chemistry and Chemical Engineering and ‡Howard Hughes Medical Institute, California Institute of Technology , Pasadena, California 91125, United States
| | - Thomas Spatzal
- Division of Chemistry and Chemical Engineering and ‡Howard Hughes Medical Institute, California Institute of Technology , Pasadena, California 91125, United States
| | - Douglas C Rees
- Division of Chemistry and Chemical Engineering and ‡Howard Hughes Medical Institute, California Institute of Technology , Pasadena, California 91125, United States
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14
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Djurdjevic I, Einsle O, Decamps L. Nitrogenase Cofactor: Inspiration for Model Chemistry. Chem Asian J 2017; 12:1447-1455. [PMID: 28425208 DOI: 10.1002/asia.201700478] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Ivana Djurdjevic
- Institute for Biochemistry; Albert-Ludwigs-University Freiburg; Albertstrasse 21 79104 Freiburg im Breisgau Germany
| | - Oliver Einsle
- Institute for Biochemistry; Albert-Ludwigs-University Freiburg; Albertstrasse 21 79104 Freiburg im Breisgau Germany
- BIOSS Centre for Biological Signalling Studies; Albert-Ludwigs-University Freiburg; Schänzlestrasse 1 79104 Freiburg im Breisgau Germany
| | - Laure Decamps
- Institute for Biochemistry; Albert-Ludwigs-University Freiburg; Albertstrasse 21 79104 Freiburg im Breisgau Germany
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15
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Rees JA, Bjornsson R, Kowalska JK, Lima FA, Schlesier J, Sippel D, Weyhermüller T, Einsle O, Kovacs JA, DeBeer S. Comparative electronic structures of nitrogenase FeMoco and FeVco. Dalton Trans 2017; 46:2445-2455. [PMID: 28154874 PMCID: PMC5322470 DOI: 10.1039/c7dt00128b] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 01/25/2017] [Indexed: 12/17/2022]
Abstract
An investigation of the active site cofactors of the molybdenum and vanadium nitrogenases (FeMoco and FeVco) was performed using high-resolution X-ray spectroscopy. Synthetic heterometallic iron-sulfur cluster models and density functional theory calculations complement the study of the MoFe and VFe holoproteins using both non-resonant and resonant X-ray emission spectroscopy. Spectroscopic data show the presence of direct iron-heterometal bonds, which are found to be weaker in FeVco. Furthermore, the interstitial carbide is found to perturb the electronic structures of the cofactors through highly covalent Fe-C bonding. The implications of these conclusions are discussed in light of the differential reactivity of the molybdenum and vanadium nitrogenases towards various substrates. Possible functional roles for both the heterometal and the interstitial carbide are detailed.
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Affiliation(s)
- Julian A Rees
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany. and Department of Chemistry, University of Washington, Box 351700, Seattle, WA 98195-1700, USA.
| | - Ragnar Bjornsson
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany. and Science Institute, University of Iceland, Dunhagi 3, 107 Reykjavik, Iceland
| | - Joanna K Kowalska
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany.
| | - Frederico A Lima
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany. and Centro Nacional de Pesquisa em Energia e Materiais Brazilian Synchrotron Light Laboratory - LNLS Rua Giuseppe Máximo Scolfaro, 10.000 13083-970 Campinas SP, Brazil
| | - Julia Schlesier
- Institute for Biochemistry and BIOSS Centre for Biological Signalling Studies, Albert Ludwigs University Freiburg, Germany.
| | - Daniel Sippel
- Institute for Biochemistry and BIOSS Centre for Biological Signalling Studies, Albert Ludwigs University Freiburg, Germany.
| | - Thomas Weyhermüller
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany.
| | - Oliver Einsle
- Institute for Biochemistry and BIOSS Centre for Biological Signalling Studies, Albert Ludwigs University Freiburg, Germany.
| | - Julie A Kovacs
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA 98195-1700, USA.
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany. and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
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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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Burger EM, Andrade SLA, Einsle O. Active sites without restraints: high-resolution analysis of metal cofactors. Curr Opin Struct Biol 2015; 35:32-40. [DOI: 10.1016/j.sbi.2015.07.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 07/24/2015] [Accepted: 07/31/2015] [Indexed: 11/29/2022]
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Zhang LM, Morrison CN, Kaiser JT, Rees DC. Nitrogenase MoFe protein from Clostridium pasteurianum at 1.08 Å resolution: comparison with the Azotobacter vinelandii MoFe protein. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:274-82. [PMID: 25664737 PMCID: PMC4321486 DOI: 10.1107/s1399004714025243] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 11/17/2014] [Indexed: 11/11/2022]
Abstract
The X-ray crystal structure of the nitrogenase MoFe protein from Clostridium pasteurianum (Cp1) has been determined at 1.08 Å resolution by multiwavelength anomalous diffraction phasing. Cp1 and the ortholog from Azotobacter vinelandii (Av1) represent two distinct families of nitrogenases, differing primarily by a long insertion in the α-subunit and a deletion in the β-subunit of Cp1 relative to Av1. Comparison of these two MoFe protein structures at atomic resolution reveals conserved structural arrangements that are significant to the function of nitrogenase. The FeMo cofactors defining the active sites of the MoFe protein are essentially identical between the two proteins. The surrounding environment is also highly conserved, suggesting that this structural arrangement is crucial for nitrogen reduction. The P clusters are likewise similar, although the surrounding protein and solvent environment is less conserved relative to that of the FeMo cofactor. The P cluster and FeMo cofactor in Av1 and Cp1 are connected through a conserved water tunnel surrounded by similar secondary-structure elements. The long α-subunit insertion loop occludes the presumed Fe protein docking surface on Cp1 with few contacts to the remainder of the protein. This makes it plausible that this loop is repositioned to open up the Fe protein docking surface for complex formation.
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Affiliation(s)
- Li-Mei Zhang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Christine N. Morrison
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jens T. Kaiser
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Douglas C. Rees
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA
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Affiliation(s)
- Luisa B. Maia
- REQUIMTE/CQFB, Departamento
de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - José J. G. Moura
- REQUIMTE/CQFB, Departamento
de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
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Einsle O. Nitrogenase FeMo cofactor: an atomic structure in three simple steps. J Biol Inorg Chem 2014; 19:737-45. [DOI: 10.1007/s00775-014-1116-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 02/07/2014] [Indexed: 10/25/2022]
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