1
|
Abstract
The Fischer-Tropsch (FT) process converts a mixture of CO and H2 into liquid hydrocarbons as a major component of the gas-to-liquid technology for the production of synthetic fuels. Contrary to the energy-demanding chemical FT process, the enzymatic FT-type reactions catalyzed by nitrogenase enzymes, their metalloclusters, and synthetic mimics utilize H+ and e- as the reducing equivalents to reduce CO, CO2, and CN- into hydrocarbons under ambient conditions. The C1 chemistry exemplified by these FT-type reactions is underscored by the structural and electronic properties of the nitrogenase-associated metallocenters, and recent studies have pointed to the potential relevance of this reactivity to nitrogenase mechanism, prebiotic chemistry, and biotechnological applications. This review will provide an overview of the features of nitrogenase enzymes and associated metalloclusters, followed by a detailed discussion of the activities of various nitrogenase-derived FT systems and plausible mechanisms of the enzymatic FT reactions, highlighting the versatility of this unique reactivity while providing perspectives onto its mechanistic, evolutionary, and biotechnological implications.
Collapse
Affiliation(s)
- Yilin Hu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine 92697-3900, USA
| | - Chi Chung Lee
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine 92697-3900, USA
| | - Mario Grosch
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine 92697-3900, USA
| | - Joseph B. Solomon
- Department of Chemistry, University of California, Irvine, CA 92697-2025, USA
| | - Wolfgang Weigand
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Markus W. Ribbe
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine 92697-3900, USA
- Department of Chemistry, University of California, Irvine, CA 92697-2025, USA
| |
Collapse
|
2
|
Quantum Mechanical Calculations of Redox Potentials of the Metal Clusters in Nitrogenase. MOLECULES (BASEL, SWITZERLAND) 2022; 28:molecules28010065. [PMID: 36615260 PMCID: PMC9822455 DOI: 10.3390/molecules28010065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/14/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
We have calculated redox potentials of the two metal clusters in Mo-nitrogenase with quantum mechanical (QM) calculations. We employ an approach calibrated for iron-sulfur clusters with 1-4 Fe ions, involving QM-cluster calculations in continuum solvent and large QM systems (400-500 atoms), based on structures from combined QM and molecular mechanics (QM/MM) geometry optimisations. Calculations on the P-cluster show that we can reproduce the experimental redox potentials within 0.33 V. This is similar to the accuracy obtained for the smaller clusters, although two of the redox reactions involve also proton transfer. The calculated P1+/PN redox potential is nearly the same independently of whether P1+ is protonated or deprotonated, explaining why redox titrations do not show any pH dependence. For the FeMo cluster, the calculations clearly show that the formal oxidation state of the cluster in the resting E0 state is MoIIIFe3IIFe4III , in agreement with previous experimental studies and QM calculations. Moreover, the redox potentials of the first five E0-E4 states are nearly constant, as is expected if the electrons are delivered by the same site (the P-cluster). However, the redox potentials are insensitive to the formal oxidation states of the Fe ion (i.e., whether the added protons bind to sulfide or Fe ions). Finally, we show that the later (E4-E8) states of the reaction mechanism have redox potential that are more positive (i.e., more exothermic) than that of the E0/E1 couple.
Collapse
|
3
|
Ribbe MW, Górecki K, Grosch M, Solomon JB, Quechol R, Liu YA, Lee CC, Hu Y. Nitrogenase Fe Protein: A Multi-Tasking Player in Substrate Reduction and Metallocluster Assembly. Molecules 2022; 27:molecules27196743. [PMID: 36235278 PMCID: PMC9571451 DOI: 10.3390/molecules27196743] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/05/2022] [Accepted: 10/06/2022] [Indexed: 11/18/2022] Open
Abstract
The Fe protein of nitrogenase plays multiple roles in substrate reduction and metallocluster assembly. Best known for its function to transfer electrons to its catalytic partner during nitrogenase catalysis, the Fe protein is also a key player in the biosynthesis of the complex metalloclusters of nitrogenase. In addition, it can function as a reductase on its own and affect the ambient reduction of CO2 or CO to hydrocarbons. This review will provide an overview of the properties and functions of the Fe protein, highlighting the relevance of this unique FeS enzyme to areas related to the catalysis, biosynthesis, and applications of the fascinating nitrogenase system.
Collapse
Affiliation(s)
- Markus W. Ribbe
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, USA
- Department of Chemistry, University of California, Irvine, CA 92697-2025, USA
- Correspondence: (M.W.R.); (Y.H.)
| | - Kamil Górecki
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, USA
| | - Mario Grosch
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, USA
| | - Joseph B. Solomon
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, USA
- Department of Chemistry, University of California, Irvine, CA 92697-2025, USA
| | - Robert Quechol
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, USA
| | - Yiling A. Liu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, USA
| | - Chi Chung Lee
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, USA
| | - Yilin Hu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, USA
- Correspondence: (M.W.R.); (Y.H.)
| |
Collapse
|
4
|
Stripp ST, Duffus BR, Fourmond V, Léger C, Leimkühler S, Hirota S, Hu Y, Jasniewski A, Ogata H, Ribbe MW. Second and Outer Coordination Sphere Effects in Nitrogenase, Hydrogenase, Formate Dehydrogenase, and CO Dehydrogenase. Chem Rev 2022; 122:11900-11973. [PMID: 35849738 PMCID: PMC9549741 DOI: 10.1021/acs.chemrev.1c00914] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Gases like H2, N2, CO2, and CO are increasingly recognized as critical feedstock in "green" energy conversion and as sources of nitrogen and carbon for the agricultural and chemical sectors. However, the industrial transformation of N2, CO2, and CO and the production of H2 require significant energy input, which renders processes like steam reforming and the Haber-Bosch reaction economically and environmentally unviable. Nature, on the other hand, performs similar tasks efficiently at ambient temperature and pressure, exploiting gas-processing metalloenzymes (GPMs) that bind low-valent metal cofactors based on iron, nickel, molybdenum, tungsten, and sulfur. Such systems are studied to understand the biocatalytic principles of gas conversion including N2 fixation by nitrogenase and H2 production by hydrogenase as well as CO2 and CO conversion by formate dehydrogenase, carbon monoxide dehydrogenase, and nitrogenase. In this review, we emphasize the importance of the cofactor/protein interface, discussing how second and outer coordination sphere effects determine, modulate, and optimize the catalytic activity of GPMs. These may comprise ionic interactions in the second coordination sphere that shape the electron density distribution across the cofactor, hydrogen bonding changes, and allosteric effects. In the outer coordination sphere, proton transfer and electron transfer are discussed, alongside the role of hydrophobic substrate channels and protein structural changes. Combining the information gained from structural biology, enzyme kinetics, and various spectroscopic techniques, we aim toward a comprehensive understanding of catalysis beyond the first coordination sphere.
Collapse
Affiliation(s)
- Sven T Stripp
- Freie Universität Berlin, Experimental Molecular Biophysics, Berlin 14195, Germany
| | | | - Vincent Fourmond
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Institut Microbiologie, Bioénergies et Biotechnologie, CNRS, Aix Marseille Université, Marseille 13402, France
| | - Christophe Léger
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Institut Microbiologie, Bioénergies et Biotechnologie, CNRS, Aix Marseille Université, Marseille 13402, France
| | - Silke Leimkühler
- University of Potsdam, Molecular Enzymology, Potsdam 14476, Germany
| | - Shun Hirota
- Nara Institute of Science and Technology, Division of Materials Science, Graduate School of Science and Technology, Nara 630-0192, Japan
| | - Yilin Hu
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California 92697-3900, United States
| | - Andrew Jasniewski
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California 92697-3900, United States
| | - Hideaki Ogata
- Nara Institute of Science and Technology, Division of Materials Science, Graduate School of Science and Technology, Nara 630-0192, Japan.,Hokkaido University, Institute of Low Temperature Science, Sapporo 060-0819, Japan.,Graduate School of Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Markus W Ribbe
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California 92697-3900, United States.,Department of Chemistry, University of California, Irvine, California 92697-2025, United States
| |
Collapse
|
5
|
Chica B, Ruzicka J, Pellows LM, Kallas H, Kisgeropoulos E, Vansuch GE, Mulder DW, Brown KA, Svedruzic D, Peters JW, Dukovic G, Seefeldt LC, King PW. Dissecting Electronic-Structural Transitions in the Nitrogenase MoFe Protein P-Cluster during Reduction. J Am Chem Soc 2022; 144:5708-5712. [PMID: 35315658 PMCID: PMC8991001 DOI: 10.1021/jacs.1c13311] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The [8Fe-7S] P-cluster of nitrogenase MoFe protein mediates electron transfer from nitrogenase Fe protein during the catalytic production of ammonia. The P-cluster transitions between three oxidation states, PN, P+, P2+ of which PN↔P+ is critical to electron exchange in the nitrogenase complex during turnover. To dissect the steps in formation of P+ during electron transfer, photochemical reduction of MoFe protein at 231-263 K was used to trap formation of P+ intermediates for analysis by EPR. In complexes with CdS nanocrystals, illumination of MoFe protein led to reduction of the P-cluster P2+ that was coincident with formation of three distinct EPR signals: S = 1/2 axial and rhombic signals, and a high-spin S = 7/2 signal. Under dark annealing the axial and high-spin signal intensities declined, which coincided with an increase in the rhombic signal intensity. A fit of the time-dependent changes of the axial and high-spin signals to a reaction model demonstrates they are intermediates in the formation of the P-cluster P+ resting state and defines how spin-state transitions are coupled to changes in P-cluster oxidation state in MoFe protein during electron transfer.
Collapse
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
| | - Lauren M Pellows
- 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
| | - Effie Kisgeropoulos
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Gregory E Vansuch
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, 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
| | - Drazenka Svedruzic
- 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
| | - Gordana Dukovic
- Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States.,Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, Colorado 80309, United States.,Materials Science and Engineering, University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Lance C Seefeldt
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Paul W King
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States.,Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, Colorado 80309, United States
| |
Collapse
|
6
|
Yuan C, Jin WT, Zhou ZH. Statistical analysis of PN clusters in Mo/VFe protein crystals using a bond valence method toward their electronic structures. RSC Adv 2022; 12:5214-5224. [PMID: 35425536 PMCID: PMC8981338 DOI: 10.1039/d1ra08507g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 01/26/2022] [Indexed: 11/21/2022] Open
Abstract
Iron valences of 129 P-clusters from FeMo/V proteins were analyzed using a bond valence method, supposing the existence of Fe3+ in a generally considered all-ferrous PN cluster in solution with excess reducing agent.
Collapse
Affiliation(s)
- Chang Yuan
- State Key Laboratory for Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Wan-Ting Jin
- State Key Laboratory for Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Zhao-Hui Zhou
- State Key Laboratory for Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| |
Collapse
|
7
|
Stich TA. Characterization of Paramagnetic Iron-Sulfur Clusters Using Electron Paramagnetic Resonance Spectroscopy. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2353:259-280. [PMID: 34292554 DOI: 10.1007/978-1-0716-1605-5_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Continuous-wave (CW) electron paramagnetic resonance (EPR) spectroscopy is a powerful ally in characterizing the multitude of redox-active iron-sulfur cluster-containing ([Fe-S]) species present in biological samples. The technique detects only those clusters that are paramagnetic-having a nonzero total electron spin (S > 0)-thus, it can discriminate between clusters in different oxidation states. The low-temperature CW-EPR spectrum of an [Fe-S] yields the three magnetic g-values that serve as a fingerprint of its electronic structure. This chapter briefly describes the underlying theory that defines this electronic structure and provides a recipe for the acquisition and analysis of EPR spectra of [Fe-S] proteins.
Collapse
Affiliation(s)
- Troy A Stich
- Department of Chemistry, Wake Forest University, Winston-Salem, NC, USA.
| |
Collapse
|
8
|
Abstract
Nitrogenase is the only enzyme capable of reducing N2 to NH3. This challenging reaction requires the coordinated transfer of multiple electrons from the reductase, Fe-protein, to the catalytic component, MoFe-protein, in an ATP-dependent fashion. In the last two decades, there have been significant advances in our understanding of how nitrogenase orchestrates electron transfer (ET) from the Fe-protein to the catalytic site of MoFe-protein and how energy from ATP hydrolysis transduces the ET processes. In this review, we summarize these advances, with focus on the structural and thermodynamic redox properties of nitrogenase component proteins and their complexes, as well as on new insights regarding the mechanism of ET reactions during catalysis and how they are coupled to ATP hydrolysis. We also discuss recently developed chemical, photochemical, and electrochemical methods for uncoupling substrate reduction from ATP hydrolysis, which may provide new avenues for studying the catalytic mechanism of nitrogenase.
Collapse
Affiliation(s)
- Hannah L Rutledge
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - F Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| |
Collapse
|
9
|
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: 105] [Impact Index Per Article: 26.3] [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.
Collapse
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
| |
Collapse
|
10
|
Jasniewski AJ, Lee CC, Ribbe MW, Hu Y. Reactivity, Mechanism, and Assembly of the Alternative Nitrogenases. Chem Rev 2020; 120:5107-5157. [PMID: 32129988 DOI: 10.1021/acs.chemrev.9b00704] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Biological nitrogen fixation is catalyzed by the enzyme nitrogenase, which facilitates the cleavage of the relatively inert triple bond of N2. Nitrogenase is most commonly associated with the molybdenum-iron cofactor called FeMoco or the M-cluster, and it has been the subject of extensive structural and spectroscopic characterization over the past 60 years. In the late 1980s and early 1990s, two "alternative nitrogenase" systems were discovered, isolated, and found to incorporate V or Fe in place of Mo. These systems are regulated by separate gene clusters; however, there is a high degree of structural and functional similarity between each nitrogenase. Limited studies with the V- and Fe-nitrogenases initially demonstrated that these enzymes were analogously active as the Mo-nitrogenase, but more recent investigations have found capabilities that are unique to the alternative systems. In this review, we will discuss the reactivity, biosynthetic, and mechanistic proposals for the alternative nitrogenases as well as their electronic and structural properties in comparison to the well-characterized Mo-dependent system. Studies over the past 10 years have been particularly fruitful, though key aspects about V- and Fe-nitrogenases remain unexplored.
Collapse
Affiliation(s)
- Andrew J Jasniewski
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, United States
| | - Chi Chung Lee
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, United States
| | - Markus W Ribbe
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, United States.,Department of Chemistry, University of California, Irvine, California 92697-2025, United States
| | - Yilin Hu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, United States
| |
Collapse
|
11
|
Li Z, Guo S, Sun Q, Chan GKL. Electronic landscape of the P-cluster of nitrogenase as revealed through many-electron quantum wavefunction simulations. Nat Chem 2019; 11:1026-1033. [PMID: 31570817 DOI: 10.1038/s41557-019-0337-3] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 08/20/2019] [Indexed: 11/09/2022]
Abstract
The electronic structure of the nitrogenase metal cofactors is central to nitrogen fixation. However, the P-cluster and FeMo cofactor, each containing eight Fe atoms, have eluded detailed characterization of their electronic properties. We report on the low-energy electronic states of the P-cluster in three oxidation states through exhaustive many-electron wavefunction simulations enabled by new theoretical methods. The energy scales of orbital and spin excitations overlap, yielding a dense spectrum with features that we trace to the underlying atomic states and recouplings. The clusters exist in superpositions of spin configurations with non-classical spin correlations, complicating interpretation of magnetic spectroscopies, whereas the charges are mostly localized from reorganization of the cluster and its surroundings. On oxidation, the opening of the P-cluster substantially increases the density of states, which is intriguing given its proposed role in electron transfer. These results demonstrate that many-electron simulations stand to provide new insights into the electronic structure of the nitrogenase cofactors.
Collapse
Affiliation(s)
- Zhendong Li
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.
| | - Sheng Guo
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Qiming Sun
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Garnet Kin-Lic Chan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.
| |
Collapse
|
12
|
Cao L, Börner MC, Bergmann J, Caldararu O, Ryde U. Geometry and Electronic Structure of the P-Cluster in Nitrogenase Studied by Combined Quantum Mechanical and Molecular Mechanical Calculations and Quantum Refinement. Inorg Chem 2019; 58:9672-9690. [DOI: 10.1021/acs.inorgchem.9b00400] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Lili Cao
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Melanie C. Börner
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
- Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, 48149 Münster, Germany
| | - Justin Bergmann
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Octav Caldararu
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| |
Collapse
|
13
|
Abstract
Biological nitrogen fixation, the conversion of dinitrogen (N2) into ammonia (NH3), stands as a particularly challenging chemical process. As the entry point into a bioavailable form of nitrogen, biological nitrogen fixation is a critical step in the global nitrogen cycle. In Nature, only one enzyme, nitrogenase, is competent in performing this reaction. Study of this complex metalloenzyme has revealed a potent substrate reduction system that utilizes some of the most sophisticated metalloclusters known. This chapter discusses the structure and function of nitrogenase, covers methods that have proven useful in the elucidation of enzyme properties, and provides an overview of the three known nitrogenase variants.
Collapse
|
14
|
Keable SM, Zadvornyy OA, Johnson LE, Ginovska B, Rasmussen AJ, Danyal K, Eilers BJ, Prussia GA, LeVan AX, Raugei S, Seefeldt LC, Peters JW. Structural characterization of the P 1+ intermediate state of the P-cluster of nitrogenase. J Biol Chem 2018; 293:9629-9635. [PMID: 29720402 PMCID: PMC6016482 DOI: 10.1074/jbc.ra118.002435] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 04/26/2018] [Indexed: 01/07/2023] Open
Abstract
Nitrogenase is the enzyme that reduces atmospheric dinitrogen (N2) to ammonia (NH3) in biological systems. It catalyzes a series of single-electron transfers from the donor iron protein (Fe protein) to the molybdenum-iron protein (MoFe protein) that contains the iron-molybdenum cofactor (FeMo-co) sites where N2 is reduced to NH3 The P-cluster in the MoFe protein functions in nitrogenase catalysis as an intermediate electron carrier between the external electron donor, the Fe protein, and the FeMo-co sites of the MoFe protein. Previous work has revealed that the P-cluster undergoes redox-dependent structural changes and that the transition from the all-ferrous resting (PN) state to the two-electron oxidized P2+ state is accompanied by protein serine hydroxyl and backbone amide ligation to iron. In this work, the MoFe protein was poised at defined potentials with redox mediators in an electrochemical cell, and the three distinct structural states of the P-cluster (P2+, P1+, and PN) were characterized by X-ray crystallography and confirmed by computational analysis. These analyses revealed that the three oxidation states differ in coordination, implicating that the P1+ state retains the serine hydroxyl coordination but lacks the backbone amide coordination observed in the P2+ states. These results provide a complete picture of the redox-dependent ligand rearrangements of the three P-cluster redox states.
Collapse
Affiliation(s)
- Stephen M. Keable
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717
| | - Oleg A. Zadvornyy
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99163
| | - Lewis E. Johnson
- Pacific Northwest National Laboratory, Richland, Washington 99352, and
| | - Bojana Ginovska
- Pacific Northwest National Laboratory, Richland, Washington 99352, and
| | - Andrew J. Rasmussen
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322
| | - Karamatullah Danyal
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322
| | - Brian J. Eilers
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717
| | - Gregory A. Prussia
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717
| | - Axl X. LeVan
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717
| | - Simone Raugei
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99163, ,Pacific Northwest National Laboratory, Richland, Washington 99352, and
| | - Lance C. Seefeldt
- Pacific Northwest National Laboratory, Richland, Washington 99352, and ,Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, To whom correspondence may be addressed:
Dept. of Chemistry and Biochemistry, Utah State University, Logan, UT 84322. Tel.:
435-797-3964; E-mail:
| | - John W. Peters
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, ,Institute of Biological Chemistry, Washington State University, Pullman, Washington 99163, ,Pacific Northwest National Laboratory, Richland, Washington 99352, and , To whom correspondence may be addressed:
Institute of Biological Chemistry, Washington State University, Pullman, WA 99163. Tel.:
509-335-3412; E-mail:
| |
Collapse
|
15
|
Jimenez-Vicente E, Yang ZY, Ray WK, Echavarri-Erasun C, Cash VL, Rubio LM, Seefeldt LC, Dean DR. Sequential and differential interaction of assembly factors during nitrogenase MoFe protein maturation. J Biol Chem 2018; 293:9812-9823. [PMID: 29724822 PMCID: PMC6016461 DOI: 10.1074/jbc.ra118.002994] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 04/24/2018] [Indexed: 11/06/2022] Open
Abstract
Nitrogenases reduce atmospheric nitrogen, yielding the basic inorganic molecule ammonia. The nitrogenase MoFe protein contains two cofactors, a [7Fe-9S-Mo-C-homocitrate] active-site species, designated FeMo-cofactor, and a [8Fe-7S] electron-transfer mediator called P-cluster. Both cofactors are essential for molybdenum-dependent nitrogenase catalysis in the nitrogen-fixing bacterium Azotobacter vinelandii. We show here that three proteins, NafH, NifW, and NifZ, copurify with MoFe protein produced by an A. vinelandii strain deficient in both FeMo-cofactor formation and P-cluster maturation. In contrast, two different proteins, NifY and NafY, copurified with MoFe protein deficient only in FeMo-cofactor formation. We refer to proteins associated with immature MoFe protein in the following as “assembly factors.” Copurifications of such assembly factors with MoFe protein produced in different genetic backgrounds revealed their sequential and differential interactions with MoFe protein during the maturation process. We found that these interactions occur in the order NafH, NifW, NifZ, and NafY/NifY. Interactions of NafH, NifW, and NifZ with immature forms of MoFe protein preceded completion of P-cluster maturation, whereas interaction of NafY/NifY preceded FeMo-cofactor insertion. Because each assembly factor could independently bind an immature form of MoFe protein, we propose that subpopulations of MoFe protein–assembly factor complexes represent MoFe protein captured at different stages of a sequential maturation process. This suggestion was supported by separate isolation of three such complexes, MoFe protein–NafY, MoFe protein–NifY, and MoFe protein–NifW. We conclude that factors involved in MoFe protein maturation sequentially bind and dissociate in a dynamic process involving several MoFe protein conformational states.
Collapse
Affiliation(s)
| | - Zhi-Yong Yang
- the Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, and
| | - W Keith Ray
- From the Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061
| | - Carlos Echavarri-Erasun
- the Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM Pozuelo de Alarcón, Madrid 28223, Spain
| | - Valerie L Cash
- From the Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061
| | - Luis M Rubio
- the Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM Pozuelo de Alarcón, Madrid 28223, Spain
| | - Lance C Seefeldt
- the Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, and
| | - Dennis R Dean
- From the Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061,
| |
Collapse
|
16
|
Rupnik K, Lee CC, Hu Y, Ribbe MW, Hales BJ. A VTVH MCD and EPR Spectroscopic Study of the Maturation of the "Second" Nitrogenase P-Cluster. Inorg Chem 2018; 57:4719-4725. [PMID: 29611695 DOI: 10.1021/acs.inorgchem.8b00428] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The P-cluster of the nitrogenase MoFe protein is a [ Fe8 S7] cluster that mediates efficient transfer of electrons to the active site for substrate reduction. Arguably the most complex homometallic FeS cluster found in nature, the biosynthetic mechanism of the P-cluster is of considerable theoretical and synthetic interest to chemists and biochemists alike. Previous studies have revealed a biphasic assembly mechanism of the two P-clusters in the MoFe protein upon incubation with Fe protein and ATP, in which the first P-cluster is formed through fast fusion of a pair of [ Fe4 S4]+ clusters within 5 min and the second P-cluster is formed through slow fusion of the second pair of [ Fe4 S4]+ clusters in a period of 2 h. Here we report a VTVH MCD and EPR spectroscopic study of the biosynthesis of the slow-forming, second P-cluster within the MoFe protein. Our results show that the first major step in the formation of the second P-cluster is the conversion of one of the precursor [ Fe4 S4]+ clusters into the integer spin cluster [ Fe4 S3-4]α, a process aided by the assembly protein NifZ, whereas the second major biosynthetic step appears to be the formation of a diamagnetic cluster with a possible structure of [ Fe8 S7-8]β, which is eventually converted into the P-cluster.
Collapse
Affiliation(s)
- Kresimir Rupnik
- Department of Chemistry , Louisiana State University , Baton Rouge , Louisiana 70803 , United States
| | - Chi Chung Lee
- Department of Molecular Biology and Biochemistry , University of California , Irvine , California 92697 , United States
| | - Yilin Hu
- Department of Molecular Biology and Biochemistry , University of California , Irvine , California 92697 , United States
| | - Markus W Ribbe
- Department of Molecular Biology and Biochemistry , University of California , Irvine , California 92697 , United States
| | - Brian J Hales
- Department of Chemistry , Louisiana State University , Baton Rouge , Louisiana 70803 , United States
| |
Collapse
|
17
|
Abstract
The Mo- and V-nitrogenases are two homologous members of the nitrogenase family that are distinguished mainly by the presence of different heterometals (Mo or V) at their respective cofactor sites (M- or V-cluster). However, the V-nitrogenase is ~600-fold more active than its Mo counterpart in reducing CO to hydrocarbons at ambient conditions. Here, we expressed an M-cluster-containing, hybrid V-nitrogenase in Azotobacter vinelandii and compared it to its native, V-cluster-containing counterpart in order to assess the impact of protein scaffold and cofactor species on the differential reactivities of Mo- and V-nitrogenases toward CO. Housed in the VFe protein component of V-nitrogenase, the M-cluster displayed electron paramagnetic resonance (EPR) features similar to those of the V-cluster and demonstrated an ~100-fold increase in hydrocarbon formation activity from CO reduction, suggesting a significant impact of protein environment on the overall CO-reducing activity of nitrogenase. On the other hand, the M-cluster was still ~6-fold less active than the V-cluster in the same protein scaffold, and it retained its inability to form detectable amounts of methane from CO reduction, illustrating a fine-tuning effect of the cofactor properties on this nitrogenase-catalyzed reaction. Together, these results provided important insights into the two major determinants for the enzymatic activity of CO reduction while establishing a useful framework for further elucidation of the essential catalytic elements for the CO reactivity of nitrogenase. This is the first report on the in vivo generation and in vitro characterization of an M-cluster-containing V-nitrogenase hybrid. The “normalization” of the protein scaffold to that of the V-nitrogenase permits a direct comparison between the cofactor species of the Mo- and V-nitrogenases (M- and V-clusters) in CO reduction, whereas the discrepancy between the protein scaffolds of the Mo- and V-nitrogenases (MoFe and VFe proteins) housing the same cofactor (M-cluster) allows for an effective assessment of the impact of the protein environment on the CO reactivity of nitrogenase. The results of this study provide a first look into the “weighted” contributions of protein environment and cofactor properties to the overall activity of CO reduction; more importantly, they establish a useful platform for further investigation of the structural elements attributing to the CO-reducing activity of nitrogenase.
Collapse
|
18
|
Holm RH, Lo W. Structural Conversions of Synthetic and Protein-Bound Iron–Sulfur Clusters. Chem Rev 2016; 116:13685-13713. [DOI: 10.1021/acs.chemrev.6b00276] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- R. H. Holm
- Department
of Chemistry and
Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Wayne Lo
- Department
of Chemistry and
Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| |
Collapse
|
19
|
Owens CP, Katz FEH, Carter CH, Oswald VF, Tezcan FA. Tyrosine-Coordinated P-Cluster in G. diazotrophicus Nitrogenase: Evidence for the Importance of O-Based Ligands in Conformationally Gated Electron Transfer. J Am Chem Soc 2016; 138:10124-7. [PMID: 27487256 DOI: 10.1021/jacs.6b06783] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The P-cluster is a unique iron-sulfur center that likely functions as a dynamic electron (e(-)) relay site between the Fe-protein and the catalytic FeMo-cofactor in nitrogenase. The P-cluster has been shown to undergo large conformational changes upon 2-e(-) oxidation which entail the coordination of two of the Fe centers to a Ser side chain and a backbone amide N, respectively. Yet, how and if this 2-e(-) oxidized state (P(OX)) is involved in catalysis by nitrogenase is not well established. Here, we present the crystal structures of reduced and oxidized MoFe-protein (MoFeP) from Gluconacetobacter diazotrophicus (Gd), which natively possesses an Ala residue in the position of the Ser ligand to the P-cluster. While reduced Gd-MoFeP is structurally identical to previously characterized counterparts around the FeMo-cofactor, oxidized Gd-MoFeP features an unusual Tyr coordination to its P-cluster along with ligation by a backbone amide nitrogen. EPR analysis of the oxidized Gd-MoFeP P-cluster confirmed that it is a 2-e(-) oxidized, integer-spin species. Importantly, we have found that the sequence positions corresponding to the Ser and Tyr ligands are almost completely covariant among Group I nitrogenases. These findings strongly support the possibility that the P(OX) state is functionally relevant in nitrogenase catalysis and that a hard, O-based anionic ligand serves to stabilize this state in a switchable fashion.
Collapse
Affiliation(s)
- Cedric P Owens
- Department of Chemistry and Biochemistry, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093-0356, United States
| | - Faith E H Katz
- Department of Chemistry and Biochemistry, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093-0356, United States
| | - Cole H Carter
- Department of Chemistry and Biochemistry, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093-0356, United States
| | - Victoria F Oswald
- Department of Chemistry, University of California , Irvine, 1102 Natural Science II, Irvine, California 92697, United States
| | - F Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093-0356, United States
| |
Collapse
|
20
|
Davydov R, Khadka N, Yang ZY, Fielding AJ, Lukoyanov D, Dean DR, Seefeldt LC, Hoffman BM. Exploring Electron/Proton Transfer and Conformational Changes in the Nitrogenase MoFe Protein and FeMo-cofactor Through Cryoreduction/EPR Measurements. Isr J Chem 2016; 56:841-851. [PMID: 27777444 DOI: 10.1002/ijch.201600026] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We combine cryoreduction/annealing/EPR measurements of nitrogenase MoFe protein with results of earlier investigations to provide a detailed view of the electron/proton transfer events and conformational changes that occur during early stages of [e-/H+] accumulation by the MoFe protein. This includes reduction of (i) the non-catalytic state of the iron-molybdenum cofactor (FeMo-co) active site that is generated by chemical oxidation of the resting-state cofactor (S = 3/2)) within resting MoFe (E0), and (ii) the catalytic state that has accumulated n =1 [e-/H+] above the resting-state level, denoted E1(1H) (S ≥ 1) in the Lowe-Thorneley kinetic scheme. FeMo-co does not undergo a major change of conformation during reduction of oxidized FeMo-co. In contrast, FeMo-co undergoes substantial conformational changes during the reduction of E0 to E1(1H), and of E1(1H) to E2(2H) (n = 2; S = 3/2). The experimental results further suggest that the E1(1H) → E2(2H) step involves coupled delivery of a proton and electron (PCET) to FeMo-co of E1(H) to generate a non-equilibrium S = ½ form E2(2H)*. This subsequently undergoes conformational relaxation and attendant change in FeMo-co spin state, to generate the equilibrium E2(2H) (S = 3/2) state. Unexpectedly, these experiments also reveal conformational coupling between FeMo-co and P-cluster, and between Fe protein binding and FeMo-co, which might play a role in gated ET from reduced Fe protein to FeMo-co.
Collapse
Affiliation(s)
- Roman Davydov
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | - Nimesh Khadka
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322
| | - Zhi-Yong Yang
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322
| | - Andrew J Fielding
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322
| | - Dmitriy Lukoyanov
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | - Dennis R Dean
- Department of Biochemistry, Virginia Tech, 110 Fralin Hall, Blacksburg, VA 24061
| | - Lance C Seefeldt
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| |
Collapse
|
21
|
Lee SC, Lo W, Holm RH. Developments in the biomimetic chemistry of cubane-type and higher nuclearity iron-sulfur clusters. Chem Rev 2014; 114:3579-600. [PMID: 24410527 PMCID: PMC3982595 DOI: 10.1021/cr4004067] [Citation(s) in RCA: 159] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
| | - Wayne Lo
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1 Canada and the Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
| | - R. H. Holm
- Corresponding Authors: S. C. Lee: . R. H. Holm:
| |
Collapse
|
22
|
Hoffman BM, Lukoyanov D, Yang ZY, Dean DR, Seefeldt LC. Mechanism of nitrogen fixation by nitrogenase: the next stage. Chem Rev 2014; 114:4041-62. [PMID: 24467365 PMCID: PMC4012840 DOI: 10.1021/cr400641x] [Citation(s) in RCA: 963] [Impact Index Per Article: 96.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Brian M Hoffman
- Department of Chemistry and Biochemistry, Utah State University , 0300 Old Main Hill, Logan, Utah 84322, United States
| | | | | | | | | |
Collapse
|