51
|
Arnett CH, Bogacz I, Chatterjee R, Yano J, Oyala PH, Agapie T. Mixed-Valent Diiron μ-Carbyne, μ-Hydride Complexes: Implications for Nitrogenase. J Am Chem Soc 2020; 142:18795-18813. [PMID: 32976708 DOI: 10.1021/jacs.0c05920] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Binding of N2 by the FeMo-cofactor of nitrogenase is believed to occur after transfer of 4 e- and 4 H+ equivalents to the active site. Although pulse EPR studies indicate the presence of two Fe-(μ-H)-Fe moieties, the structural and electronic features of this mixed valent intermediate remain poorly understood. Toward an improved understanding of this bioorganometallic cluster, we report herein that diiron μ-carbyne complex (P6ArC)Fe2(μ-H) can be oxidized and reduced, allowing for the first time spectral characterization of two EPR-active Fe(μ-C)(μ-H)Fe model complexes linked by a 2 e- transfer which bear some resemblance to a pair of En and En+2 states of nitrogenase. Both species populate S = 1/2 states at low temperatures, and the influence of valence (de)localization on the spectroscopic signature of the μ-hydride ligand was evaluated by pulse EPR studies. Compared to analogous data for the {Fe2(μ-H)}2 state of FeMoco (E4(4H)), the data and analysis presented herein suggest that the hydride ligands in E4(4H) bridge isovalent (most probably FeIII) metal centers. Although electron transfer involves metal-localized orbitals, investigations of [(P6ArC)Fe2(μ-H)]+1 and [(P6ArC)Fe2(μ-H)]-1 by pulse EPR revealed that redox chemistry induces significant changes in Fe-C covalency (-50% upon 2 e- reduction), a conclusion further supported by X-ray absorption spectroscopy, 57Fe Mössbauer studies, and DFT calculations. Combined, our studies demonstrate that changes in covalency buffer against the accumulation of excess charge density on the metals by partially redistributing it to the bridging carbon, thereby facilitating multielectron transformations.
Collapse
Affiliation(s)
- Charles H Arnett
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Isabel Bogacz
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Paul H Oyala
- 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
| |
Collapse
|
52
|
Liedtke J, Lee CC, Tanifuji K, Jasniewski AJ, Ribbe MW, Hu Y. Characterization of a Mo-Nitrogenase Variant Containing a Citrate-Substituted Cofactor. Chembiochem 2020; 22:151-155. [PMID: 32918851 DOI: 10.1002/cbic.202000598] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/04/2020] [Indexed: 11/10/2022]
Abstract
Nitrogenase converts N2 to NH3 , and CO to hydrocarbons, at its cofactor site. Herein, we report a biochemical and spectroscopic characterization of a Mo-nitrogenase variant expressed in an Azotobacter vinelandii strain containing a deletion of nifV, the gene encoding the homocitrate synthase. Designated NifDKCit , the catalytic component of this Mo-nitrogenase variant contains a citrate-substituted cofactor analogue. Activity analysis of NifDKCit reveals a shift of CO reduction from H2 evolution toward hydrocarbon formation and an opposite shift of N2 reduction from NH3 formation toward H2 evolution. Consistent with a shift in the Mo K-edge energy of NifDKCit relative to that of its wild-type counterpart, EPR analysis demonstrates a broadening of the line-shape and a decrease in the intensity of the cofactor-originated S=3/2 signal, suggesting a change in the spin properties of the cofactor upon citrate substitution. These observations point to a crucial role of homocitrate in substrate reduction by nitrogenase and the possibility to tune product profiles of nitrogenase reactions via organic ligand substitution.
Collapse
Affiliation(s)
- Jasper Liedtke
- Department of Molecular Biology & Biochemistry, University of California, Irvine, 2236 McGaugh Hall, Irvine, CA 92697-3900, USA
| | - Chi Chung Lee
- Department of Molecular Biology & Biochemistry, University of California, Irvine, 2236 McGaugh Hall, Irvine, CA 92697-3900, USA
| | - Kazuki Tanifuji
- Department of Molecular Biology & Biochemistry, University of California, Irvine, 2236 McGaugh Hall, Irvine, CA 92697-3900, USA
| | - Andrew J Jasniewski
- Department of Molecular Biology & Biochemistry, University of California, Irvine, 2236 McGaugh Hall, Irvine, CA 92697-3900, USA
| | - Markus W Ribbe
- Department of Molecular Biology & Biochemistry, University of California, Irvine, 2236 McGaugh Hall, Irvine, CA 92697-3900, USA.,Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, USA
| | - Yilin Hu
- Department of Molecular Biology & Biochemistry, University of California, Irvine, 2236 McGaugh Hall, Irvine, CA 92697-3900, USA
| |
Collapse
|
53
|
Rohde M, Grunau K, Einsle O. Bindung von CO am FeV‐Cofaktor der CO‐reduzierenden Vanadium‐Nitrogenase bei atomarer Auflösung. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202010790] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Michael Rohde
- Institut für Biochemie Fakultät für Chemie und Pharmazie Albert-Ludwigs-Universität Freiburg Albertstrasse 21 79104 Freiburg im Breisgau Deutschland
| | - Katharina Grunau
- Institut für Biochemie Fakultät für Chemie und Pharmazie Albert-Ludwigs-Universität Freiburg Albertstrasse 21 79104 Freiburg im Breisgau Deutschland
| | - Oliver Einsle
- Institut für Biochemie Fakultät für Chemie und Pharmazie Albert-Ludwigs-Universität Freiburg Albertstrasse 21 79104 Freiburg im Breisgau Deutschland
| |
Collapse
|
54
|
Rohde M, Grunau K, Einsle O. CO Binding to the FeV Cofactor of CO-Reducing Vanadium Nitrogenase at Atomic Resolution. Angew Chem Int Ed Engl 2020; 59:23626-23630. [PMID: 32915491 PMCID: PMC7756900 DOI: 10.1002/anie.202010790] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Indexed: 11/24/2022]
Abstract
Nitrogenases reduce N2, the most abundant element in Earth's atmosphere that is otherwise resistant to chemical conversions due to its stable triple bond. Vanadium nitrogenase stands out in that it additionally processes carbon monoxide, a known inhibitor of the reduction of all substrates other than H+. The reduction of CO leads to the formation of hydrocarbon products, holding the potential for biotechnological applications in analogy to the industrial Fischer–Tropsch process. Here we report the most highly resolved structure of vanadium nitrogenase to date at 1.0 Å resolution, with CO bound to the active site cofactor after catalytic turnover. CO bridges iron ions Fe2 and Fe6, replacing sulfide S2B, in a binding mode that is in line with previous reports on the CO complex of molybdenum nitrogenase. We discuss the structural consequences of continued turnover when CO is removed, which involve the replacement of CO possibly by OH−, the movement of Q176D and K361D, the return of sulfide and the emergence of two additional water molecules that are absent in the CO‐bound state.
Collapse
Affiliation(s)
- Michael Rohde
- Institut für Biochemie, Fakultät für Chemie und Pharmazie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg im Breisgau, Germany
| | - Katharina Grunau
- Institut für Biochemie, Fakultät für Chemie und Pharmazie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg im Breisgau, Germany
| | - Oliver Einsle
- Institut für Biochemie, Fakultät für Chemie und Pharmazie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg im Breisgau, Germany
| |
Collapse
|
55
|
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
|
56
|
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: 111] [Impact Index Per Article: 27.8] [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.
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
|
57
|
Kang W, Lee CC, Jasniewski AJ, Ribbe MW, Hu Y. Structural evidence for a dynamic metallocofactor during N 2 reduction by Mo-nitrogenase. Science 2020; 368:1381-1385. [PMID: 32554596 PMCID: PMC8410457 DOI: 10.1126/science.aaz6748] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 03/11/2020] [Accepted: 04/20/2020] [Indexed: 01/06/2023]
Abstract
The enzyme nitrogenase uses a suite of complex metallocofactors to reduce dinitrogen (N2) to ammonia. Mechanistic details of this reaction remain sparse. We report a 1.83-angstrom crystal structure of the nitrogenase molybdenum-iron (MoFe) protein captured under physiological N2 turnover conditions. This structure reveals asymmetric displacements of the cofactor belt sulfurs (S2B or S3A and S5A) with distinct dinitrogen species in the two αβ dimers of the protein. The sulfur-displaced sites are distinct in the ability of protein ligands to donate protons to the bound dinitrogen species, as well as the elongation of either the Mo-O5 (carboxyl) or Mo-O7 (hydroxyl) distance that switches the Mo-homocitrate ligation from bidentate to monodentate. These results highlight the dynamic nature of the cofactor during catalysis and provide evidence for participation of all belt-sulfur sites in this process.
Collapse
Affiliation(s)
- Wonchull Kang
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697-3900, USA
| | - Chi Chung Lee
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697-3900, USA
| | - Andrew J Jasniewski
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697-3900, USA
| | - Markus W Ribbe
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697-3900, USA.
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, USA
| | - Yilin Hu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697-3900, USA.
| |
Collapse
|
58
|
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
| |
Collapse
|
59
|
Rupnik K, Tanifuji K, Rettberg L, Ribbe MW, Hu Y, Hales BJ. Electron Paramagnetic Resonance and Magnetic Circular Dichroism Spectra of the Nitrogenase M Cluster Precursor Suggest Sulfur Migration upon Oxidation: A Proposal for Substrate and Inhibitor Binding. Chembiochem 2020; 21:1767-1772. [PMID: 31881119 PMCID: PMC7481019 DOI: 10.1002/cbic.201900681] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Indexed: 02/01/2023]
Abstract
The active site of the nitrogen-fixing enzyme Mo-nitrogenase is the M cluster ([MoFe7 S9 C⋅R-homocitrate]), also known as the FeMo cofactor or FeMoco. The biosynthesis of this highly complex metallocluster involves a series of proteins. Among them, NifB, a radical-SAM enzyme, is instrumental in the assembly of the L cluster ([Fe8 S9 C]), a precursor and all-iron core of the M cluster. In the absence of sulfite, NifB assembles a precursor form of the L cluster called the L* cluster ([Fe8 S8 C]), which lacks the final ninth sulfur. EPR and MCD spectroscopies are used to probe the electronic structures of the paramagnetic, oxidized forms of both the L and L* clusters, labeled LOx and [L*]Ox . This study shows that both LOx and [L*]Ox have nearly identical EPR and MCD spectra, thus suggesting that the two clusters have identical structures upon oxidation; in other words, a sulfur migrates away from LOx following oxidation, thereby rendering the cluster identical to [L*]Ox . It is proposed that a similar migration could occur to the M cluster upon oxidation, and that this is an instrumental part of both M cluster formation and nitrogenase substrate/inhibitor binding.
Collapse
Affiliation(s)
- Kresimir Rupnik
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Kazuki Tanifuji
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
| | - Lee Rettberg
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
| | - Markus W Ribbe
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
- Department of Chemistry, University of California, Irvine, Irvine, CA, 92697-2025, USA
| | - Yilin Hu
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
| | - Brian J Hales
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
| |
Collapse
|
60
|
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.
Collapse
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
| |
Collapse
|
61
|
Arnett CH, Agapie T. Activation of an Open Shell, Carbyne-Bridged Diiron Complex Toward Binding of Dinitrogen. J Am Chem Soc 2020; 142:10059-10068. [DOI: 10.1021/jacs.0c01896] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Charles H. Arnett
- 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
| |
Collapse
|
62
|
Spiller N, Chilkuri VG, DeBeer S, Neese F. Sulfur vs. Selenium as Bridging Ligand in Di‐Iron Complexes: A Theoretical Analysis. Eur J Inorg Chem 2020. [DOI: 10.1002/ejic.202000033] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Nico Spiller
- Department of Molecular Theory and Spectroscopy Max‐Planck‐Institut für Kohlenforschung Kaiser‐Wilhelm‐Platz 1 45470 Mülheim an der Ruhr Germany
| | - Vijay Gopal Chilkuri
- Department of Molecular Theory and Spectroscopy Max‐Planck‐Institut für Kohlenforschung Kaiser‐Wilhelm‐Platz 1 45470 Mülheim an der Ruhr Germany
| | - Serena DeBeer
- Department of Inorganic Spectroscopy Max Planck Institute for Chemical Energy Conversion Stiftstr. 34‐36 45470 Mülheim an der Ruhr Germany
| | - Frank Neese
- Department of Molecular Theory and Spectroscopy Max‐Planck‐Institut für Kohlenforschung Kaiser‐Wilhelm‐Platz 1 45470 Mülheim an der Ruhr Germany
| |
Collapse
|
63
|
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: 177] [Impact Index Per Article: 44.3] [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.
Collapse
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
| |
Collapse
|
64
|
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: 107] [Impact Index Per Article: 26.8] [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
|
65
|
Dance I. Computational Investigations of the Chemical Mechanism of the Enzyme Nitrogenase. Chembiochem 2020; 21:1671-1709. [DOI: 10.1002/cbic.201900636] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Ian Dance
- School of Chemistry UNSW Sydney Sydney 2052 Australia
| |
Collapse
|
66
|
Nagelski AL, Fataftah MS, Bollmeyer MM, McWilliams SF, MacMillan SN, Mercado BQ, Lancaster KM, Holland PL. The influences of carbon donor ligands on biomimetic multi-iron complexes for N 2 reduction. Chem Sci 2020; 11:12710-12720. [PMID: 34094466 PMCID: PMC8163302 DOI: 10.1039/d0sc03447a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The active site clusters of nitrogenase enzymes possess the only examples of carbides in biology. These are the only biological FeS clusters that are capable of reducing N2 to NH4+, implicating the central carbon and its interaction with Fe as important in the mechanism of N2 reduction. This biological question motivates study of the influence of carbon donors on the electronic structure and reactivity of unsaturated, high-spin iron centers. Here, we present functional and structural models that test the impacts of carbon donors and sulfide donors in simpler iron compounds. We report the first example of a diiron complex that is bridged by an alkylidene and a sulfide, which serves as a high-fidelity structural and spectroscopic model of a two-iron portion of the active-site cluster (FeMoco) in the resting state of Mo-nitrogenase. The model complexes have antiferromagnetically coupled pairs of high-spin iron centers, and sulfur K-edge X-ray absorption spectroscopy shows comparable covalency of the sulfide for C and S bridged species. The sulfur-bridged compound does not interact with N2 even upon reduction, but upon removal of the sulfide it becomes capable of reducing N2 to NH4+ with the addition of protons and electrons. This provides synthetic support for sulfide extrusion in the activation of nitrogenase cofactors. High-spin diiron alkylidenes give insight into the electronic structure and functional relevance of carbon in the FeMoco active site of nitrogenase.![]()
Collapse
Affiliation(s)
| | | | - Melissa M. Bollmeyer
- Department of Chemistry and Chemical Biology
- Baker Laboratory
- Cornell University
- Ithaca
- USA
| | | | - Samantha N. MacMillan
- Department of Chemistry and Chemical Biology
- Baker Laboratory
- Cornell University
- Ithaca
- USA
| | | | - Kyle M. Lancaster
- Department of Chemistry and Chemical Biology
- Baker Laboratory
- Cornell University
- Ithaca
- USA
| | | |
Collapse
|
67
|
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.
Collapse
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
| |
Collapse
|
68
|
Van Stappen C, Thorhallsson AT, Decamps L, Bjornsson R, DeBeer S. Resolving the structure of the E 1 state of Mo nitrogenase through Mo and Fe K-edge EXAFS and QM/MM calculations. Chem Sci 2019; 10:9807-9821. [PMID: 32055350 PMCID: PMC6984330 DOI: 10.1039/c9sc02187f] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 09/03/2019] [Indexed: 11/21/2022] Open
Abstract
Biological nitrogen fixation is predominately accomplished through Mo nitrogenase, which utilizes a complex MoFe7S9C catalytic cluster to reduce N2 to NH3. This cluster requires the accumulation of three to four reducing equivalents prior to binding N2; however, despite decades of research, the intermediate states formed prior to N2 binding are still poorly understood. Herein, we use Mo and Fe K-edge X-ray absorption spectroscopy and QM/MM calculations to investigate the nature of the E1 state, which is formed following the addition of the first reducing equivalent to Mo nitrogenase. By analyzing the extended X-ray absorption fine structure (EXAFS) region, we provide structural insight into the changes that occur in the metal clusters of the protein when forming the E1 state, and use these metrics to assess a variety of possible models of the E1 state. The combination of our experimental and theoretical results supports that formation of E1 involves an Fe-centered reduction combined with the protonation of a belt-sulfide of the cluster. Hence, these results provide critical experiment and computational insight into the mechanism of this important enzyme.
Collapse
Affiliation(s)
- Casey Van Stappen
- Max-Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36 , 45470 Mülheim an der Ruhr , NRW , Germany . ;
| | - Albert Thor Thorhallsson
- Max-Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36 , 45470 Mülheim an der Ruhr , NRW , Germany . ;
| | - Laure Decamps
- Max-Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36 , 45470 Mülheim an der Ruhr , NRW , Germany . ;
| | - Ragnar Bjornsson
- Max-Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36 , 45470 Mülheim an der Ruhr , NRW , Germany . ;
| | - Serena DeBeer
- Max-Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36 , 45470 Mülheim an der Ruhr , NRW , Germany . ;
| |
Collapse
|
69
|
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]
|
70
|
Jasniewski AJ, Wilcoxen J, Tanifuji K, Hedman B, Hodgson KO, Britt RD, Hu Y, Ribbe MW. Spectroscopic Characterization of an Eight-Iron Nitrogenase Cofactor Precursor that Lacks the "9 th Sulfur". Angew Chem Int Ed Engl 2019; 58:14703-14707. [PMID: 31411369 DOI: 10.1002/anie.201907593] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Indexed: 01/09/2023]
Abstract
Nitrogenases catalyze the reduction of N2 to NH4 + at its cofactor site. Designated the M-cluster, this [MoFe7 S9 C(R-homocitrate)] cofactor is synthesized via the transformation of a [Fe4 S4 ] cluster pair into an [Fe8 S9 C] precursor (designated the L-cluster) prior to insertion of Mo and homocitrate. We report the characterization of an eight-iron cofactor precursor (designated the L*-cluster), which is proposed to have the composition [Fe8 S8 C] and lack the "9th sulfur" in the belt region of the L-cluster. Our X-ray absorption and electron spin echo envelope modulation (ESEEM) analyses strongly suggest that the L*-cluster represents a structural homologue to the l-cluster except for the missing belt sulfur. The absence of a belt sulfur from the L*-cluster may prove beneficial for labeling the catalytically important belt region, which could in turn facilitate investigations into the reaction mechanism of nitrogenases.
Collapse
Affiliation(s)
- Andrew J Jasniewski
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
| | - Jarett Wilcoxen
- Department of Chemistry, University of California, Davis, Davis, CA, 95616, USA
| | - Kazuki Tanifuji
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
| | - Britt Hedman
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, 94025, USA
| | - Keith O Hodgson
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, 94025, USA.,Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - R David Britt
- Department of Chemistry, University of California, Davis, Davis, CA, 95616, USA
| | - Yilin Hu
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
| | - Markus W Ribbe
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA.,Department Chemistry, University of California, Irvine, Irvine, CA, 92697-2025, USA
| |
Collapse
|
71
|
Jasniewski AJ, Wilcoxen J, Tanifuji K, Hedman B, Hodgson KO, Britt RD, Hu Y, Ribbe MW. Spectroscopic Characterization of an Eight‐Iron Nitrogenase Cofactor Precursor that Lacks the “9
th
Sulfur”. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201907593] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Andrew J. Jasniewski
- Department of Molecular Biology & Biochemistry University of California, Irvine Irvine CA 92697-3900 USA
| | - Jarett Wilcoxen
- Department of Chemistry University of California, Davis Davis CA 95616 USA
| | - Kazuki Tanifuji
- Department of Molecular Biology & Biochemistry University of California, Irvine Irvine CA 92697-3900 USA
| | - Britt Hedman
- Stanford Synchrotron Radiation Lightsource SLAC National Accelerator Laboratory Stanford University Menlo Park CA 94025 USA
| | - Keith O. Hodgson
- Stanford Synchrotron Radiation Lightsource SLAC National Accelerator Laboratory Stanford University Menlo Park CA 94025 USA
- Department of Chemistry Stanford University Stanford CA 94305 USA
| | - R. David Britt
- Department of Chemistry University of California, Davis Davis CA 95616 USA
| | - Yilin Hu
- Department of Molecular Biology & Biochemistry University of California, Irvine Irvine CA 92697-3900 USA
| | - Markus W. Ribbe
- Department of Molecular Biology & Biochemistry University of California, Irvine Irvine CA 92697-3900 USA
- Department Chemistry University of California, Irvine Irvine CA 92697-2025 USA
| |
Collapse
|
72
|
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.
Collapse
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
| |
Collapse
|
73
|
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: 28] [Impact Index Per Article: 5.6] [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.
Collapse
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
| |
Collapse
|
74
|
DeRosha DE, Arnet NA, Mercado BQ, Holland PL. A [2Fe-1S] Complex That Affords Access to Bimetallic and Higher-Nuclearity Iron-Sulfur Clusters. Inorg Chem 2019; 58:8829-8834. [PMID: 31247861 DOI: 10.1021/acs.inorgchem.9b01212] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Small, coordinatively unsaturated iron-sulfur clusters are conceived as building blocks for the diverse set of shapes of iron-sulfur clusters in biological and synthetic chemistry. Here we describe a synthetic method for preparing [2Fe-1S] clusters containing two iron(II) ions, which are supported by a relatively unhindered β-diketiminate supporting ligand. The [2Fe-1S] cluster can be isolated in the presence of trimethylphosphine, and the compound with one PMe3 on each iron(II) ion has been crystallographically characterized. The PMe3 ligands may be removed with B(C6F5)3 to give a spectroscopically characterized species with solvent ligands. This species is a versatile synthon for [2Fe-2S], [4Fe-3S], and [10Fe-8S] clusters. Crystallographic characterization of the 10Fe cluster shows that it has all iron(II) ions, and the core has two [4Fe-4S] cubes that share a face in a novel arrangement. This cluster also has two iron sites that are coordinated to solvent donors, suggesting the potential for using this type of cluster for reactivity in the future.
Collapse
Affiliation(s)
- Daniel E DeRosha
- Department of Chemistry , Yale University , 225 Prospect Street , New Haven , Connecticut 06511 , United States
| | - Nicholas A Arnet
- Department of Chemistry , Yale University , 225 Prospect Street , New Haven , Connecticut 06511 , United States
| | - Brandon Q Mercado
- Department of Chemistry , Yale University , 225 Prospect Street , New Haven , Connecticut 06511 , United States
| | - Patrick L Holland
- Department of Chemistry , Yale University , 225 Prospect Street , New Haven , Connecticut 06511 , United States
| |
Collapse
|
75
|
Wittkamp F, Mishra N, Wang H, Wille HC, Steinbrügge R, Kaupp M, Cramer SP, Apfel UP, Pelmenschikov V. Insights from 125Te and 57Fe nuclear resonance vibrational spectroscopy: a [4Fe-4Te] cluster from two points of view. Chem Sci 2019; 10:7535-7541. [PMID: 31588304 PMCID: PMC6761874 DOI: 10.1039/c9sc02025j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 06/22/2019] [Indexed: 11/21/2022] Open
Abstract
Can sulfur-to-tellurium exchange serve as a method to understand iron–sulfur clusters of enzymatic systems?
Iron–sulfur clusters are common building blocks for electron transport and active sites of metalloproteins. Their comprehensive investigation is crucial for understanding these enzymes, which play important roles in modern biomimetic catalysis and biotechnology applications. We address this issue by utilizing (Et4N)3[Fe4Te4(SPh)4], a tellurium modified version of a conventional reduced [4Fe–4S]+ cluster, and performed both 57Fe- and 125Te-NRVS to reveal its characteristic vibrational features. Our analysis exposed major differences in the resulting 57Fe spectrum profile as compared to that of the respective [4Fe–4S] cluster, and between the 57Fe and 125Te profiles. DFT calculations are applied to rationalize structural, electronic, vibrational, and redox-dependent properties of the [4Fe–4Te]+ core. We herein highlight the potential of sulfur/tellurium exchange as a method to isolate the iron-only motion in enzymatic systems.
Collapse
Affiliation(s)
- Florian Wittkamp
- Department of Chemistry and Biochemistry , Inorganic Chemistry I , Ruhr-Universität Bochum , Universitätsstraße 150 , 44801 Bochum , Germany .
| | - Nakul Mishra
- Department of Chemistry , University of California , Davis, One Shields Avenue , Davis , California 95616 , USA .
| | - Hongxin Wang
- Department of Chemistry , University of California , Davis, One Shields Avenue , Davis , California 95616 , USA .
| | - Hans-Christian Wille
- Deutsches Elektronen-Synchrotron DESY , Notkestraße 85 , 22607 Hamburg , Germany
| | - René Steinbrügge
- Deutsches Elektronen-Synchrotron DESY , Notkestraße 85 , 22607 Hamburg , Germany
| | - Martin Kaupp
- Institute of Chemistry , Theoretical Chemistry/Quantum Chemistry , Technical University of Berlin , Sekr. C7, Straße des 17. Juni 135 , 10623 Berlin , Germany .
| | - Stephen P Cramer
- Department of Chemistry , University of California , Davis, One Shields Avenue , Davis , California 95616 , USA .
| | - Ulf-Peter Apfel
- Department of Chemistry and Biochemistry , Inorganic Chemistry I , Ruhr-Universität Bochum , Universitätsstraße 150 , 44801 Bochum , Germany . .,Fraunhofer UMSICHT , Osterfelder Straße 3 , 46047 Oberhausen , Germany
| | - Vladimir Pelmenschikov
- Institute of Chemistry , Theoretical Chemistry/Quantum Chemistry , Technical University of Berlin , Sekr. C7, Straße des 17. Juni 135 , 10623 Berlin , Germany .
| |
Collapse
|
76
|
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.
Collapse
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
| |
Collapse
|
77
|
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
| |
Collapse
|
78
|
Rutledge HL, Rittle J, Williamson LM, Xu WA, Gagnon DM, Tezcan FA. Redox-Dependent Metastability of the Nitrogenase P-Cluster. J Am Chem Soc 2019; 141:10091-10098. [PMID: 31146522 DOI: 10.1021/jacs.9b04555] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Molybdenum nitrogenase catalyzes the reduction of dinitrogen into ammonia, which requires the coordinated transfer of eight electrons to the active site cofactor (FeMoco) through the intermediacy of an [8Fe-7S] cluster (P-cluster), both housed in the molybdenum-iron protein (MoFeP). Previous studies on MoFeP from two different organisms, Azotobacter vinelandii ( Av) and Gluconacetobacter diazotrophicus ( Gd), have established that the P-cluster is conformationally flexible and can undergo substantial structural changes upon two-electron oxidation to the POX state, whereby a backbone amidate and an oxygenic residue (Ser or Tyr) ligate to two of the cluster's Fe centers. This redox-dependent change in coordination has been implicated in the conformationally gated electron transfer in nitrogenase. Here, we have investigated the role of the oxygenic ligand in Av MoFeP, which natively contains a Ser ligand (βSer188) to the P-cluster. Three variants were generated in which (1) the oxygenic ligand was eliminated (βSer188Ala), (2) the P-cluster environment was converted to the one in Gd MoFeP (βPhe99Tyr/βSer188Ala), and (3) two oxygenic ligands were simultaneously included (βPhe99Tyr). Our studies have revealed that the P-cluster can become compositionally labile upon oxidation and reversibly lose one or two Fe centers in the absence of the oxygenic ligand, while still retaining wild-type-like dinitrogen reduction activity. Our findings also suggest that Av and Gd MoFePs evolved with specific preferences for Ser and Tyr ligands, respectively, and that the structural control of these ligands must extend beyond the primary and secondary coordination spheres of the P-cluster. The P-cluster adds to the increasing number of examples of inherently labile Fe-S clusters whose compositional instability may be an obligatory feature to enable redox-linked conformational changes to facilitate multielectron redox reactions.
Collapse
Affiliation(s)
- Hannah L Rutledge
- Department of Chemistry and Biochemistry , University of California, San Diego , 9500 Gilman Drive , La Jolla , California 92093-0356 , United States
| | - Jonathan Rittle
- Department of Chemistry and Biochemistry , University of California, San Diego , 9500 Gilman Drive , La Jolla , California 92093-0356 , United States
| | - Laura M Williamson
- Department of Chemistry and Biochemistry , University of California, San Diego , 9500 Gilman Drive , La Jolla , California 92093-0356 , United States
| | - Wanqing A Xu
- Department of Chemistry and Biochemistry , University of California, San Diego , 9500 Gilman Drive , La Jolla , California 92093-0356 , United States
| | - Derek M Gagnon
- Department of Chemistry and Biochemistry , University of California, San Diego , 9500 Gilman Drive , La Jolla , California 92093-0356 , 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
|
79
|
Wenke BB, Spatzal T, Rees DC. Site-Specific Oxidation State Assignments of the Iron Atoms in the [4Fe:4S] 2+/1+/0 States of the Nitrogenase Fe-Protein. Angew Chem Int Ed Engl 2019; 58:3894-3897. [PMID: 30698901 PMCID: PMC6519357 DOI: 10.1002/anie.201813966] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Indexed: 12/05/2022]
Abstract
The nitrogenase iron protein (Fe-protein) contains an unusual [4Fe:4S] iron-sulphur cluster that is stable in three oxidation states: 2+, 1+, and 0. Here, we use spatially resolved anomalous dispersion (SpReAD) refinement to determine oxidation assignments for the individual irons for each state. Additionally, we report the 1.13-Å resolution structure for the ADP bound Fe-protein, the highest resolution Fe-protein structure presently determined. In the dithionite-reduced [4Fe:4S]1+ state, our analysis identifies a solvent exposed, delocalized Fe2.5+ pair and a buried Fe2+ pair. We propose that ATP binding by the Fe-protein promotes an internal redox rearrangement such that the solvent-exposed Fe pair becomes reduced, thereby facilitating electron transfer to the nitrogenase molybdenum iron-protein. In the [4Fe:4S]0 and [4Fe:4S]2+ states, the SpReAD analysis supports oxidation states assignments for all irons in these clusters of Fe2+ and valence delocalized Fe2.5+ , respectively.
Collapse
Affiliation(s)
- Belinda B. Wenke
- Division of Chemistry and Chemical EngineeringCalifornia Institute of TechnologyPasadenaCA91125USA
| | - Thomas Spatzal
- Howard Hughes Medical InstituteCalifornia Institute of TechnologyPasadenaCA91125USA
- Division of Chemistry and Chemical EngineeringCalifornia Institute of TechnologyPasadenaCA91125USA
| | - Douglas C. Rees
- Howard Hughes Medical InstituteCalifornia Institute of TechnologyPasadenaCA91125USA
- Division of Chemistry and Chemical EngineeringCalifornia Institute of TechnologyPasadenaCA91125USA
| |
Collapse
|
80
|
Wenke BB, Spatzal T, Rees DC. Site‐Specific Oxidation State Assignments of the Iron Atoms in the [4Fe:4S]
2+/1+/0
States of the Nitrogenase Fe‐Protein. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201813966] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Belinda B. Wenke
- Division of Chemistry and Chemical EngineeringCalifornia Institute of Technology Pasadena CA 91125 USA
| | - Thomas Spatzal
- Howard Hughes Medical InstituteCalifornia Institute of Technology Pasadena CA 91125 USA
- Division of Chemistry and Chemical EngineeringCalifornia Institute of Technology Pasadena CA 91125 USA
| | - Douglas C. Rees
- Howard Hughes Medical InstituteCalifornia Institute of Technology Pasadena CA 91125 USA
- Division of Chemistry and Chemical EngineeringCalifornia Institute of Technology Pasadena CA 91125 USA
| |
Collapse
|
81
|
Survey of the Geometric and Electronic Structures of the Key Hydrogenated Forms of FeMo-co, the Active Site of the Enzyme Nitrogenase: Principles of the Mechanistically Significant Coordination Chemistry. INORGANICS 2019. [DOI: 10.3390/inorganics7010008] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The enzyme nitrogenase naturally hydrogenates N2 to NH3, achieved through the accumulation of H atoms on FeMo-co, the Fe7MoS9C(homocitrate) cluster that is the catalytically active site. Four intermediates, E1H1, E2H2, E3H3, and E4H4, carry these hydrogen atoms. I report density functional calculations of the numerous possibilities for the geometric and electronic structures of these poly-hydrogenated forms of FeMo-co. This survey involves more than 100 structures, including those with bound H2, and assesses their relative energies and most likely electronic states. Twelve locations for bound H atoms in the active domain of FeMo-co, including Fe–H–Fe and Fe–H–S bridges, are studied. A significant result is that transverse Fe–H–Fe bridges (transverse to the pseudo-threefold axis of FeMo-co and shared with triply-bridging S) are not possible geometrically unless the S is hydrogenated to become doubly-bridging. The favourable Fe–H–Fe bridges are shared with doubly-bridging S. ENDOR data for an E4H4 intermediate trapped at low temperature, and interpretations in terms of the geometrical and electronic structure of E4H4, are assessed in conjunction with the calculated possibilities. The results reported here yield a set of 24 principles for the mechanistically significant coordination chemistry of H and H2 on FeMo-co, in the stages prior to N2 binding.
Collapse
|
82
|
Dance I. How feasible is the reversible S-dissociation mechanism for the activation of FeMo-co, the catalytic site of nitrogenase? Dalton Trans 2019; 48:1251-1262. [PMID: 30607401 DOI: 10.1039/c8dt04531c] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The active site of the enzyme nitrogenase (N2→ NH3) is a Fe7MoS9C cluster that contains three doubly-bridging μ-S atoms around a central belt. A vanadium nitrogenase variant has a slightly different cluster, containing two μ-S atoms. Recent crystal structures have revealed substitution of one μ-S (S2B, bridging Fe2 and Fe6), by CO in Mo-nitrogenase and an uncertain light atom in V-nitrogenase. These systems retained catalytic activity, and were able to recover the lost μ-S atom. Electron density attributed to the dissociated S is displaced by 7 Å in the crystal structure of the non-standard V-protein. The hypothesis arising from these observations is that the chemical mechanism of nitrogenase involves reversible dissociation of S2B, leaving Fe2 and Fe6 seriously under-coordinated and reactive in trapping N2 and binding reaction intermediates. Accumulated experimental evidence points to the Fe2-S2B-Fe6 domain as the centre of catalytic hydrogenation of N2. Using DFT simulations of a large model (>488 atoms) containing all relevant surrounding protein residues, I have investigated the chemical steps that could allow dissociation of S2B. The participation of H atoms is crucial, as is involvement of the nearby side chain of His195 that can function as proton donor to S2B and hydrogen-bonding supporter of displaced S2B. A significant result is that after ingress and binding of N2 at Fe2 the breaking of the Fe2-S2B bond can be strongly exergonic with negligible kinetic barrier. Subsequent extension of the Fe6-S2B bond and dissociation as H2S (or SH-) is endergonic by 20-25 kcal mol-1, partly because the separating H2S is restricted by surrounding amino-acids. I present a number of reaction sequences and energy landscapes, and derive thirteen chemical principles relevant to the postulated S-dissociation mechanism. A key conclusion is that unhooking of S2BH or S2BH2 from Fe2 is favourable, likely, and propitious for subsequent H transfer to bound N2 or reaction intermediates. The space between Fe2 and Fe6 supports two bridging ligands, and another H atom on Fe6 can move without kinetic barrier to occupy the bridging position vacated by S2B.
Collapse
Affiliation(s)
- Ian Dance
- School of Chemistry, UNSW Sydney, Sydney 2000, Australia.
| |
Collapse
|
83
|
Hiller CJ, Lee CC, Stiebritz MT, Rettberg LA, Hu Y. Strategies Towards Capturing Nitrogenase Substrates and Intermediates via Controlled Alteration of Electron Fluxes. Chemistry 2018; 25:2389-2395. [PMID: 30225894 DOI: 10.1002/chem.201803735] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Indexed: 11/07/2022]
Abstract
Nitrogenase utilizes an ATP-dependent reductase to deliver electrons to its catalytic component to enable two important reactions: the reduction of N2 to NH4 + , and the reduction of CO to hydrocarbons. The two nitrogenase-based reactions parallel the industrial Haber-Bosch and Fischer-Tropsch processes, yet they occur under ambient conditions. As such, understanding the enzymatic mechanism of nitrogenase is crucial for the future development of biomimetic strategies for energy-efficient production of valuable chemical commodities. Mechanistic investigations of nitrogenase has long been hampered by the difficulty to trap substrates and intermediates relevant to the nitrogenase reactions. Recently, we have successfully captured CO on the Azotobacter vinelandii V-nitrogenase via two approaches that alter the electron fluxes in a controlled manner: one approach utilizes an artificial electron donor to trap CO on the catalytic component of V-nitrogenase in the resting state; whereas the other employs a mismatched reductase component to reduce the electron flux through the system and consequently accumulate CO on the catalytic component of V-nitrogenase. Here we summarize the major outcome of these recent studies, which not only clarified the catalytic relevance of the one-CO (lo-CO) and multi-CO (hi-CO) bound states of nitrogenase, but also pointed to a potential competition between N2 and CO for binding to the same pair of reactive Fe sites across the sulfur belt of the cofactor. Together, these results highlight the utility of these strategies in poising the cofactor at a well-defined state for substrate- or intermediate-trapping via controlled alteration of electron fluxes, which could prove beneficial for further elucidation of the mechanistic details of nitrogenase-catalyzed reactions.
Collapse
Affiliation(s)
- Caleb J Hiller
- 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
| | - Chi Chung Lee
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, 92697-3900, USA
| | - Martin T Stiebritz
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, 92697-3900, USA
| | - Lee A Rettberg
- 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
| |
Collapse
|
84
|
Crystallization of Nitrogenase Proteins. Methods Mol Biol 2018. [PMID: 30317480 DOI: 10.1007/978-1-4939-8864-8_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Nitrogenase is the only known enzymatic system capable of reducing atmospheric dinitrogen to ammonia. This unique reaction requires tightly choreographed interactions between the nitrogenase component proteins, the molybdenum-iron (MoFe)- and iron (Fe)-proteins, as well as regulation of electron transfer between multiple metal centers that are only found in these components. Several decades of research beginning in the 1950s yielded substantial information of how nitrogenase manages the task of N2 fixation. However, key mechanistic steps in this highly oxygen-sensitive and ATP-intensive reaction have only recently been identified at an atomic level. A critical part in any mechanistic elucidation is the necessity to connect spectroscopic and functional properties of the component proteins to the detailed three-dimensional structures. Structural information derived from X-ray diffraction (XRD) methods has provided detailed atomic insights into the enzyme system and, in particular, its active site FeMo-cofactor. The following chapter outlines the general protocols for the crystallization of Azotobacter vinelandii (Av) nitrogenase component proteins, with a special emphasis on different applications, such as high-resolution XRD, single-crystal spectroscopy, and the structural characterization of bound inhibitors.
Collapse
|
85
|
Wittenborn EC, Merrouch M, Ueda C, Fradale L, Léger C, Fourmond V, Pandelia ME, Dementin S, Drennan CL. Redox-dependent rearrangements of the NiFeS cluster of carbon monoxide dehydrogenase. eLife 2018; 7:39451. [PMID: 30277213 PMCID: PMC6168284 DOI: 10.7554/elife.39451] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 08/23/2018] [Indexed: 01/03/2023] Open
Abstract
The C-cluster of the enzyme carbon monoxide dehydrogenase (CODH) is a structurally distinctive Ni-Fe-S cluster employed to catalyze the reduction of CO2 to CO as part of the Wood-Ljungdahl carbon fixation pathway. Using X-ray crystallography, we have observed unprecedented conformational dynamics in the C-cluster of the CODH from Desulfovibrio vulgaris, providing the first view of an oxidized state of the cluster. Combined with supporting spectroscopic data, our structures reveal that this novel, oxidized cluster arrangement plays a role in avoiding irreversible oxidative degradation at the C-cluster. Furthermore, mutagenesis of a conserved cysteine residue that binds the C-cluster in the oxidized state but not in the reduced state suggests that the oxidized conformation could be important for proper cluster assembly, in particular Ni incorporation. Together, these results lay a foundation for future investigations of C-cluster activation and assembly, and contribute to an emerging paradigm of metallocluster plasticity.
Collapse
Affiliation(s)
- Elizabeth C Wittenborn
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
| | - Mériem Merrouch
- Aix Marseille Univ, CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines, Marseille, France
| | - Chie Ueda
- Department of Biochemistry, Brandeis University, Waltham, United States
| | - Laura Fradale
- Aix Marseille Univ, CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines, Marseille, France
| | - Christophe Léger
- Aix Marseille Univ, CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines, Marseille, France
| | - Vincent Fourmond
- Aix Marseille Univ, CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines, Marseille, France
| | | | - Sébastien Dementin
- Aix Marseille Univ, CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines, Marseille, France
| | - Catherine L Drennan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States.,Bio-inspired Solar Energy Program, Canadian Institute for Advanced Research, Toronto, Canada
| |
Collapse
|
86
|
Tanifuji K, Lee CC, Sickerman NS, Tatsumi K, Ohki Y, Hu Y, Ribbe MW. Tracing the 'ninth sulfur' of the nitrogenase cofactor via a semi-synthetic approach. Nat Chem 2018; 10:568-572. [PMID: 29662207 PMCID: PMC5910187 DOI: 10.1038/s41557-018-0029-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 02/16/2018] [Indexed: 11/23/2022]
Abstract
The M-cluster is the [(homocitrate)MoFe7S9C] active site of nitrogenase that is derived from an 8Fe core assembled via coupling and rearrangement of two [Fe4S4] clusters concomitant with the insertion of an interstitial carbon and a ‘9th sulfur’. Combining synthetic [Fe4S4] clusters with an assembly protein template, here we show that sulfite can give rise to the ‘9th sulfur’ that is incorporated in the catalytically important belt region of the cofactor after the radical SAM-dependent carbide insertion and the concurrent 8Fe-core rearrangement have already taken place. Based on the differential reactivity of the formed cluster species, we also propose a new [Fe8S8C] cluster intermediate, the L*-cluster, that is similar to the [Fe8S9C] L- cluster but lacks the ‘9th S’ from sulfite. This work provides a semi-synthetic tool for protein reconstitution that could be widely applicable for the functional analysis of other FeS systems.
Collapse
Affiliation(s)
- Kazuki Tanifuji
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
| | - Chi Chung Lee
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
| | - Nathaniel S Sickerman
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
| | - Kazuyuki Tatsumi
- Department of Chemistry, Graduate School of Science and Research Center for Materials Science, Nagoya University, Nagoya, Japan
| | - Yasuhiro Ohki
- Department of Chemistry, Graduate School of Science and Research Center for Materials Science, Nagoya University, Nagoya, Japan
| | - Yilin Hu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA.
| | - Markus W Ribbe
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA. .,Department of Chemistry, University of California, Irvine, CA, USA.
| |
Collapse
|
87
|
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
|
88
|
Lee CC, Wilcoxen J, Hiller CJ, Britt RD, Hu Y. Evaluation of the Catalytic Relevance of the CO-Bound States of V-Nitrogenase. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201800189] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Chi Chung Lee
- Department of Molecular Biology and Biochemistry; University of California, Irvine; Irvine CA 92697-3900 USA
| | - Jarett Wilcoxen
- Department of Chemistry; University of California, Davis; Davis CA 95616 USA
| | - Caleb J. Hiller
- Department of Molecular Biology and Biochemistry; University of California, Irvine; Irvine CA 92697-3900 USA
- Department of Chemistry; University of California, Irvine; Irvine CA 92697-2025 USA
| | - R. David Britt
- Department of Chemistry; University of California, Davis; Davis CA 95616 USA
| | - Yilin Hu
- Department of Molecular Biology and Biochemistry; University of California, Irvine; Irvine CA 92697-3900 USA
| |
Collapse
|
89
|
ATP-dependent substrate reduction at an [Fe 8S 9] double-cubane cluster. Proc Natl Acad Sci U S A 2018; 115:2994-2999. [PMID: 29507223 DOI: 10.1073/pnas.1720489115] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chemically demanding reductive conversions in biology, such as the reduction of dinitrogen to ammonia or the Birch-type reduction of aromatic compounds, depend on Fe/S-cluster-containing ATPases. These reductions are typically catalyzed by two-component systems, in which an Fe/S-cluster-containing ATPase energizes an electron to reduce a metal site on the acceptor protein that drives the reductive reaction. Here, we show a two-component system featuring a double-cubane [Fe8S9]-cluster [{Fe4S4(SCys)3}2(μ2-S)]. The double-cubane-cluster-containing enzyme is capable of reducing small molecules, such as acetylene (C2H2), azide (N3-), and hydrazine (N2H4). We thus present a class of metalloenzymes akin in fold, metal clusters, and reactivity to nitrogenases.
Collapse
|
90
|
Lee CC, Wilcoxen J, Hiller CJ, Britt RD, Hu Y. Evaluation of the Catalytic Relevance of the CO-Bound States of V-Nitrogenase. Angew Chem Int Ed Engl 2018; 57:3411-3414. [PMID: 29409145 DOI: 10.1002/anie.201800189] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Indexed: 11/08/2022]
Abstract
Binding and activation of CO by nitrogenase is a topic of interest because CO is isoelectronic to N2 , the physiological substrate of this enzyme. The catalytic relevance of one- and multi-CO-bound states (the lo-CO and hi-CO states) of V-nitrogenase to C-C coupling and N2 reduction was examined. Enzymatic and spectroscopic studies demonstrate that the multiple CO moieties in the hi-CO state cannot be coupled as they are, suggesting that C-C coupling requires further activation and/or reduction of the bound CO entity. Moreover, these studies reveal an interesting correlation between decreased activity of N2 reduction and increased population of the lo-CO state, pointing to the catalytic relevance of the belt Fe atoms that are bridged by the single CO moiety in the lo-CO state. Together, these results provide a useful framework for gaining insights into the nitrogenase-catalyzed reaction via further exploration of the utility of the lo-CO conformation of V-nitrogenase.
Collapse
Affiliation(s)
- Chi Chung Lee
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
| | - Jarett Wilcoxen
- Department of Chemistry, University of California, Davis, Davis, CA, 95616, USA
| | - Caleb J Hiller
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA.,Department of Chemistry, University of California, Irvine, Irvine, CA, 92697-2025, USA
| | - R David Britt
- Department of Chemistry, University of California, Davis, Davis, CA, 95616, USA
| | - Yilin Hu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
| |
Collapse
|
91
|
Wang SY, Jin WT, Chen HB, Zhou ZH. Comparison of hydroxycarboxylato imidazole molybdenum(iv) complexes and nitrogenase protein structures: indirect evidence for the protonation of homocitrato FeMo-cofactors. Dalton Trans 2018; 47:7412-7421. [DOI: 10.1039/c8dt00278a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Glycolato and lactato imidazole molybdenum(iv) complexes are used for structural comparison with FeMo-cofactors of MoFe-protein structures.
Collapse
Affiliation(s)
- Si-Yuan Wang
- State Key Laboratory for Physical Chemistry of Solid Surfaces
- College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen
- China
| | - Wan-Ting Jin
- State Key Laboratory for Physical Chemistry of Solid Surfaces
- College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen
- China
| | - Hong-Bin Chen
- State Key Laboratory for Physical Chemistry of Solid Surfaces
- College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen
- China
| | - Zhao-Hui Zhou
- State Key Laboratory for Physical Chemistry of Solid Surfaces
- College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen
- China
| |
Collapse
|
92
|
Artz JH, Zadvornyy OA, Mulder DW, King PW, Peters JW. Structural Characterization of Poised States in the Oxygen Sensitive Hydrogenases and Nitrogenases. Methods Enzymol 2017; 595:213-259. [PMID: 28882202 DOI: 10.1016/bs.mie.2017.07.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The crystallization of FeS cluster-containing proteins has been challenging due to their oxygen sensitivity, and yet these enzymes are involved in many critical catalytic reactions. The last few years have seen a wealth of innovative experiments designed to elucidate not just structural but mechanistic insights into FeS cluster enzymes. Here, we focus on the crystallization of hydrogenases, which catalyze the reversible reduction of protons to hydrogen, and nitrogenases, which reduce dinitrogen to ammonia. A specific focus is given to the different experimental parameters and strategies that are used to trap distinct enzyme states, specifically, oxidants, reductants, and gas treatments. Other themes presented here include the recent use of Cryo-EM, and how coupling various spectroscopies to crystallization is opening up new approaches for structural and mechanistic analysis.
Collapse
Affiliation(s)
- Jacob H Artz
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Oleg A Zadvornyy
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - David W Mulder
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO, United States
| | - Paul W King
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO, United States
| | - John W Peters
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States.
| |
Collapse
|
93
|
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.
Collapse
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
| |
Collapse
|
94
|
Sippel D, Einsle O. The structure of vanadium nitrogenase reveals an unusual bridging ligand. Nat Chem Biol 2017; 13:956-960. [PMID: 28692069 PMCID: PMC5563456 DOI: 10.1038/nchembio.2428] [Citation(s) in RCA: 176] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 05/22/2017] [Indexed: 12/28/2022]
Abstract
Nitrogenases catalyze the reduction of N2 gas to ammonium at a complex heterometallic cofactor. Most commonly this is the FeMo cofactor (FeMoco), a [Mo:7Fe:9S:C] cluster whose exact reactivity and substrate binding mode remain unknown. Alternative nitrogenases replace molybdenum with either vanadium or iron and differ in reactivity, prominently in the ability of vanadium nitrogenase to reduce CO to hydrocarbons. Here we report the 1.35 Å structure of vanadium nitrogenase from Azotobacter vinelandii. The 240 kDa protein contains an additional α-helical subunit not present in molybdenum nitrogenase. The FeV cofactor (FeVco) is a [V:7Fe:8S:C] cluster with a homocitrate ligand to vanadium. Unexpectedly, it lacks one sulfide ion compared to FeMoco that is replaced by a bridging ligand, likely a μ-1,3-carbonate. The anion fits into a pocket within the protein that is obstructed in molybdenum nitrogenase, and its different chemical character helps to rationalize the altered chemical properties of this unique N2- and CO-fixing enzyme.
Collapse
Affiliation(s)
- Daniel Sippel
- Lehrstuhl Biochemie, Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg Research Institute for Advanced Studies (FRIAS), and BIOSS Centre for Biological Signalling Studies, Freiburg, Germany
| | - Oliver Einsle
- Lehrstuhl Biochemie, Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg Research Institute for Advanced Studies (FRIAS), and BIOSS Centre for Biological Signalling Studies, Freiburg, Germany
| |
Collapse
|
95
|
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
| |
Collapse
|
96
|
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.
Collapse
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
| |
Collapse
|
97
|
Cupp-Sutton KA, Ashby MT. Biological Chemistry of Hydrogen Selenide. Antioxidants (Basel) 2016; 5:E42. [PMID: 27879667 PMCID: PMC5187540 DOI: 10.3390/antiox5040042] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 11/04/2016] [Accepted: 11/08/2016] [Indexed: 12/13/2022] Open
Abstract
There are no two main-group elements that exhibit more similar physical and chemical properties than sulfur and selenium. Nonetheless, Nature has deemed both essential for life and has found a way to exploit the subtle unique properties of selenium to include it in biochemistry despite its congener sulfur being 10,000 times more abundant. Selenium is more easily oxidized and it is kinetically more labile, so all selenium compounds could be considered to be "Reactive Selenium Compounds" relative to their sulfur analogues. What is furthermore remarkable is that one of the most reactive forms of selenium, hydrogen selenide (HSe- at physiologic pH), is proposed to be the starting point for the biosynthesis of selenium-containing molecules. This review contrasts the chemical properties of sulfur and selenium and critically assesses the role of hydrogen selenide in biological chemistry.
Collapse
Affiliation(s)
- Kellye A Cupp-Sutton
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA.
| | - Michael T Ashby
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA.
| |
Collapse
|
98
|
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
|
99
|
Dance I. Mechanisms of the S/CO/Se interchange reactions at FeMo-co, the active site cluster of nitrogenase. Dalton Trans 2016; 45:14285-300. [PMID: 27534727 DOI: 10.1039/c6dt03159e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The active site of the N2 fixing enzyme nitrogenase is a C-centred Fe7MoS cluster (FeMo-co) containing a trigonal prism of six Fe atoms connected by a central belt of three doubly-bridging S atoms. The trigonal faces of the prism are capped via triply-bridging S atoms to Fe1 at one end and Mo at the other end. One of the central belt atoms, S2B, considered to be important in the chemical mechanism of the enzyme, has been shown by Spatzal, Rees et al. to undergo substitution by CO, and also substitution by Se in the presence of SeCN(-), under turnover conditions. Further, when turning over under C2H2 or N2/CO there is migration of Se to the other two belt bridging positions. These reactions are extraordinary, and unprecedented in metal chalcogenide cluster chemistry. Using density functional simulations, mechanisms for all of these reactions have been developed, involving the small molecules SCO, SeCO, C2H2S, C2H2Se, SeCN(-), SCN(-) functioning as carriers of S and Se atoms. The possibility that the S2B bridge position is vacant is discounted, because the barrier to formation of a bridge-void intermediate with two contiguous three-coordinate Fe atoms is too large. A bridging ligand is retained throughout the proposed mechanisms. Intermediates with Fe-C(O)-S/Se-Fe cycles and with SCO/SeCO C-bound to Fe are predicted. The energetics of the reaction trajectories show them to be feasible and easily reversible, consistent with experiment. Alternative mechanisms involving intramolecular differential rotatory rearrangements of the cluster to scramble the Se bridges are also examined, and shown to be very unlikely. The implications of these new facets of the reactivity of the FeMo-co cluster are discussed: it is considered that they are unlikely to be part of the mechanism of the physiological reactions of nitrogenase.
Collapse
Affiliation(s)
- Ian Dance
- School of Chemistry, UNSW Australia, Sydney 2052, Australia.
| |
Collapse
|
100
|
Čorić I, Holland PL. Insight into the Iron-Molybdenum Cofactor of Nitrogenase from Synthetic Iron Complexes with Sulfur, Carbon, and Hydride Ligands. J Am Chem Soc 2016; 138:7200-11. [PMID: 27171599 PMCID: PMC5508211 DOI: 10.1021/jacs.6b00747] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Nitrogenase enzymes are used by microorganisms for converting atmospheric N2 to ammonia, which provides an essential source of N atoms for higher organisms. The active site of the molybdenum-dependent nitrogenase is the unique carbide-containing iron-sulfur cluster called the iron-molybdenum cofactor (FeMoco). On the FeMoco, N2 binding is suggested to occur at one or more iron atoms, but the structures of the catalytic intermediates are not clear. In order to establish the feasibility of different potential mechanistic steps during biological N2 reduction, chemists have prepared iron complexes that mimic various structural aspects of the iron sites in the FeMoco. This reductionist approach gives mechanistic insight, and also uncovers fundamental principles that could be used more broadly for small-molecule activation. Here, we discuss recent results and highlight directions for future research. In one direction, synthetic iron complexes have now been shown to bind N2, break the N-N triple bond, and produce ammonia catalytically. Carbon- and sulfur-based donors have been incorporated into the ligand spheres of Fe-N2 complexes to show how these atoms may influence the structure and reactivity of the FeMoco. Hydrides have been incorporated into synthetic systems, which can bind N2, reduce some nitrogenase substrates, and/or reductively eliminate H2 to generate reduced iron centers. Though some carbide-containing iron clusters are known, none yet have sulfide bridges or high-spin iron atoms like the FeMoco.
Collapse
Affiliation(s)
- Ilija Čorić
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Patrick L. Holland
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| |
Collapse
|