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Warmack RA, Rees DC. Nitrogenase beyond the Resting State: A Structural Perspective. Molecules 2023; 28:7952. [PMID: 38138444 PMCID: PMC10745740 DOI: 10.3390/molecules28247952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
Nitrogenases have the remarkable ability to catalyze the reduction of dinitrogen to ammonia under physiological conditions. How does this happen? The current view of the nitrogenase mechanism focuses on the role of hydrides, the binding of dinitrogen in a reductive elimination process coupled to loss of dihydrogen, and the binding of substrates to a binuclear site on the active site cofactor. This review focuses on recent experimental characterizations of turnover relevant forms of the enzyme determined by cryo-electron microscopy and other approaches, and comparison of these forms to the resting state enzyme and the broader family of iron sulfur clusters. Emerging themes include the following: (i) The obligatory coupling of protein and electron transfers does not occur in synthetic and small-molecule iron-sulfur clusters. The coupling of these processes in nitrogenase suggests that they may involve unique features of the cofactor, such as hydride formation on the trigonal prismatic arrangement of irons, protonation of belt sulfurs, and/or protonation of the interstitial carbon. (ii) Both the active site cofactor and protein are dynamic under turnover conditions; the changes are such that more highly reduced forms may differ in key ways from the resting-state structure. Homocitrate appears to play a key role in coupling cofactor and protein dynamics. (iii) Structural asymmetries are observed in nitrogenase under turnover-relevant conditions by cryo-electron microscopy, although the mechanistic relevance of these states (such as half-of-sites reactivity) remains to be established.
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Affiliation(s)
- Rebeccah A. Warmack
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Douglas C. Rees
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA
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2
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Dance I. The HD Reaction of Nitrogenase: a Detailed Mechanism. Chemistry 2023; 29:e202202502. [PMID: 36274057 PMCID: PMC10099629 DOI: 10.1002/chem.202202502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Indexed: 11/06/2022]
Abstract
Nitrogenase is the enzyme that converts N2 to NH3 under ambient conditions. The chemical mechanism of this catalysis at the active site FeMo-co [Fe7 S9 CMo(homocitrate)] is unknown. An obligatory co-product is H2 , while exogenous H2 is a competitive inhibitor. Isotopic substitution using exogenous D2 revealed the N2 -dependent reaction D2 +2H+ +2e- →2HD (the 'HD reaction'), together with a collection of additional experimental characteristics and requirements. This paper describes a detailed mechanism for the HD reaction, developed and elaborated using density functional simulations with a 486-atom model of the active site and surrounding protein. First D2 binds at one Fe atom (endo-Fe6 coordination position), where it is flanked by H-Fe6 (exo position) and H-Fe2 (endo position). Then there is synchronous transfer of these two H atoms to bound D2 , forming one HD bound to Fe2 and a second HD bound to Fe6. These two HD dissociate sequentially. The final phase is recovery of the two flanking H atoms. These H atoms are generated, sequentially, by translocation of a proton from the protein surface to S3B of FeMo-co and combination with introduced electrons. The first H atom migrates from S3B to exo-Fe6 and the second from S3B to endo-Fe2. Reaction energies and kinetic barriers are reported for all steps. This mechanism accounts for the experimental data: (a) stoichiometry; (b) the N2 -dependence results from promotional N2 bound at exo-Fe2; (c) different N2 binding Km for the HD reaction and the NH3 formation reaction results from involvement of two different sites; (d) inhibition by CO; (e) the non-occurrence of 2HD→H2 +D2 results from the synchronicity of the two transfers of H to D2 ; (f) inhibition of HD production at high pN2 is by competitive binding of N2 at endo-Fe6; (g) the non-leakage of D to solvent follows from the hydrophobic environment and irreversibility of proton introduction.
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Affiliation(s)
- Ian Dance
- School of Chemistry, UNSW, Sydney, Australia
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3
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Decamps L, Rice DB, DeBeer S. An Fe 6 C Core in All Nitrogenase Cofactors. Angew Chem Int Ed Engl 2022; 61:e202209190. [PMID: 35975943 PMCID: PMC9826452 DOI: 10.1002/anie.202209190] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Indexed: 01/11/2023]
Abstract
The biological process of dinitrogen reduction to ammonium occurs at the cofactors of nitrogenases, the only enzymes that catalyze this challenging chemical reaction. Three types of nitrogenases have been described, named according to the heterometal in their cofactor: molybdenum, vanadium or iron nitrogenases. Spectroscopic and structural characterization allowed the unambiguous identification of the cofactors of molybdenum and vanadium nitrogenases and revealed a central μ6 -carbide in both of them. Although genetic studies suggested that the cofactor of the iron nitrogenase contains a similar Fe6 C core, this has not been experimentally demonstrated. Here we report Valence-to-Core X-ray Emission Spectroscopy providing experimental evidence that this cofactor contains a carbide, thereby making the Fe6 C core a feature of all nitrogenase cofactors.
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Affiliation(s)
- Laure Decamps
- Department of Inorganic SpectroscopyMax Planck Institute for Chemical Energy ConversionStiftstrasse 34–3645470Mülheim an derRuhrGermany
| | - Derek B. Rice
- Department of Inorganic SpectroscopyMax Planck Institute for Chemical Energy ConversionStiftstrasse 34–3645470Mülheim an derRuhrGermany
| | - Serena DeBeer
- Department of Inorganic SpectroscopyMax Planck Institute for Chemical Energy ConversionStiftstrasse 34–3645470Mülheim an derRuhrGermany
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4
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Decamps L, Rice D, DeBeer S. An Fe6C Core in All Nitrogenase Cofactors. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202209190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Laure Decamps
- Max-Planck-Institute for Chemical Energy Conversion: Max-Planck-Institut fur chemische Energiekonversion Inorganic Spectroscopy GERMANY
| | - Derek Rice
- Max-Planck-Institute for Chemical Energy Conversion: Max-Planck-Institut fur chemische Energiekonversion Inorganic Spectroscopy GERMANY
| | - Serena DeBeer
- MPI CEC Molecular Theory and Spectroscopy Stidtstr. 34-36 45470 Muelheim an der Ruhr GERMANY
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5
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Patra D, Pal A, Nath S, Kundu R, Drew MGB, Ghosh T. Insights into the transformation of VO 2+ motif to VO 3+, V 2O 34+ and VO 2+ motifs and their interconversion along with a detailed mechanistic study of their anti-cancer activity in SiHa cervical cancer cells. J Inorg Biochem 2022; 234:111900. [PMID: 35717882 DOI: 10.1016/j.jinorgbio.2022.111900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 05/30/2022] [Accepted: 06/05/2022] [Indexed: 11/29/2022]
Abstract
The basic criteria for the formation of complexes with VO3+, V2O34+ and VO2+ motifs from the VO2+ motif and their interconversion were explored utilizing two multidentate O,N-donor hydrazone ligands namely, E-2-Hydroxy-N'-(4-oxopentan-2-ylidine)benzohydrazide (H3L1) and E-2-Hydroxy-N'-(4-oxo-4-phenylbutan-2-ylidine)benzohydrazide (H3L2), derived from the condensation of 2-hydroxybenzoylhydrazide with acetylacetone and benzoylacetone respectively. Under aerobic condition, the possibility of forming complexes with different motifs in different solvents with varying pH was examined theoretically by computational methods with results that were verified experimentally. This study reveals that under aerobic condition, complexes with VO3+ (1,2) and V2O34+ (3, 4) motifs were formed in protic CH3OH and neutral CHCl3 solvent respectively while the formation of complexes (5-14) with VO2+ motif required protic CH3OH solvent and higher pH (≥ 7). Interconversion of VO3+, V2O34+ and VO2+ motifs are associated with specific acid-base equilibria, substantiated by 51V NMR titrations. Complexes containing these three motifs exhibited promising in vitro anticancer activity in SiHa cervical cancer cells without affecting healthy cells; among them complexes (5-14) with VO2+ motif are more potent. A detailed systematic mechanistic study was carried out, utilizing the two most potent complexes 5 and 6 (IC50 = 13, 6 μM respectively), which indicates that cytotoxicity and anti-proliferative activity of these complexes are manifested through oxidative stress induced apoptotic pathways (caspase mediated).
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Affiliation(s)
- Debashis Patra
- Post Graduate Department of Chemistry, Ramakrishna Mission Vivekananda Centenary College, Rahara, Kolkata 700118, India
| | - Asmita Pal
- Department of Botany, University of Calcutta, 35 Ballyguange Circular Road, Kolkata 700019, India
| | - Sonali Nath
- Department of Botany, University of Calcutta, 35 Ballyguange Circular Road, Kolkata 700019, India
| | - Rita Kundu
- Department of Botany, University of Calcutta, 35 Ballyguange Circular Road, Kolkata 700019, India
| | - Michael G B Drew
- Department of Chemistry, The University of Reading, PO Box 224, Whiteknights, Reading, RG6 6AD, UK
| | - Tapas Ghosh
- Post Graduate Department of Chemistry, Ramakrishna Mission Vivekananda Centenary College, Rahara, Kolkata 700118, India.
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Khare R, Weindl R, Jentys A, Reuter K, Shi H, Lercher JA. Di- and Tetrameric Molybdenum Sulfide Clusters Activate and Stabilize Dihydrogen as Hydrides. JACS AU 2022; 2:613-622. [PMID: 35373212 PMCID: PMC8965828 DOI: 10.1021/jacsau.1c00507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Indexed: 06/14/2023]
Abstract
NaY zeolite-encapsulated dimeric (Mo2S4) and tetrameric (Mo4S4) molybdenum sulfide clusters stabilize hydrogen as hydride binding to Mo atoms. Density functional theory (DFT) calculations and adsorption measurements suggest that stabilization of hydrogen as sulfhydryl (SH) groups, as typical for layered MoS2, is thermodynamically disfavored. Competitive adsorption of H2 and ethene on Mo was probed by quantifying adsorbed CO on partly hydrogen and/or ethene covered samples with IR spectroscopy. During hydrogenation, experiment and theory suggest that Mo is covered predominately with ethene and sparsely with hydride. DFT calculations further predict that, under reaction conditions, each Mo x S y cluster can activate only one H2, suggesting that the entire cluster (irrespective of its nuclearity) acts as one active site for hydrogenation. The nearly identical turnover frequencies (24.7 ± 3.3 molethane·h-1·molcluster -1), apparent activation energies (31-32 kJ·mol-1), and reaction orders (∼0.5 in ethene and ∼1.0 in H2) show that the active sites in both clusters are catalytically indistinguishable.
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Affiliation(s)
- Rachit Khare
- Department
of Chemistry and Catalysis Research Center, Technical University of Munich, 85747 Garching, Germany
| | - Roland Weindl
- Department
of Chemistry and Catalysis Research Center, Technical University of Munich, 85747 Garching, Germany
| | - Andreas Jentys
- Department
of Chemistry and Catalysis Research Center, Technical University of Munich, 85747 Garching, Germany
| | - Karsten Reuter
- Department
of Chemistry and Catalysis Research Center, Technical University of Munich, 85747 Garching, Germany
- Fritz
Haber Institute of the Max Planck Society, 14195 Berlin, Germany
| | - Hui Shi
- School
of Chemistry and Chemical Engineering, Yangzhou
University, Yangzhou, 225009 Jiangsu China
| | - Johannes A. Lercher
- Department
of Chemistry and Catalysis Research Center, Technical University of Munich, 85747 Garching, Germany
- Institute
for Integrated Catalysis, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
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Oehlmann NN, Rebelein JG. The Conversion of Carbon Monoxide and Carbon Dioxide by Nitrogenases. Chembiochem 2021; 23:e202100453. [PMID: 34643977 PMCID: PMC9298215 DOI: 10.1002/cbic.202100453] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/13/2021] [Indexed: 12/02/2022]
Abstract
Nitrogenases are the only known family of enzymes that catalyze the reduction of molecular nitrogen (N2) to ammonia (NH3). The N2 reduction drives biological nitrogen fixation and the global nitrogen cycle. Besides the conversion of N2, nitrogenases catalyze a whole range of other reductions, including the reduction of the small gaseous substrates carbon monoxide (CO) and carbon dioxide (CO2) to hydrocarbons. However, it remains an open question whether these ‘side reactivities’ play a role under environmental conditions. Nonetheless, these reactivities and particularly the formation of hydrocarbons have spurred the interest in nitrogenases for biotechnological applications. There are three different isozymes of nitrogenase: the molybdenum and the alternative vanadium and iron‐only nitrogenase. The isozymes differ in their metal content, structure, and substrate‐dependent activity, despite their homology. This minireview focuses on the conversion of CO and CO2 to methane and higher hydrocarbons and aims to specify the differences in activity between the three nitrogenase isozymes.
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Affiliation(s)
- Niels N Oehlmann
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043, Marburg, Germany
| | - Johannes G Rebelein
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043, Marburg, Germany
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