1
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Kang W. Structural Insights and Mechanistic Understanding of Iron-Molybdenum Cofactor Biosynthesis by NifB in Nitrogenase Assembly Process. Mol Cells 2023; 46:736-742. [PMID: 38052488 PMCID: PMC10701300 DOI: 10.14348/molcells.2023.0140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/13/2023] [Accepted: 09/13/2023] [Indexed: 12/07/2023] Open
Abstract
NifB, a radical S-adenosylmethionine (SAM) enzyme, is pivotal in the biosynthesis of the iron-molybdenum cofactor (FeMo-co), commonly referred to as the M-cluster. This cofactor, located within the active site of nitrogenase, is essential for the conversion of dinitrogen (N2) to NH3. Recognized as the most intricate metallocluster in nature, FeMo-co biosynthesis involves multiple proteins and a sequence of steps. Of particular significance, NifB directs the fusion of two [Fe4S4] clusters to assemble the 8Fe core, while also incorporating an interstitial carbide. Although NifB has been extensively studied, its molecular mechanisms remain elusive. In this review, we explore recent structural analyses of NifB and provide a comprehensive overview of the established catalytic mechanisms. We propose prospective directions for future research, emphasizing the relevance to biochemistry, agriculture, and environmental science. The goal of this review is to lay a solid foundation for future endeavors aimed at elucidating the atomic details of FeMo-co biosynthesis.
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Affiliation(s)
- Wonchull Kang
- Department of Chemistry, College of Natural Sciences, Soongsil University, Seoul 06978, Korea
- Department of Green Chemistry and Materials Engineering, Soongsil University, Seoul 06978, Korea
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2
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Einsle O. Catalysis and structure of nitrogenases. Curr Opin Struct Biol 2023; 83:102719. [PMID: 37802004 DOI: 10.1016/j.sbi.2023.102719] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/03/2023] [Accepted: 09/06/2023] [Indexed: 10/08/2023]
Abstract
In providing bioavailable nitrogen as building blocks for all classes of biomacromolecules, biological nitrogen fixation is an essential process for all organismic life. Only a single enzyme, nitrogenase, performs this task at ambient conditions and with ATP as an energy source. The assembly of the complex iron-sulfur enzyme nitrogenase and its catalytic mechanism remains a matter of intense study. Recent progress in the structural analysis of the three known isoforms of nitrogenase-differentiated primarily by the heterometal in their active site cofactor-has revealed a degree of structural plasticity of these clusters that suggest two distinct binding sites for substrates and reaction intermediates. A mechanistic proposal based on this finding integrates most of the available experimental data. Furthermore, the first applications of high-resolution cryo-electron microscopy have highlighted further dynamic conformational changes. Structures obtained under turnover conditions support the proposed alternating half-site reactivity in the C2-symmetric nitrogenase complex.
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Affiliation(s)
- Oliver Einsle
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104 Freiburg im Breisgau, Germany.
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3
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Nicolet Y, Cherrier MV, Amara P. Radical SAM Enzymes and Metallocofactor Assembly: A Structural Point of View. ACS BIO & MED CHEM AU 2022; 2:36-52. [PMID: 37102176 PMCID: PMC10114646 DOI: 10.1021/acsbiomedchemau.1c00044] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
This Review focuses on the structure-function relationship of radical S-adenosyl-l-methionine (SAM) enzymes involved in the assembly of metallocofactors corresponding to the active sites of [FeFe]-hydrogenase and nitrogenase [MoFe]-protein. It does not claim to correspond to an extensive review on the assembly machineries of these enzyme active sites, for which many good reviews are already available, but instead deals with the contribution of structural data to the understanding of their chemical mechanism (Buren et al. Chem. Rev.2020, 142 ( (25), ) 11006-11012; Britt et al. Chem. Sci.2020, 11 ( (38), ), 10313-10323). Hence, we will present the history and current knowledge about the radical SAM maturases HydE, HydG, and NifB as well as what, in our opinion, should be done in the near future to overcome the existing barriers in our understanding of this fascinating chemistry that intertwine organic radicals and organometallic complexes.
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Affiliation(s)
- Yvain Nicolet
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000 Grenoble, France
| | - Mickael V. Cherrier
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000 Grenoble, France
| | - Patricia Amara
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000 Grenoble, France
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4
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Abstract
Carbide complexes remain a rare class of molecules. Their paucity does not reflect exceptional instability but is rather due to the generally narrow scope of synthetic procedures for constructing carbide complexes. The preparation of carbide complexes typically revolves around generating LnM-CEx fragments, followed by cleavage of the C-E bonds of the coordinated carbon-based ligands (the alternative being direct C atom transfer). Prime examples involve deoxygenation of carbonyl ligands and deprotonation of methyl ligands, but several other p-block fragments can be cleaved off to afford carbide ligands. This Review outlines synthetic strategies toward terminal carbide complexes, bridging carbide complexes, as well as carbide-carbonyl cluster complexes. It then surveys the reactivity of carbide complexes, covering stoichiometric reactions where the carbide ligands act as C1 reagents, engage in cross-coupling reactions, and enact Fischer-Tropsch-like chemistry; in addition, we discuss carbide complexes in the context of catalysis. Finally, we examine spectroscopic features of carbide complexes, which helps to establish the presence of the carbide functionality and address its electronic structure.
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Affiliation(s)
- Anders Reinholdt
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Jesper Bendix
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
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5
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Postbiosynthetic modification of a precursor to the nitrogenase iron-molybdenum cofactor. Proc Natl Acad Sci U S A 2021; 118:2015361118. [PMID: 33836573 DOI: 10.1073/pnas.2015361118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nitrogenases utilize Fe-S clusters to reduce N2 to NH3 The large number of Fe sites in their catalytic cofactors has hampered spectroscopic investigations into their electronic structures, mechanisms, and biosyntheses. To facilitate their spectroscopic analysis, we are developing methods for incorporating 57Fe into specific sites of nitrogenase cofactors, and we report herein site-selective 57Fe labeling of the L-cluster-a carbide-containing, [Fe8S9C] precursor to the Mo nitrogenase catalytic cofactor. Treatment of the isolated L-cluster with the chelator ethylenediaminetetraacetate followed by reconstitution with 57Fe2+ results in 57Fe labeling of the terminal Fe sites in high yield and with high selectivity. This protocol enables the generation of L-cluster samples in which either the two terminal or the six belt Fe sites are selectively labeled with 57Fe. Mössbauer spectroscopic analysis of these samples bound to the nitrogenase maturase Azotobacter vinelandii NifX reveals differences in the primary coordination sphere of the terminal Fe sites and that one of the terminal sites of the L-cluster binds to H35 of Av NifX. This work provides molecular-level insights into the electronic structure and biosynthesis of the L-cluster and introduces postbiosynthetic modification as a promising strategy for studies of nitrogenase cofactors.
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6
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Burén S, Jiménez-Vicente E, Echavarri-Erasun C, Rubio LM. Biosynthesis of Nitrogenase Cofactors. Chem Rev 2020; 120:4921-4968. [PMID: 31975585 PMCID: PMC7318056 DOI: 10.1021/acs.chemrev.9b00489] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Indexed: 12/30/2022]
Abstract
Nitrogenase harbors three distinct metal prosthetic groups that are required for its activity. The simplest one is a [4Fe-4S] cluster located at the Fe protein nitrogenase component. The MoFe protein component carries an [8Fe-7S] group called P-cluster and a [7Fe-9S-C-Mo-R-homocitrate] group called FeMo-co. Formation of nitrogenase metalloclusters requires the participation of the structural nitrogenase components and many accessory proteins, and occurs both in situ, for the P-cluster, and in external assembly sites for FeMo-co. The biosynthesis of FeMo-co is performed stepwise and involves molecular scaffolds, metallochaperones, radical chemistry, and novel and unique biosynthetic intermediates. This review provides a critical overview of discoveries on nitrogenase cofactor structure, function, and activity over the last four decades.
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Affiliation(s)
- Stefan Burén
- Centro
de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto
Nacional de Investigación y Tecnología Agraria
y Alimentaria (INIA), Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Emilio Jiménez-Vicente
- Department
of Biochemistry, Virginia Polytechnic Institute, Blacksburg, Virginia 24061, United States
| | - Carlos Echavarri-Erasun
- Centro
de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto
Nacional de Investigación y Tecnología Agraria
y Alimentaria (INIA), Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Luis M. Rubio
- Centro
de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto
Nacional de Investigación y Tecnología Agraria
y Alimentaria (INIA), Pozuelo de Alarcón, 28223 Madrid, Spain
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7
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Van Stappen C, Decamps L, Cutsail GE, Bjornsson R, Henthorn JT, Birrell JA, DeBeer S. The Spectroscopy of Nitrogenases. Chem Rev 2020; 120:5005-5081. [PMID: 32237739 PMCID: PMC7318057 DOI: 10.1021/acs.chemrev.9b00650] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Indexed: 01/08/2023]
Abstract
Nitrogenases are responsible for biological nitrogen fixation, a crucial step in the biogeochemical nitrogen cycle. These enzymes utilize a two-component protein system and a series of iron-sulfur clusters to perform this reaction, culminating at the FeMco active site (M = Mo, V, Fe), which is capable of binding and reducing N2 to 2NH3. In this review, we summarize how different spectroscopic approaches have shed light on various aspects of these enzymes, including their structure, mechanism, alternative reactivity, and maturation. Synthetic model chemistry and theory have also played significant roles in developing our present understanding of these systems and are discussed in the context of their contributions to interpreting the nature of nitrogenases. Despite years of significant progress, there is still much to be learned from these enzymes through spectroscopic means, and we highlight where further spectroscopic investigations are needed.
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Affiliation(s)
- Casey Van Stappen
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Laure Decamps
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - George E. Cutsail
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Ragnar Bjornsson
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Justin T. Henthorn
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - James A. Birrell
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Serena DeBeer
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
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8
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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.
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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 . ;
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9
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Jin WT, Wang H, Wang SY, Dapper CH, Li X, Newton WE, Zhou ZH, Cramer SP. Preliminary Assignment of Protonated and Deprotonated Homocitrates in Extracted FeMo-Cofactors by Comparisons with Molybdenum(IV) Lactates and Oxidovanadium Glycolates. Inorg Chem 2019; 58:2523-2532. [PMID: 30726074 DOI: 10.1021/acs.inorgchem.8b03108] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A similar pair of protonated and deprotonated mononuclear oxidovanadium glycolates [VO(Hglyc)(phen)(H2O)]Cl·2H2O (1) and [VO(glyc)(bpy)(H2O)] (2) and a mixed-(de)protonated oxidovanadium triglycolate (NH4)2[VO(Hglyc)2(glyc)]·H2O (3) were isolated and examined. The ≡C-O(H) (≡C-OH or ≡C-O) groups coordinated to vanadium were spectroscopically and structurally identified. The glycolate in 1 features a bidentate chelation through protonated α-hydroxy and α-carboxy groups, whereas the glycolate in 2 coordinates through deprotonated α-alkoxy and α-carboxy groups. The glycolates in 3 coordinate to vanadium through α-alkoxy or α-hydroxy and α-carboxy groups and thus have both protonated ≡C-OH and deprotonated ≡C-O bonds simultaneously. Structural investigations revealed that the longer protonated V-Oα-hydroxy bonds [2.234(2) Å and 2.244(2) Å] in 1 and 3 are close to those of FeV-cofactor (FeV-co) 2.17 Å1 (FeMo-co 2.17 Å2), while deprotonated V-Oα-alkoxy bonds [2, 1.930(2); 3, 1.927(2) Å] were obviously shorter. This shows a similar elongated trend as the Mo-O distances in the previously reported deprotonated vs protonated molybdenum lactates (Wang, S. Y. et al. Dalton Trans. 2018, 47, 7412-7421) and these vanadium and molybdenum complexes have the same local V/Mo-homocitrate structures as those of FeV/Mo-cos of nitrogenases. The IR spectra of these oxidovanadium and the previously synthesized molybdenum complexes including different substituted ≡C-O(H) model compounds show red-shifts for ≡C-OH vs ≡C-O alternation, which further assign the two IR bands of extracted FeMo-co at 1084 and 1031 cm-1 to ≡C-O and ≡C-OH vibrations, respectively. Although the structural data or IR spectra for some of the previously synthesized Mo/V complexes and extracted FeMo-co were measured earlier, this is the first time that the ≡C-O(H) coordinated peaks are assigned. The overall structural and IR results well suggest the coexistence of homocitrates coordinated with α-alkoxy (deprotonated) and α-hydroxy (protonated) groups in the extracted FeMo-co.
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Affiliation(s)
- Wan-Ting Jin
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 361005 , China
| | - Hongxin Wang
- Department of Chemistry , University of California , Davis , California 95616 , United States.,Physical Biosciences Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Si-Yuan Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 361005 , China
| | - Christie H Dapper
- Department of Biochemistry , Virginia Polytechnic Institute and State University , Blacksburg , Virginia 24061 , United States
| | - Xing Li
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 361005 , China
| | - William E Newton
- Department of Biochemistry , Virginia Polytechnic Institute and State University , Blacksburg , Virginia 24061 , United States
| | - Zhao-Hui Zhou
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 361005 , China
| | - Stephen P Cramer
- Department of Chemistry , University of California , Davis , California 95616 , United States.,Physical Biosciences Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
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10
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Probing the coordination and function of Fe 4S 4 modules in nitrogenase assembly protein NifB. Nat Commun 2018; 9:2824. [PMID: 30026506 PMCID: PMC6053413 DOI: 10.1038/s41467-018-05272-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 06/21/2018] [Indexed: 11/08/2022] Open
Abstract
NifB is an essential radical S-adenosylmethionine (SAM) enzyme for nitrogenase cofactor assembly. Previous studies show that NifB couples a putative pair of [Fe4S4] modules (designated K1 and K2) into an [Fe8S9C] cofactor precursor concomitant with radical SAM-dependent carbide insertion through the action of its SAM-binding [Fe4S4] module. However, the coordination and function of the NifB cluster modules remain unknown. Here, we use continuous wave and pulse electron paramagnetic resonance spectroscopy to show that K1- and K2-modules are 3-cysteine-coordinated [Fe4S4] clusters, with a histidine-derived nitrogen serving as the fourth ligand to K1 that is lost upon K1/K2-coupling. Further, we demonstrate that coexistence of SAM/K2-modules is a prerequisite for methyltransfer to K2 and hydrogen abstraction from the K2-associated methyl by a 5′-deoxyadenosyl radical. These results establish an important framework for mechanistic explorations of NifB while highlighting the utility of a synthetic-cluster-based reconstitution approach employed herein in functional analyses of iron–sulfur (FeS) enzymes. NifB is a key enzyme in the biosynthesis pathway of the nitrogenase FeMo cofactor. Here, the authors investigate the maturation of its iron-sulfur clusters by EPR and biochemical analyses, showing how individual precursor clusters participate in the formation of the final iron-sulfur cluster.
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11
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George SJ, Hernandez JA, Jimenez-Vicente E, Echavarri-Erasun C, Rubio LM. EXAFS reveals two Mo environments in the nitrogenase iron-molybdenum cofactor biosynthetic protein NifQ. Chem Commun (Camb) 2018; 52:11811-11814. [PMID: 27711309 DOI: 10.1039/c6cc06370e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Mo and Fe K-edge EXAFS analysis of NifQ shows the presence of a [MoFe3S4] cluster and a second independent Mo environment that includes Mo-O bonds and Mo-S bonds. Both environments are relevant to FeMo-co biosynthesis and may represent different stages of Mo biochemical transformations catalyzed by NifQ.
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Affiliation(s)
| | - Jose A Hernandez
- Department of Biochemistry, Midwestern University, Glendale, Arizona 85308, USA
| | - Emilio Jimenez-Vicente
- Centro de Biotecnología y Genómica de Plantas, Universidad Politénica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223, Pozuelo de Alarcón, Madrid, Spain.
| | - Carlos Echavarri-Erasun
- Centro de Biotecnología y Genómica de Plantas, Universidad Politénica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223, Pozuelo de Alarcón, Madrid, Spain.
| | - Luis M Rubio
- Centro de Biotecnología y Genómica de Plantas, Universidad Politénica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223, Pozuelo de Alarcón, Madrid, Spain.
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12
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Mus F, Alleman AB, Pence N, Seefeldt LC, Peters JW. Exploring the alternatives of biological nitrogen fixation. Metallomics 2018; 10:523-538. [DOI: 10.1039/c8mt00038g] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Most biological nitrogen fixation (BNF) results from the activity of the molybdenum nitrogenase (Mo-nitrogenase, Nif), an oxygen-sensitive metalloenzyme complex found in all known diazotrophs.
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Affiliation(s)
- Florence Mus
- Institute of Biological Chemistry, Washington State University
- Pullman
- USA
| | | | - Natasha Pence
- Department of Chemistry and Biochemistry, Montana State University
- Bozeman
- USA
| | - Lance C. Seefeldt
- Department of Chemistry and Biochemistry, Utah State University
- Logan
- USA
| | - John W. Peters
- Institute of Biological Chemistry, Washington State University
- Pullman
- USA
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13
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Arragain S, Jiménez-Vicente E, Scandurra AA, Burén S, Rubio LM, Echavarri-Erasun C. Diversity and Functional Analysis of the FeMo-Cofactor Maturase NifB. FRONTIERS IN PLANT SCIENCE 2017; 8:1947. [PMID: 29250084 PMCID: PMC5715403 DOI: 10.3389/fpls.2017.01947] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 10/30/2017] [Indexed: 06/07/2023]
Abstract
One of the main hurdles to engineer nitrogenase in a non-diazotrophic host is achieving NifB activity. NifB is an extremely unstable and oxygen sensitive protein that catalyzes a low-potential SAM-radical dependent reaction. The product of NifB activity is called NifB-co, a complex [8Fe-9S-C] cluster that serves as obligate intermediate in the biosyntheses of the active-site cofactors of all known nitrogenases. Here we study the diversity and phylogeny of naturally occurring NifB proteins, their protein architecture and the functions of the distinct NifB domains in order to understand what defines a catalytically active NifB. Focus is on NifB from the thermophile Chlorobium tepidum (two-domain architecture), the hyperthermophile Methanocaldococcus infernus (single-domain architecture) and the mesophile Klebsiella oxytoca (two-domain architecture), showing in silico characterization of their nitrogen fixation (nif) gene clusters, conserved NifB motifs, and functionality. C. tepidum and M. infernus NifB were able to complement an Azotobacter vinelandii (ΔnifB) mutant restoring the Nif+ phenotype and thus demonstrating their functionality in vivo. In addition, purified C. tepidum NifB exhibited activity in the in vitro NifB-dependent nitrogenase reconstitution assay. Intriguingly, changing the two-domain K. oxytoca NifB to single-domain by removal of the C-terminal NifX-like extension resulted in higher in vivo nitrogenase activity, demonstrating that this domain is not required for nitrogen fixation in mesophiles.
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Affiliation(s)
| | | | | | | | - Luis M. Rubio
- *Correspondence: Carlos Echavarri-Erasun, Luis M. Rubio,
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14
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Guo Y, Echavarri-Erasun C, Demuez M, Jiménez-Vicente E, Bominaar EL, Rubio LM. The Nitrogenase FeMo-Cofactor Precursor Formed by NifB Protein: A Diamagnetic Cluster Containing Eight Iron Atoms. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201606447] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Yisong Guo
- Department of Chemistry; Carnegie Mellon University; 4400 Fifth Ave Pittsburgh PA 15213 USA
| | - Carlos Echavarri-Erasun
- Centro de Biotecnología y Genómica de Plantas; Universidad Politénica de Madrid (UPM)-; Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA); Campus Montegancedo UPM 28223-Pozuelo de Alarcón Madrid Spain
| | - Marie Demuez
- Centro de Biotecnología y Genómica de Plantas; Universidad Politénica de Madrid (UPM)-; Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA); Campus Montegancedo UPM 28223-Pozuelo de Alarcón Madrid Spain
| | - Emilio Jiménez-Vicente
- Centro de Biotecnología y Genómica de Plantas; Universidad Politénica de Madrid (UPM)-; Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA); Campus Montegancedo UPM 28223-Pozuelo de Alarcón Madrid Spain
| | - Emile L. Bominaar
- Department of Chemistry; Carnegie Mellon University; 4400 Fifth Ave Pittsburgh PA 15213 USA
| | - Luis M. Rubio
- Centro de Biotecnología y Genómica de Plantas; Universidad Politénica de Madrid (UPM)-; Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA); Campus Montegancedo UPM 28223-Pozuelo de Alarcón Madrid Spain
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15
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Guo Y, Echavarri-Erasun C, Demuez M, Jiménez-Vicente E, Bominaar EL, Rubio LM. The Nitrogenase FeMo-Cofactor Precursor Formed by NifB Protein: A Diamagnetic Cluster Containing Eight Iron Atoms. Angew Chem Int Ed Engl 2016; 55:12764-7. [PMID: 27611968 DOI: 10.1002/anie.201606447] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Indexed: 11/10/2022]
Abstract
The biological activation of N2 occurs at the FeMo-cofactor, a 7Fe-9S-Mo-C-homocitrate cluster. FeMo-cofactor formation involves assembly of a Fe6-8 -SX -C core precursor, NifB-co, which occurs on the NifB protein. Characterization of NifB-co in NifB is complicated by the dynamic nature of the assembly process and the presence of a permanent [4Fe-4S] cluster associated with the radical SAM chemistry for generating the central carbide. We have used the physiological carrier protein, NifX, which has been proposed to bind NifB-co and deliver it to the NifEN protein, upon which FeMo-cofactor assembly is ultimately completed. Preparation of NifX in a fully NifB-co-loaded form provided an opportunity for Mössbauer analysis of NifB-co. The results indicate that NifB-co is a diamagnetic (S=0) 8-Fe cluster, containing two spectroscopically distinct Fe sites that appear in a 3:1 ratio. DFT analysis of the (57) Fe electric hyperfine interactions deduced from the Mössbauer analysis suggests that NifB-co is either a 4Fe(2+) -4Fe(3+) or 6Fe(2+) -2Fe(3+) cluster having valence-delocalized states.
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Affiliation(s)
- Yisong Guo
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Ave, Pittsburgh, PA, 15213, USA.
| | - Carlos Echavarri-Erasun
- Centro de Biotecnología y Genómica de Plantas, Universidad Politénica de Madrid (UPM)-, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223-Pozuelo de Alarcón, Madrid, Spain
| | - Marie Demuez
- Centro de Biotecnología y Genómica de Plantas, Universidad Politénica de Madrid (UPM)-, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223-Pozuelo de Alarcón, Madrid, Spain
| | - Emilio Jiménez-Vicente
- Centro de Biotecnología y Genómica de Plantas, Universidad Politénica de Madrid (UPM)-, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223-Pozuelo de Alarcón, Madrid, Spain
| | - Emile L Bominaar
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Ave, Pittsburgh, PA, 15213, USA.
| | - Luis M Rubio
- Centro de Biotecnología y Genómica de Plantas, Universidad Politénica de Madrid (UPM)-, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223-Pozuelo de Alarcón, Madrid, Spain.
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16
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Wilcoxen J, Arragain S, Scandurra AA, Jimenez-Vicente E, Echavarri-Erasun C, Pollmann S, Britt RD, Rubio LM. Electron Paramagnetic Resonance Characterization of Three Iron-Sulfur Clusters Present in the Nitrogenase Cofactor Maturase NifB from Methanocaldococcus infernus. J Am Chem Soc 2016; 138:7468-71. [PMID: 27268267 DOI: 10.1021/jacs.6b03329] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
NifB utilizes two equivalents of S-adenosyl methionine (SAM) to insert a carbide atom and fuse two substrate [Fe-S] clusters forming the NifB cofactor (NifB-co), which is then passed to NifEN for further modification to form the iron-molybdenum cofactor (FeMo-co) of nitrogenase. Here, we demonstrate that NifB from the methanogen Methanocaldococcus infernus is a radical SAM enzyme able to reductively cleave SAM to 5'-deoxyadenosine radical and is competent in FeMo-co maturation. Using electron paramagnetic resonance spectroscopy we have characterized three [4Fe-4S] clusters, one SAM binding cluster, and two auxiliary clusters probably acting as substrates for NifB-co formation. Nitrogen coordination to one or more of the auxiliary clusters in NifB was observed, and its mechanistic implications for NifB-co dissociation from the maturase are discussed.
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Affiliation(s)
- Jarett Wilcoxen
- Department of Chemistry, University of California , Davis, California 95616, United States
| | - Simon Arragain
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid , Pozuelo de Alarcón, Madrid 28223, Spain
| | - Alessandro A Scandurra
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid , Pozuelo de Alarcón, Madrid 28223, Spain
| | - Emilio Jimenez-Vicente
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid , Pozuelo de Alarcón, Madrid 28223, Spain
| | - Carlos Echavarri-Erasun
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid , Pozuelo de Alarcón, Madrid 28223, Spain
| | - Stephan Pollmann
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid , Pozuelo de Alarcón, Madrid 28223, Spain
| | - R David Britt
- Department of Chemistry, University of California , Davis, California 95616, United States
| | - Luis M Rubio
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid , Pozuelo de Alarcón, Madrid 28223, Spain
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17
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Affiliation(s)
- Yilin Hu
- Department of Molecular Biology and Biochemistry and
| | - Markus W. Ribbe
- Department of Molecular Biology and Biochemistry and
- Department of Chemistry, University of California, Irvine, California 92697-2025; ,
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18
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Echavarri-Erasun C, Arragain S, Scandurra AA, Rubio LM. Expression and purification of NifB proteins from aerobic and anaerobic sources. Methods Mol Biol 2015; 1122:19-31. [PMID: 24639251 DOI: 10.1007/978-1-62703-794-5_3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
NifB is the key protein in the biosynthesis of nitrogenase iron-molybdenum cofactor. Due to its extreme sensitivity to O2 and inherent protein instability, NifB proteins must be purified under strict anaerobic conditions by using affinity chromatography methods. We describe here the methods for NifB purification from cells of the strict aerobic nitrogen-fixing bacterium Azotobacter vinelandii, the facultative anaerobic nitrogen-fixing bacterium Klebsiella pneumoniae, and the facultative anaerobic non-nitrogen fixing bacterium Escherichia coli recombinantly expressing a nifB gene of thermophilic origin.
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Affiliation(s)
- Carlos Echavarri-Erasun
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
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19
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Liu K, Rykov AI, Wang J, Zhang T. Recent Advances in the Application of Mößbauer Spectroscopy in Heterogeneous Catalysis. ADVANCES IN CATALYSIS 2015. [DOI: 10.1016/bs.acat.2015.09.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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20
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The role of X-ray spectroscopy in understanding the geometric and electronic structure of nitrogenase. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1853:1406-15. [PMID: 25486459 DOI: 10.1016/j.bbamcr.2014.11.027] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 11/22/2014] [Accepted: 11/24/2014] [Indexed: 10/24/2022]
Abstract
X-ray absorption (XAS) and X-ray emission spectroscopy (XES) provide element specific probes of the geometric and electronic structures of metalloprotein active sites. As such, these methods have played an integral role in nitrogenase research beginning with the first EXAFS studies on nitrogenase in the late 1970s. Herein, we briefly explain the information that can be extracted from XAS and XES. We then highlight the recent applications of these methods in nitrogenase research. The influence of X-ray spectroscopy on our current understanding of the atomic structure and electronic structure of iron molybdenum cofactor (FeMoco) is emphasized. Contributions of X-ray spectroscopy to understanding substrate interactions and cluster biosynthesis are also discussed. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.
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21
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Byer AS, Shepard EM, Peters JW, Broderick JB. Radical S-adenosyl-L-methionine chemistry in the synthesis of hydrogenase and nitrogenase metal cofactors. J Biol Chem 2014; 290:3987-94. [PMID: 25477518 DOI: 10.1074/jbc.r114.578161] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nitrogenase, [FeFe]-hydrogenase, and [Fe]-hydrogenase enzymes perform catalysis at metal cofactors with biologically unusual non-protein ligands. The FeMo cofactor of nitrogenase has a MoFe7S9 cluster with a central carbon, whereas the H-cluster of [FeFe]-hydrogenase contains a 2Fe subcluster coordinated by cyanide and CO ligands as well as dithiomethylamine; the [Fe]-hydrogenase cofactor has CO and guanylylpyridinol ligands at a mononuclear iron site. Intriguingly, radical S-adenosyl-L-methionine enzymes are vital for the assembly of all three of these diverse cofactors. This minireview presents and discusses the current state of knowledge of the radical S-adenosylmethionine enzymes required for synthesis of these remarkable metal cofactors.
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Affiliation(s)
- Amanda S Byer
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717
| | - Eric M Shepard
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717
| | - John W Peters
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717
| | - Joan B Broderick
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717
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22
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Scott A, Pelmenschikov V, Guo Y, Yan L, Wang H, George SJ, Dapper CH, Newton WE, Yoda Y, Tanaka Y, Cramer SP. Structural characterization of CO-inhibited Mo-nitrogenase by combined application of nuclear resonance vibrational spectroscopy, extended X-ray absorption fine structure, and density functional theory: new insights into the effects of CO binding and the role of the interstitial atom. J Am Chem Soc 2014; 136:15942-54. [PMID: 25275608 PMCID: PMC4235365 DOI: 10.1021/ja505720m] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Indexed: 01/21/2023]
Abstract
The properties of CO-inhibited Azotobacter vinelandii (Av) Mo-nitrogenase (N2ase) have been examined by the combined application of nuclear resonance vibrational spectroscopy (NRVS), extended X-ray absorption fine structure (EXAFS), and density functional theory (DFT). Dramatic changes in the NRVS are seen under high-CO conditions, especially in a 188 cm(-1) mode associated with symmetric breathing of the central cage of the FeMo-cofactor. Similar changes are reproduced with the α-H195Q N2ase variant. In the frequency region above 450 cm(-1), additional features are seen that are assigned to Fe-CO bending and stretching modes (confirmed by (13)CO isotope shifts). The EXAFS for wild-type N2ase shows evidence for a significant cluster distortion under high-CO conditions, most dramatically in the splitting of the interaction between Mo and the shell of Fe atoms originally at 5.08 Å in the resting enzyme. A DFT model with both a terminal -CO and a partially reduced -CHO ligand bound to adjacent Fe sites is consistent with both earlier FT-IR experiments, and the present EXAFS and NRVS observations for the wild-type enzyme. Another DFT model with two terminal CO ligands on the adjacent Fe atoms yields Fe-CO bands consistent with the α-H195Q variant NRVS. The calculations also shed light on the vibrational "shake" modes of the interstitial atom inside the central cage, and their interaction with the Fe-CO modes. Implications for the CO and N2 reactivity of N2ase are discussed.
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Affiliation(s)
- Aubrey
D. Scott
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | | | - Yisong Guo
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Lifen Yan
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Hongxin Wang
- Department
of Chemistry, University of California, Davis, California 95616, United States
- Physical
Biosciences Division, Lawrence Berkeley
National Laboratory, Berkeley, California 94720, United States
| | - Simon J. George
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Christie H. Dapper
- Department
of Biochemistry, Virginia Polytechnic Institute
& State University, Blacksburg, Virginia 24061, United States
| | - William E. Newton
- Department
of Biochemistry, Virginia Polytechnic Institute
& State University, Blacksburg, Virginia 24061, United States
| | - Yoshitaka Yoda
- Research
and Utilization Division, SPring-8/JASRI, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Yoshihito Tanaka
- SR
Materials Science Instrumentation Unit, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Stephen P. Cramer
- Department
of Chemistry, University of California, Davis, California 95616, United States
- Physical
Biosciences Division, Lawrence Berkeley
National Laboratory, Berkeley, California 94720, United States
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23
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Broderick JB, Duffus B, Duschene KS, Shepard EM. Radical S-adenosylmethionine enzymes. Chem Rev 2014; 114:4229-317. [PMID: 24476342 PMCID: PMC4002137 DOI: 10.1021/cr4004709] [Citation(s) in RCA: 584] [Impact Index Per Article: 58.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Indexed: 12/22/2022]
Affiliation(s)
- Joan B. Broderick
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Benjamin
R. Duffus
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Kaitlin S. Duschene
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Eric M. Shepard
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
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24
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Happe T, Hemschemeier A. Metalloprotein mimics – old tools in a new light. Trends Biotechnol 2014; 32:170-6. [DOI: 10.1016/j.tibtech.2014.02.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 02/07/2014] [Accepted: 02/07/2014] [Indexed: 01/03/2023]
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25
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Jiménez-Vicente E, Navarro-Rodríguez M, Poza-Carrión C, Rubio LM. Role of Azotobacter vinelandii FdxN in FeMo-co biosynthesis. FEBS Lett 2013; 588:512-6. [PMID: 24374338 DOI: 10.1016/j.febslet.2013.12.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 12/11/2013] [Accepted: 12/12/2013] [Indexed: 11/20/2022]
Abstract
Biosynthesis of metal clusters for the nitrogenase component proteins NifH and NifDK involves electron donation events. Yet, electron donors specific to the biosynthetic pathways of the [4Fe-4S] cluster of NifH, or the P-cluster and the FeMo-co of NifDK, have not been identified. Here we show that an Azotobacter vinelandii mutant lacking fdxN was specifically impaired in FeMo-co biosynthesis. The ΔfdxN mutant produced 5-fold less NifB-co, an early FeMo-co biosynthetic intermediate, than wild type. As a consequence, it accumulated FeMo-co-deficient apo-NifDK and was impaired in NifDK activity. We conclude that FdxN plays a role in FeMo-co biosynthesis, presumably by donating electrons to support NifB-co synthesis by NifB. This is the first role in nitrogenase biosynthesis unequivocally assigned to any A. vinelandii ferredoxin.
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Affiliation(s)
- Emilio Jiménez-Vicente
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Pozuelo de Alarcón 28223, Madrid, Spain
| | - Mónica Navarro-Rodríguez
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Pozuelo de Alarcón 28223, Madrid, Spain
| | - César Poza-Carrión
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Pozuelo de Alarcón 28223, Madrid, Spain
| | - Luis M Rubio
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Pozuelo de Alarcón 28223, Madrid, Spain.
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26
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Ribbe MW, Hu Y, Hodgson KO, Hedman B. Biosynthesis of nitrogenase metalloclusters. Chem Rev 2013; 114:4063-80. [PMID: 24328215 DOI: 10.1021/cr400463x] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Markus W Ribbe
- Department of Molecular Biology and Biochemistry, University of California , Irvine, California 92697-3900, United States
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27
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Mitra D, George SJ, Guo Y, Kamali S, Keable S, Peters JW, Pelmenschikov V, Case DA, Cramer SP. Characterization of [4Fe-4S] cluster vibrations and structure in nitrogenase Fe protein at three oxidation levels via combined NRVS, EXAFS, and DFT analyses. J Am Chem Soc 2013; 135:2530-43. [PMID: 23282058 DOI: 10.1021/ja307027n] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Azotobacter vinelandii nitrogenase Fe protein (Av2) provides a rare opportunity to investigate a [4Fe-4S] cluster at three oxidation levels in the same protein environment. Here, we report the structural and vibrational changes of this cluster upon reduction using a combination of NRVS and EXAFS spectroscopies and DFT calculations. Key to this work is the synergy between these three techniques as each generates highly complementary information and their analytical methodologies are interdependent. Importantly, the spectroscopic samples contained no glassing agents. NRVS and DFT reveal a systematic 10-30 cm(-1) decrease in Fe-S stretching frequencies with each added electron. The "oxidized" [4Fe-4S](2+) state spectrum is consistent with and extends previous resonance Raman spectra. For the "reduced" [4Fe-4S](1+) state in Fe protein, and for any "all-ferrous" [4Fe-4S](0) cluster, these NRVS spectra are the first available vibrational data. NRVS simulations also allow estimation of the vibrational disorder for Fe-S and Fe-Fe distances, constraining the EXAFS analysis and allowing structural disorder to be estimated. For oxidized Av2, EXAFS and DFT indicate nearly equal Fe-Fe distances, while addition of one electron decreases the cluster symmetry. However, addition of the second electron to form the all-ferrous state induces significant structural change. EXAFS data recorded to k = 21 Å(-1) indicates a 1:1 ratio of Fe-Fe interactions at 2.56 Å and 2.75 Å, a result consistent with DFT. Broken symmetry (BS) DFT rationalizes the interplay between redox state and the Fe-S and Fe-Fe distances as predominantly spin-dependent behavior inherent to the [4Fe-4S] cluster and perturbed by the Av2 protein environment.
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Affiliation(s)
- Devrani Mitra
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA
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28
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Chen QL, Chen HB, Cao ZX, Zhou ZH. Synthesis, spectral, and structural characterizations of imidazole oxalato molybdenum(IV/V/VI) complexes. Dalton Trans 2013; 42:1627-36. [PMID: 23143282 DOI: 10.1039/c2dt31566a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Substitutions of trans-Na(Him)[Mo(2)O(4)(ox)(2)(H(2)O)(2)]·H(2)O (1) and trans-(Him)(2)[Mo(2)O(4)(ox)(2)(H(2)O)(2)] (2) with imidazole result in the formation of the mixed-ligand molybdenum complexes cis-Na(2)[Mo(2)O(4)(ox)(2)(im)(2)]·4.5H(2)O (3), cis-K(2)[Mo(2)O(4)(ox)(2)(im)(2)]·3H(2)O (4), respectively (H(2)ox = oxalic acid; im = imidazole). Further reduction of cis-K(2)[Mo(2)O(4)(ox)(2)(im)(2)]·3H(2)O (4) gives a trinuclear molybdenum(IV) complex K(Him)[Mo(3)O(4)(ox)(3)(im)(3)]·3H(2)O (5), which contains an incomplete cubane cluster [Mo(IV)(3)O(4)](4+). Two novel trinuclear mixed-valence imidazole compounds [Mo(3)O(8)(im)(4)](im)·H(2)O (6) and [Mo(3)O(8)(im)(4)]·H(2)O (7) were obtained by the reduction of (Him)(4)[Mo(8)O(26)(im)(2)] (8). Both 6 and 7 contain a novel Mo(VI)O(4)(Mo(V)(2)O(4)) center, where the [Mo(V)(2)O(4)](2+) unit is linked by [Mo(VI)O(4)](2-) anion. The Mo-Mo bond distances in 1-7 decrease with the decrease of oxidation state of molybdenum. Solid and solution NMR spectra show that imidazole molybdenum compounds 6-8 fully dissociate in solution, where solvated imidazole and imidazolium groups in 6 and 8 could be served as internal references in their solid (13)C NMR spectra. Furthermore, mixed-ligand molybdenum species 3 and 4 are stable in water. Stabilities of 3 and 4 in solution may be attributed to the strong coordination of bidentate oxalate and the formation of hydrogen bond. Dimers 2 and 4 display quasi-reversible redox process, while trimer 6 is irreversible. Bond valence calculations for 1-8 are consistent with their oxidation states of molybdenum atoms. Calculation of the oxidation state in recent structure of iron molybdenum cofactor [MoFe(7)S(9)C(R-homocit)] (FeMo-co) is 3.318.
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Affiliation(s)
- Quan-Liang Chen
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
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29
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Lancaster KM, Hu Y, Bergmann U, Ribbe MW, DeBeer S. X-ray spectroscopic observation of an interstitial carbide in NifEN-bound FeMoco precursor. J Am Chem Soc 2013; 135:610-2. [PMID: 23276198 DOI: 10.1021/ja309254g] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The iron-molybdenum cofactor (FeMoco) of nitrogenase contains a biologically unprecedented μ(6)-coordinated C(4-) ion. Although the role of this interstitial atom in nitrogenase catalysis is unknown, progress in understanding its biosynthetic origins has been made. Here we report valence-to-core Fe Kβ X-ray emission spectroscopy data to show that this C(4-) ion is present in the Fe(8)S(9) "L-cluster," which is the immediate precursor to FeMoco prior to the insertion of molybdenum and coordination by homocitrate. These results accord with recent evidence supporting a role for the S-adenosylmethionine-dependent enzyme NifB in the incorporation of carbon into the FeMoco center of nitrogenase.
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Affiliation(s)
- Kyle M Lancaster
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
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30
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31
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Guo Y, Brecht E, Aznavour K, Nix JC, Xiao Y, Wang H, George SJ, Bau R, Keable S, Peters JW, Adams MWW, Jenney F, Sturhahn W, Alp EE, Zhao J, Yoda Y, Cramer SP. Nuclear resonance vibrational spectroscopy (NRVS) of rubredoxin and MoFe protein crystals. ACTA ACUST UNITED AC 2012; 222:77-90. [PMID: 26052177 DOI: 10.1007/s10751-012-0643-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We have applied 57Fe nuclear resonance vibrational spectroscopy (NRVS) for the first time to study the dynamics of Fe centers in Fe-S protein crystals, including oxidized wild type rubredoxin crystals from Pyrococcus furiosus, and the MoFe protein of nitrogenase from Azotobacter vinelandii. Thanks to the NRVS selection rule, selectively probed vibrational modes have been observed in both oriented rubredoxin and MoFe protein crystals. The NRVS work was complemented by extended X-ray absorption fine structure spectroscopy (EXAFS) measurements on oxidized wild type rubredoxin crystals from Pyrococcus furiosus. The EXAFS spectra revealed the Fe-S bond length difference in oxidized Pf Rd protein, which is qualitatively consistent with the X-ray crystal structure.
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Affiliation(s)
- Yisong Guo
- Department of Applied Science, University of California, Davis, CA 95616
| | - Eric Brecht
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717
| | - Kristen Aznavour
- Department of Chemistry, University of Southern California, Los Angeles, CA 90033
| | - Jay C Nix
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Yuming Xiao
- Department of Applied Science, University of California, Davis, CA 95616
| | - Hongxin Wang
- Department of Applied Science, University of California, Davis, CA 95616 ; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Simon J George
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Robert Bau
- Department of Chemistry, University of Southern California, Los Angeles, CA 90033
| | - Stephen Keable
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717
| | - John W Peters
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717
| | | | - Francis Jenney
- Georgia Campus, Philadelphia College of Osteopathic Medicine, Suwanee, GA 30024
| | - Wolfgang Sturhahn
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439
| | - Ercan E Alp
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439
| | - Jiyong Zhao
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439
| | - Yoshitaka Yoda
- JASRI, SPring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Stephen P Cramer
- Department of Applied Science, University of California, Davis, CA 95616 ; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 ; Department of Chemistry, University of California, Davis, CA 95616
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32
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Peters JW, Broderick JB. Emerging paradigms for complex iron-sulfur cofactor assembly and insertion. Annu Rev Biochem 2012; 81:429-50. [PMID: 22482905 DOI: 10.1146/annurev-biochem-052610-094911] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
[FeFe]-hydrogenses and molybdenum (Mo)-nitrogenase are evolutionarily unrelated enzymes with unique complex iron-sulfur cofactors at their active sites. The H cluster of [FeFe]-hydrogenases and the FeMo cofactor of Mo-nitrogenase require specific maturation machinery for their proper synthesis and insertion into the structural enzymes. Recent insights reveal striking similarities in the biosynthetic pathways of these complex cofactors. For both systems, simple iron-sulfur cluster precursors are modified on assembly scaffolds by the activity of radical S-adenosylmethionine (SAM) enzymes. Radical SAM enzymes are responsible for the synthesis and insertion of the unique nonprotein ligands presumed to be key structural determinants for their respective catalytic activities. Maturation culminates in the transfer of the intact cluster assemblies to a cofactor-less structural protein recipient. Required roles for nucleotide binding and hydrolysis have been implicated in both systems, but the specific role for these requirements remain unclear. In this review, we highlight the progress on [FeFe]-hydrogenase H cluster and nitrogenase FeMo-cofactor assembly in the context of these emerging paradigms.
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Affiliation(s)
- John W Peters
- Department of Chemistry and Biochemistry and the Astrobiology Biogeocatalysis Research Center, Montana State University, Bozeman, Montana 59717, USA.
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33
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George SJ, Barney BM, Mitra D, Igarashi RY, Guo Y, Dean DR, Cramer SP, Seefeldt LC. EXAFS and NRVS reveal a conformational distortion of the FeMo-cofactor in the MoFe nitrogenase propargyl alcohol complex. J Inorg Biochem 2012; 112:85-92. [PMID: 22564272 DOI: 10.1016/j.jinorgbio.2012.02.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2011] [Revised: 01/03/2012] [Accepted: 02/07/2012] [Indexed: 10/14/2022]
Abstract
We have used EXAFS and NRVS spectroscopies to examine the structural changes in the FeMo-cofactor active site of the α-70(Ala) variant of Azotobacter vinelandii nitrogenase on binding and reduction of propargyl alcohol (PA). The Mo K-edge near-edge and EXAFS spectra are very similar in the presence and absence of PA, suggesting PA does not bind at Mo. By contrast, Fe EXAFS spectra show a clear and reproducible change in the long Fe-Fe interaction at ~3.7 Å on PA binding with the apparent appearance of a new Fe-Fe interaction at 3.99 Å. An analogous change in the long Mo-Fe 5.1 Å interaction is not seen. The NRVS spectra exclude the possibility of large-scale structural change of the FeMo-cofactor involving breaking the μ(2) Fe-S-Fe bonds of the Fe(6)S(9)X core. The simplest chemically consistent structural change is that the bound form of PA is coordinated at Fe atoms (Fe6 or Fe7) adjacent to the Mo terminus, with a concomitant movement of the Fe away from the central atom X and along the Fe-X bond by about 0.35 Å. This study comprises the first experimental evidence of the conformational changes of the FeMo-cofactor active site on binding a substrate or product.
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Affiliation(s)
- Simon J George
- Department of Chemistry, University of California, Davis, CA 95616, USA.
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34
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Duffus BR, Hamilton TL, Shepard EM, Boyd ES, Peters JW, Broderick JB. Radical AdoMet enzymes in complex metal cluster biosynthesis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1824:1254-63. [PMID: 22269887 DOI: 10.1016/j.bbapap.2012.01.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Accepted: 01/01/2012] [Indexed: 10/14/2022]
Abstract
Radical S-adenosylmethionine (AdoMet) enzymes comprise a large superfamily of proteins that engage in a diverse series of biochemical transformations through generation of the highly reactive 5'-deoxyadenosyl radical intermediate. Recent advances into the biosynthesis of unique iron-sulfur (FeS)-containing cofactors such as the H-cluster in [FeFe]-hydrogenase, the FeMo-co in nitrogenase, as well as the iron-guanylylpyridinol (FeGP) cofactor in [Fe]-hydrogenase have implicated new roles for radical AdoMet enzymes in the biosynthesis of complex inorganic cofactors. Radical AdoMet enzymes in conjunction with scaffold proteins engage in modifying ubiquitous FeS precursors into unique clusters, through novel amino acid decomposition and sulfur insertion reactions. The ability of radical AdoMet enzymes to modify common metal centers to unusual metal cofactors may provide important clues into the stepwise evolution of these and other complex bioinorganic catalysts. This article is part of a Special Issue entitled: Radical SAM enzymes and Radical Enzymology.
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Affiliation(s)
- Benjamin R Duffus
- The Department of Chemistry and Biochemistry and the Astrobiology Biogeocatalysis Research Center, Montana State University, Bozeman, MT 59717, USA
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35
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Paulsen H, Trautwein AX, Wegner P, Schmidt C, Chumakov AI, Schünemann V. Interpretation of Nuclear Resonant Vibrational Spectra of Rubredoxin Using a Combined Quantum Mechanics and Molecular Mechanics Approach. Chemphyschem 2011; 12:3434-41. [DOI: 10.1002/cphc.201100595] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Indexed: 11/06/2022]
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36
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Fay AW, Blank MA, Lee CC, Hu Y, Hodgson KO, Hedman B, Ribbe MW. Spectroscopic characterization of the isolated iron-molybdenum cofactor (FeMoco) precursor from the protein NifEN. Angew Chem Int Ed Engl 2011; 50:7787-90. [PMID: 21726031 DOI: 10.1002/anie.201102724] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Indexed: 11/07/2022]
Affiliation(s)
- Aaron W Fay
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697, USA
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37
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Fay AW, Blank MA, Lee CC, Hu Y, Hodgson KO, Hedman B, Ribbe MW. Spectroscopic Characterization of the Isolated Iron-Molybdenum Cofactor (FeMoco) Precursor from the Protein NifEN. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201102724] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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38
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Biosynthesis of complex iron–sulfur enzymes. Curr Opin Chem Biol 2011; 15:319-27. [DOI: 10.1016/j.cbpa.2011.02.012] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2010] [Revised: 01/31/2011] [Accepted: 02/10/2011] [Indexed: 11/21/2022]
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39
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Martínez-Noël G, Curatti L, Hernandez JA, Rubio LM. NifB and NifEN protein levels are regulated by ClpX2 under nitrogen fixation conditions in Azotobacter vinelandii. Mol Microbiol 2011; 79:1182-93. [PMID: 21231969 PMCID: PMC3104958 DOI: 10.1111/j.1365-2958.2011.07540.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The major part of biological nitrogen fixation is catalysed by the molybdenum nitrogenase that carries at its active site the iron and molybdenum cofactor (FeMo-co). The nitrogen fixation (nif) genes required for the biosynthesis of FeMo-co are derepressed in the absence of a source of fixed nitrogen. The nifB gene product is remarkable because it assembles NifB-co, a complex cluster proposed to comprise a [6Fe-9S-X] cluster, from simpler [Fe-S] clusters common to other metabolic pathways. NifB-co is a common intermediate of the biosyntheses of the cofactors present in the molybdenum, vanadium and iron nitrogenases. In this work, the expression of the Azotobacter vinelandii nifB gene was uncoupled from its natural nif regulation to show that NifB protein levels are lower in cells growing diazotrophically than in cells growing at the expense of ammonium. A. vinelandii carries a duplicated copy of the ATPase component of the ubiquitous ClpXP protease (ClpX2), which is induced under nitrogen fixing conditions. Inactivation of clpX2 resulted in the accumulation of NifB and NifEN and a defect in diazotrophic growth, especially when iron was in short supply. Mutations in nifE, nifN and nifX or in nifA also affected NifB accumulation, suggesting that NifB susceptibility to degradation might vary during its catalytic cycle.
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Affiliation(s)
- Giselle Martínez-Noël
- Fundación IMDEA Energía, Centro de Biotecnología y Genómica de Plantas, Campus Montegancedo, Pozuelo de Alarcón 28223 Madrid, Spain
| | - Leonardo Curatti
- Centro de Investigaciones Biológicas, FIBA, Mar del Plata, Argentina and Centro de Estudios de Biodiversidad y Biotecnología de Mar del Plata, CONICET, Argentina
| | - Jose A. Hernandez
- Department of Biochemistry, AZCOM, Midwestern University, Glendale, AZ 85308, USA
| | - Luis M. Rubio
- Fundación IMDEA Energía, Centro de Biotecnología y Genómica de Plantas, Campus Montegancedo, Pozuelo de Alarcón 28223 Madrid, Spain
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40
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Abstract
X-ray absorption spectroscopy (XAS) involves the excitation of core electrons to bound states localized on the photoabsorber and the eventual excitation of the photoelectron to the continuum. The resulting spectra are typically divided into two regions: (1) the edge region which provides electronic structure information and (2) the extended X-ray absorption fine structure (EXAFS) region, which provides information about the distance, number, and type of ligands. Here, a basic introduction to XAS theory, the information that can be obtained, and the experimental consideration are presented. The application of XAS to biological systems and the impact this has had on nitrogenase research are briefly highlighted. New experimental advances are described.
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Affiliation(s)
- Serena Debeer
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.
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41
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Abstract
Nitrogenase is the enzyme responsible for biological reduction of dinitrogen (N(2)) to ammonia, a form usable for life. Playing a central role in the global biogeochemical nitrogen cycle, this enzyme has been the focus of intensive research for over 60 years. This chapter provides an overview of the features of nitrogenase as a background to the subsequent chapters of this volume that detail the many methods that have been applied in an attempt to gain a deeper understanding of this complex enzyme.
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Affiliation(s)
- Zhi-Yong Yang
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322, USA.
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42
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Hernandez JA, Phillips AH, Erbil WK, Zhao D, Demuez M, Zeymer C, Pelton JG, Wemmer DE, Rubio LM. A sterile alpha-motif domain in NafY targets apo-NifDK for iron-molybdenum cofactor delivery via a tethered domain. J Biol Chem 2010; 286:6321-8. [PMID: 21156797 DOI: 10.1074/jbc.m110.168732] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
NafY participates in the final steps of nitrogenase maturation, having a dual role as iron-molybdenum cofactor (FeMo-co) carrier and as chaperone to the FeMo-co-deficient apo-NifDK (apo-dinitrogenase). NafY contains an N-terminal domain of unknown function (n-NafY) and a C-terminal domain (core-NafY) necessary for FeMo-co binding. We show here that n-NafY and core-NafY have very weak interactions in intact NafY. The NMR structure of n-NafY reveals that it belongs to the sterile α-motif (SAM) family of domains, which are frequently involved in protein-protein interactions. The presence of a SAM domain in NafY was unexpected and could not be inferred from its amino acid sequence. Although SAM domains are very commonly found in eukaryotic proteins, they have rarely been identified in prokaryotes. The n-NafY SAM domain binds apo-NifDK. As opposed to full-length NafY, n-NafY impaired FeMo-co insertion when present in molar excess relative to FeMo-co and apo-NifDK. The implications of these observations are discussed to offer a plausible mechanism of FeMo-co insertion. NafY domain structure, molecular tumbling, and interdomain motion, as well as NafY interaction with apo-NifDK are consistent with the function of NafY in FeMo-co delivery to apo-NifDK.
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Affiliation(s)
- Jose A Hernandez
- Department of Biochemistry, Arizona College of Osteopathic Medicine, Midwestern University Arizona, Glendale, Arizona 85308, USA
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43
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Delfino I, Cerullo G, Cannistraro S, Manzoni C, Polli D, Dapper C, Newton WE, Guo Y, Cramer SP. Observation of terahertz vibrations in the nitrogenase FeMo cofactor by femtosecond pump-probe spectroscopy. Angew Chem Int Ed Engl 2010; 49:3912-5. [PMID: 20411554 PMCID: PMC3129498 DOI: 10.1002/anie.200906787] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We have used Impulsive Coherent Vibrational Spectroscopy (ICVS) to study the FeMo-cofactor of nitrogenase from Azotobacter vinelandii as the extracted small molecule ‘FeMoco’. In the ICVS experiment, a 15 fs visible laser pulse pumps the sample to an excited electronic state, and a second <10 fs pulse probes the change in transmission as a function of the time delay. FeMoco was observed to relax to the ground state by a single exponential decay with a time constant of ~200 fs. Superimposed on this relaxation are oscillations caused by the coherent excitation of vibrational modes in both excited and ground electronic states. Fourier transformation reveals the FeMoco vibrational frequencies that are coherently excited by the short laser pulse. The frequencies obtained by the ICVS technique were compared with values from normal mode calculations. The strongest ICVS bands are at 215 and 420 cm−1. The 420 cm−1 band is attributed to Fe-S stretching motion, whereas the 215 cm−1 band, which is the strongest feature in the spectrum, is attributed to a breathing mode of FeMoco. Over the years, nitrogenase and FeMoco have resisted characterization by resonance Raman spectroscopy. The current results demonstrate the promise of ICVS as an alternative probe of FeMoco dynamics.
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Affiliation(s)
- Ines Delfino
- Biophysics & Nanoscience Centre, CNISM, Facoltà di Scienze, Università della Tuscia, Largo dell’Università, I-01100 Viterbo, Italy
| | - Giulio Cerullo
- National Laboratory for Ultrafast and Ultraintense Optical Science-CNR-INFM, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Salvatore Cannistraro
- Biophysics & Nanoscience Centre, CNISM, Facoltà di Scienze, Università della Tuscia, Largo dell’Università, I-01100 Viterbo, Italy
| | - Cristian Manzoni
- National Laboratory for Ultrafast and Ultraintense Optical Science-CNR-INFM, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Dario Polli
- National Laboratory for Ultrafast and Ultraintense Optical Science-CNR-INFM, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Christie Dapper
- Department of Biochemistry, Virginia Polytechnic Institute & State University, Blacksburg, VA 24061
| | - William E. Newton
- Department of Biochemistry, Virginia Polytechnic Institute & State University, Blacksburg, VA 24061
| | - Yisong Guo
- Department of Applied Science, University of California, Davis, CA 95616
| | - Stephen P. Cramer
- Department of Applied Science, University of California, Davis, CA 95616
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
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44
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Delfino I, Cerullo G, Cannistraro S, Manzoni C, Polli D, Dapper C, Newton W, Guo Y, Cramer S. Observation of Terahertz Vibrations in the Nitrogenase FeMo Cofactor by Femtosecond Pump-Probe Spectroscopy. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200906787] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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45
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Substrate specificity and evolutionary implications of a NifDK enzyme carrying NifB-co at its active site. FEBS Lett 2010; 584:1487-92. [PMID: 20219465 DOI: 10.1016/j.febslet.2010.02.064] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2010] [Revised: 02/04/2010] [Accepted: 02/23/2010] [Indexed: 11/24/2022]
Abstract
The in vitro reconstitution of molybdenum nitrogenase was manipulated to generate a chimeric enzyme in which the active site iron-molybdenum cofactor (FeMo-co) is replaced by NifB-co. The NifDK/NifB-co enzyme was unable to reduce N(2) to NH(3), while exhibiting residual C(2)H(4) and considerable H(2) production activities. Production of H(2) by NifDK/NifB-co was stimulated by N(2) and was dependent on NifH and ATP hydrolysis. Thus, NifDK/NifB-co is a useful tool to gain insights into the catalytic mechanism of nitrogenase. Furthermore, phylogenetic analysis of D and K homologs indicates that several early emerging lineages, which contain NifB, NifH and NifDK encoding genes but which lack other genes required for processing NifB-co into FeMo-co, might encode an enzyme with similar catalytic properties to NifDK/NifB-co.
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46
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Applications of X-ray absorption spectroscopy to biologically relevant metal-based chemistry. Radiat Phys Chem Oxf Engl 1993 2010. [DOI: 10.1016/j.radphyschem.2009.03.072] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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47
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Hernandez JA, George SJ, Rubio LM. Molybdenum trafficking for nitrogen fixation. Biochemistry 2009; 48:9711-21. [PMID: 19772354 DOI: 10.1021/bi901217p] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The molybdenum nitrogenase is responsible for most biological nitrogen fixation, a prokaryotic metabolic process that determines the global biogeochemical cycles of nitrogen and carbon. Here we describe the trafficking of molybdenum for nitrogen fixation in the model diazotrophic bacterium Azotobacter vinelandii. The genes and proteins involved in molybdenum uptake, homeostasis, storage, regulation, and nitrogenase cofactor biosynthesis are reviewed. Molybdenum biochemistry in A. vinelandii reveals unexpected mechanisms and a new role for iron-sulfur clusters in the sequestration and delivery of molybdenum.
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Affiliation(s)
- Jose A Hernandez
- Department of Biochemistry, Midwestern University, Glendale, Arizona 85308, USA
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48
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Asthalter T, Rajagopalan S, Kauf T, Rabe V, Christoffers J. Monitoring Reaction Intermediates in the FeCl3-Catalyzed Michael Reaction by Nuclear Inelastic Scattering. J Phys Chem A 2008; 112:11514-8. [DOI: 10.1021/jp806878x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- T. Asthalter
- Institut für Physikalische Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany, Institut für Organische Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany, and Institut für Reine and Angewandte Chemie, Carl-von-Ossietzky-Universität Oldenburg, Carl-von-Ossietzky-Strasse 9-11, D-26111 Oldenburg, Germany
| | - S. Rajagopalan
- Institut für Physikalische Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany, Institut für Organische Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany, and Institut für Reine and Angewandte Chemie, Carl-von-Ossietzky-Universität Oldenburg, Carl-von-Ossietzky-Strasse 9-11, D-26111 Oldenburg, Germany
| | - Th. Kauf
- Institut für Physikalische Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany, Institut für Organische Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany, and Institut für Reine and Angewandte Chemie, Carl-von-Ossietzky-Universität Oldenburg, Carl-von-Ossietzky-Strasse 9-11, D-26111 Oldenburg, Germany
| | - V. Rabe
- Institut für Physikalische Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany, Institut für Organische Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany, and Institut für Reine and Angewandte Chemie, Carl-von-Ossietzky-Universität Oldenburg, Carl-von-Ossietzky-Strasse 9-11, D-26111 Oldenburg, Germany
| | - J. Christoffers
- Institut für Physikalische Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany, Institut für Organische Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany, and Institut für Reine and Angewandte Chemie, Carl-von-Ossietzky-Universität Oldenburg, Carl-von-Ossietzky-Strasse 9-11, D-26111 Oldenburg, Germany
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49
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Abstract
The iron-molybdenum cofactor (FeMo-co), located at the active site of the molybdenum nitrogenase, is one of the most complex metal cofactors known to date. During the past several years, an intensive effort has been made to purify the proteins involved in FeMo-co synthesis and incorporation into nitrogenase. This effort is starting to provide insights into the structures of the FeMo-co biosynthetic intermediates and into the biochemical details of FeMo-co synthesis.
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Affiliation(s)
- Luis M Rubio
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA.
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