101
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Grunenberg J. Der interstitiell gebundene Kohlenstoff der Nitrogenase ist deutlich stabiler als bisher angenommen. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701790] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jörg Grunenberg
- TU Braunschweig; Fakultät für Lebenswissenschaften; Institut für Organische Chemie; Abteilung Computerchemie; Hagenring 30 38106 Braunschweig Deutschland
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102
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Cluster assembly in nitrogenase. Essays Biochem 2017; 61:271-279. [DOI: 10.1042/ebc20160071] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 02/23/2017] [Accepted: 03/01/2017] [Indexed: 11/17/2022]
Abstract
The versatile enzyme system nitrogenase accomplishes the challenging reduction of N2and other substrates through the use of two main metalloclusters. For molybdenum nitrogenase, the catalytic component NifDK contains the [Fe8S7]-core P-cluster and a [MoFe7S9C-homocitrate] cofactor called the M-cluster. These chemically unprecedented metalloclusters play a critical role in the reduction of N2, and both originate from [Fe4S4] clusters produced by the actions of NifS and NifU. Maturation of P-cluster begins with a pair of these [Fe4S4] clusters on NifDK called the P*-cluster. An accessory protein NifZ aids in P-cluster fusion, and reductive coupling is facilitated by NifH in a stepwise manner to form P-cluster on each half of NifDK. For M-cluster biosynthesis, two [Fe4S4] clusters on NifB are coupled with a carbon atom in a radical-SAM dependent process, and concomitant addition of a ‘ninth’ sulfur atom generates the [Fe8S9C]-core L-cluster. On the scaffold protein NifEN, L-cluster is matured to M-cluster by the addition of Mo and homocitrate provided by NifH. Finally, matured M-cluster in NifEN is directly transferred to NifDK, where a conformational change locks the cofactor in place. Mechanistic insights into these fascinating biosynthetic processes are detailed in this chapter.
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103
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Eizawa A, Arashiba K, Tanaka H, Kuriyama S, Matsuo Y, Nakajima K, Yoshizawa K, Nishibayashi Y. Remarkable catalytic activity of dinitrogen-bridged dimolybdenum complexes bearing NHC-based PCP-pincer ligands toward nitrogen fixation. Nat Commun 2017; 8:14874. [PMID: 28374835 PMCID: PMC5382288 DOI: 10.1038/ncomms14874] [Citation(s) in RCA: 158] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 02/10/2017] [Indexed: 12/24/2022] Open
Abstract
Intensive efforts for the transformation of dinitrogen using transition metal-dinitrogen complexes as catalysts under mild reaction conditions have been made. However, limited systems have succeeded in the catalytic formation of ammonia. Here we show that newly designed and prepared dinitrogen-bridged dimolybdenum complexes bearing N-heterocyclic carbene- and phosphine-based PCP-pincer ligands [{Mo(N2)2(PCP)}2(μ-N2)] (1) work as so far the most effective catalysts towards the formation of ammonia from dinitrogen under ambient reaction conditions, where up to 230 equiv. of ammonia are produced based on the catalyst. DFT calculations on 1 reveal that the PCP-pincer ligand serves as not only a strong σ-donor but also a π-acceptor. These electronic properties are responsible for a solid connection between the molybdenum centre and the pincer ligand, leading to the enhanced catalytic activity for nitrogen fixation.
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Affiliation(s)
- Aya Eizawa
- Department of Systems Innovation, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Kazuya Arashiba
- Department of Systems Innovation, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Hiromasa Tanaka
- Institute for Materials Chemistry and Engineering, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
| | - Shogo Kuriyama
- Department of Systems Innovation, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yuki Matsuo
- Institute for Materials Chemistry and Engineering, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
| | - Kazunari Nakajima
- Department of Systems Innovation, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Kazunari Yoshizawa
- Institute for Materials Chemistry and Engineering, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
- Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Nishikyo-ku, Kyoto 615-8520, Japan
| | - Yoshiaki Nishibayashi
- Department of Systems Innovation, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
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104
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Wang D, Xu A, Elmerich C, Ma LZ. Biofilm formation enables free-living nitrogen-fixing rhizobacteria to fix nitrogen under aerobic conditions. ISME JOURNAL 2017; 11:1602-1613. [PMID: 28338674 DOI: 10.1038/ismej.2017.30] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 12/26/2016] [Accepted: 01/22/2017] [Indexed: 12/14/2022]
Abstract
The multicellular communities of microorganisms known as biofilms are of high significance in agricultural setting, yet it is largely unknown about the biofilm formed by nitrogen-fixing bacteria. Here we report the biofilm formation by Pseudomonas stutzeri A1501, a free-living rhizospheric bacterium, capable of fixing nitrogen under microaerobic and nitrogen-limiting conditions. P. stutzeri A1501 tended to form biofilm in minimal media, especially under nitrogen depletion condition. Under such growth condition, the biofilms formed at the air-liquid interface (termed as pellicles) and the colony biofilms on agar plates exhibited nitrogenase activity in air. The two kinds of biofilms both contained large ovoid shape 'cells' that were multiple living bacteria embedded in a sac of extracellular polymeric substances (EPSs). We proposed to name such large 'cells' as A1501 cyst. Our results suggest that the EPS, especially exopolysaccharides enabled the encased bacteria to fix nitrogen while grown under aerobic condition. The formation of A1501 cysts was reversible in response to the changes of carbon or nitrogen source status. A1501 cyst formation depended on nitrogen-limiting signaling and the presence of sufficient carbon sources, yet was independent of an active nitrogenase. The pellicles formed by Azospirillum brasilense, another free-living nitrogen-fixing rhizobacterium, which also exhibited nitrogenase activity and contained the large EPS-encapsuled A1501 cyst-like 'cells'. Our data imply that free-living nitrogen-fixing bacteria could convert the easy-used carbon sources to exopolysaccharides in order to enable nitrogen fixation in a natural aerobic environment.
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Affiliation(s)
- Di Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Anming Xu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | | | - Luyan Z Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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105
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Mulliez E, Duarte V, Arragain S, Fontecave M, Atta M. On the Role of Additional [4Fe-4S] Clusters with a Free Coordination Site in Radical-SAM Enzymes. Front Chem 2017; 5:17. [PMID: 28361051 PMCID: PMC5352715 DOI: 10.3389/fchem.2017.00017] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 03/03/2017] [Indexed: 11/13/2022] Open
Abstract
The canonical CysXXXCysXXCys motif is the hallmark of the Radical-SAM superfamily. This motif is responsible for the ligation of a [4Fe-4S] cluster containing a free coordination site available for SAM binding. The five enzymes MoaA, TYW1, MiaB, RimO and LipA contain in addition a second [4Fe-4S] cluster itself bound to three other cysteines and thus also displaying a potentially free coordination site. This review article summarizes recent important achievements obtained on these five enzymes with the main focus to delineate the role of this additional [4Fe-4S] cluster in catalysis.
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Affiliation(s)
- Etienne Mulliez
- Biosciences and Biotechnology Institute of Grenoble, Laboratoire de Chimie et Biologie des Métaux, UMR 5249 CEA-Centre National de la Recherche Scientifique-UGA Grenoble, France
| | - Victor Duarte
- Biosciences and Biotechnology Institute of Grenoble, Laboratoire de Chimie et Biologie des Métaux, UMR 5249 CEA-Centre National de la Recherche Scientifique-UGA Grenoble, France
| | - Simon Arragain
- Laboratoire de Chimie des Processus Biologiques, UMR 8229, Collége de France-Centre National de la Recherche Scientifique-Université P. et M. Curie Paris, France
| | - Marc Fontecave
- Biosciences and Biotechnology Institute of Grenoble, Laboratoire de Chimie et Biologie des Métaux, UMR 5249 CEA-Centre National de la Recherche Scientifique-UGAGrenoble, France; Laboratoire de Chimie des Processus Biologiques, UMR 8229, Collége de France-Centre National de la Recherche Scientifique-Université P. et M. CurieParis, France
| | - Mohamed Atta
- Biosciences and Biotechnology Institute of Grenoble, Laboratoire de Chimie et Biologie des Métaux, UMR 5249 CEA-Centre National de la Recherche Scientifique-UGA Grenoble, France
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106
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Burén S, Jiang X, López-Torrejón G, Echavarri-Erasun C, Rubio LM. Purification and In Vitro Activity of Mitochondria Targeted Nitrogenase Cofactor Maturase NifB. FRONTIERS IN PLANT SCIENCE 2017; 8:1567. [PMID: 28955359 PMCID: PMC5601070 DOI: 10.3389/fpls.2017.01567] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 08/28/2017] [Indexed: 05/13/2023]
Abstract
Active NifB is a milestone in the process of engineering nitrogen fixing plants. NifB is an extremely O2-sensitive S-adenosyl methionine (SAM)-radical enzyme that provides the key metal cluster intermediate (NifB-co) for the biosyntheses of the active-site cofactors of all three types of nitrogenases. NifB and NifB-co are unique to diazotrophic organisms. In this work, we have expressed synthetic codon-optimized versions of NifB from the γ-proteobacterium Azotobacter vinelandii and the thermophilic methanogen Methanocaldococcus infernus in Saccharomyces cerevisiae and in Nicotiana benthamiana. NifB proteins were targeted to the mitochondria, where O2 consumption is high and bacterial-like [Fe-S] cluster assembly operates. In yeast, NifB proteins were co-expressed with NifU, NifS, and FdxN proteins that are involved in NifB [Fe-S] cluster assembly and activity. The synthetic version of thermophilic NifB accumulated in soluble form within the yeast cell, while the A. vinelandii version appeared to form aggregates. Similarly, NifB from M. infernus was expressed at higher levels in leaves of Nicotiana benthamiana and accumulated as a soluble protein while A. vinelandii NifB was mainly associated with the non-soluble cell fraction. Soluble M. infernus NifB was purified from aerobically grown yeast and biochemically characterized. The purified protein was functional in the in vitro FeMo-co synthesis assay. This work presents the first active NifB protein purified from a eukaryotic cell, and highlights the importance of screening nif genes from different organisms in order to sort the best candidates to assemble a functional plant nitrogenase.
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107
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Holm RH, Lo W. Structural Conversions of Synthetic and Protein-Bound Iron–Sulfur Clusters. Chem Rev 2016; 116:13685-13713. [DOI: 10.1021/acs.chemrev.6b00276] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- R. H. Holm
- Department
of Chemistry and
Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Wayne Lo
- Department
of Chemistry and
Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
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108
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Reinholdt A, Vosch T, Bendix J. Modification of σ-Donor Properties of Terminal Carbide Ligands Investigated Through Carbide-Iodine Adduct Formation. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201606551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Anders Reinholdt
- Department of Chemistry; University of Copenhagen; Universitetsparken 5 2100 Copenhagen Denmark
| | - Tom Vosch
- Department of Chemistry; University of Copenhagen; Universitetsparken 5 2100 Copenhagen Denmark
| | - Jesper Bendix
- Department of Chemistry; University of Copenhagen; Universitetsparken 5 2100 Copenhagen Denmark
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109
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Reinholdt A, Vosch T, Bendix J. Modification of σ-Donor Properties of Terminal Carbide Ligands Investigated Through Carbide-Iodine Adduct Formation. Angew Chem Int Ed Engl 2016; 55:12484-7. [DOI: 10.1002/anie.201606551] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Anders Reinholdt
- Department of Chemistry; University of Copenhagen; Universitetsparken 5 2100 Copenhagen Denmark
| | - Tom Vosch
- Department of Chemistry; University of Copenhagen; Universitetsparken 5 2100 Copenhagen Denmark
| | - Jesper Bendix
- Department of Chemistry; University of Copenhagen; Universitetsparken 5 2100 Copenhagen Denmark
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110
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Katz FEH, Owens CP, Tezcan FA. Electron Transfer Reactions in Biological Nitrogen Fixation. Isr J Chem 2016. [DOI: 10.1002/ijch.201600020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Faith E. H. Katz
- Department of Chemistry and Biochemistry; University of California, San Diego; 9500 Gilman Drive San Diego CA 92093 USA
| | - Cedric P. Owens
- Department of Chemistry and Biochemistry; University of California, San Diego; 9500 Gilman Drive San Diego CA 92093 USA
| | - F. A. Tezcan
- Department of Chemistry and Biochemistry; University of California, San Diego; 9500 Gilman Drive San Diego CA 92093 USA
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111
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Čorić I, Holland PL. Insight into the Iron-Molybdenum Cofactor of Nitrogenase from Synthetic Iron Complexes with Sulfur, Carbon, and Hydride Ligands. J Am Chem Soc 2016; 138:7200-11. [PMID: 27171599 PMCID: PMC5508211 DOI: 10.1021/jacs.6b00747] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Nitrogenase enzymes are used by microorganisms for converting atmospheric N2 to ammonia, which provides an essential source of N atoms for higher organisms. The active site of the molybdenum-dependent nitrogenase is the unique carbide-containing iron-sulfur cluster called the iron-molybdenum cofactor (FeMoco). On the FeMoco, N2 binding is suggested to occur at one or more iron atoms, but the structures of the catalytic intermediates are not clear. In order to establish the feasibility of different potential mechanistic steps during biological N2 reduction, chemists have prepared iron complexes that mimic various structural aspects of the iron sites in the FeMoco. This reductionist approach gives mechanistic insight, and also uncovers fundamental principles that could be used more broadly for small-molecule activation. Here, we discuss recent results and highlight directions for future research. In one direction, synthetic iron complexes have now been shown to bind N2, break the N-N triple bond, and produce ammonia catalytically. Carbon- and sulfur-based donors have been incorporated into the ligand spheres of Fe-N2 complexes to show how these atoms may influence the structure and reactivity of the FeMoco. Hydrides have been incorporated into synthetic systems, which can bind N2, reduce some nitrogenase substrates, and/or reductively eliminate H2 to generate reduced iron centers. Though some carbide-containing iron clusters are known, none yet have sulfide bridges or high-spin iron atoms like the FeMoco.
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Affiliation(s)
- Ilija Čorić
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Patrick L. Holland
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
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112
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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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113
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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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114
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Affiliation(s)
- Yilin Hu
- Department of Molecular Biology and Biochemistry;, Department of Chemistry University of California, Irvine Irvine CA 92697-3900 USA
| | - Markus W. Ribbe
- Department of Molecular Biology and Biochemistry;, Department of Chemistry University of California, Irvine Irvine CA 92697-3900 USA
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115
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Abstract
Named after its ability to catalyze the reduction of nitrogen to ammonia, nitrogenase has a surprising rapport with carbon-both through the interstitial carbide that resides in the central cavity of its cofactor and through its ability to catalyze the reductive carbon-carbon coupling of small carbon compounds into hydrocarbon products. Recently, a radical-SAM-dependent pathway was revealed for the insertion of carbide, which signifies a novel biosynthetic route to complex bridged metalloclusters. Moreover, a sulfur-displacement mechanism was proposed for the activation of carbon monoxide by nitrogenase, which suggests an essential role of the interstitial carbide in maintaining the stability while permitting a certain flexibility of the cofactor structure during substrate turnover.
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Affiliation(s)
- Yilin Hu
- Department of Molecular Biology and Biochemistry, Department of Chemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA.
| | - Markus W Ribbe
- Department of Molecular Biology and Biochemistry, Department of Chemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA.
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116
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Nitrogenase FeMoco investigated by spatially resolved anomalous dispersion refinement. Nat Commun 2016; 7:10902. [PMID: 26973151 PMCID: PMC4793075 DOI: 10.1038/ncomms10902] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 01/31/2016] [Indexed: 02/06/2023] Open
Abstract
The [Mo:7Fe:9S:C] iron-molybdenum cofactor (FeMoco) of nitrogenase is the largest known metal cluster and catalyses the 6-electron reduction of dinitrogen to ammonium in biological nitrogen fixation. Only recently its atomic structure was clarified, while its reactivity and electronic structure remain under debate. Here we show that for its resting S=3/2 state the common iron oxidation state assignments must be reconsidered. By a spatially resolved refinement of the anomalous scattering contributions of the 7 Fe atoms of FeMoco, we conclude that three irons (Fe1/3/7) are more reduced than the other four (Fe2/4/5/6). Our data are in agreement with the recently revised oxidation state assignment for the molybdenum ion, providing the first spatially resolved picture of the resting-state electron distribution within FeMoco. This might provide the long-sought experimental basis for a generally accepted theoretical description of the cluster that is in line with available spectroscopic and functional data. The [Mo:7Fe:9S:C] iron-molybdenum cofactor (FeMoco) of nitrogenase is a large metal cluster with an important role in biological nitrogen fixation. Here, the authors use spatially resolved refinement of the anomalous scattering contributions of the iron atoms to determine the resting-state electron distribution of FeMoco.
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117
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Hu Y, Ribbe MW. Maturation of nitrogenase cofactor-the role of a class E radical SAM methyltransferase NifB. Curr Opin Chem Biol 2016; 31:188-94. [PMID: 26969410 DOI: 10.1016/j.cbpa.2016.02.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 02/23/2016] [Accepted: 02/24/2016] [Indexed: 10/22/2022]
Abstract
Nitrogenase catalyzes the important reactions of N2-reduction, CO-reduction and CO2-reduction at its active cofactor site. Designated the M-cluster, this complex metallocofactor is assembled through the generation of a characteristic 8Fe-core before the insertion of Mo and homocitrate that completes the stoichiometry of the M-cluster. NifB catalyzes the crucial step of radical SAM-dependent carbide insertion that occurs concomitant with the insertion a '9th' sulfur and the rearrangement/coupling of two 4Fe-clusters into a complete 8Fe-core of the M-cluster. Further categorization of a family of NifB proteins as a new class of radical SAM methyltransferases suggests a general function of these proteins in complex metallocofactor assembly and provides a new platform for unveiling unprecedented chemical reactions catalyzed by biological systems.
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Affiliation(s)
- Yilin Hu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, United States.
| | - Markus W Ribbe
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, United States; Department of Chemistry, University of California, Irvine, CA 92697-2025, United States.
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118
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Rao L, Xu X, Adamo C. Theoretical Investigation on the Role of the Central Carbon Atom and Close Protein Environment on the Nitrogen Reduction in Mo Nitrogenase. ACS Catal 2016. [DOI: 10.1021/acscatal.5b02577] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Li Rao
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Xin Xu
- Shanghai
Key Laboratory of Molecular Catalysis and Innovative Materials, MOE
Laboratory for Computational Physical Science, Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Carlo Adamo
- Chimie ParisTech,
PSL Research University, CNRS, Institut de Recherche de Chimie Paris
(IRCP), F-75005 Paris, France
- Institut Universitaire de France, 103 Boulevard Saint Michel, F-75005 Paris, France
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119
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Application of 93Nb NMR spectroscopy to (silox)3Nb(Xn/Lm) complexes (silox =tBu3SiO): Where does (silox)3Nb(NN)Nb(silox)3 appear? Polyhedron 2016. [DOI: 10.1016/j.poly.2015.10.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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120
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Walter M. Recent Advances in Transition Metal-Catalyzed Dinitrogen Activation. ADVANCES IN ORGANOMETALLIC CHEMISTRY 2016. [DOI: 10.1016/bs.adomc.2016.03.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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121
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Reinholdt A, Herbst K, Bendix J. Delivering carbide ligands to sulfide-rich clusters. Chem Commun (Camb) 2016; 52:2015-8. [DOI: 10.1039/c5cc08918b] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The propensity of the terminal ruthenium carbide Ru(C)Cl2(PCy3)2 (RuC) to form carbide bridges to electron-rich transition metals enables synthetic routes to metal clusters with coexisting carbide and sulfide ligands.
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Affiliation(s)
- Anders Reinholdt
- Department of Chemistry
- University of Copenhagen
- DK-2100 Copenhagen
- Denmark
| | | | - Jesper Bendix
- Department of Chemistry
- University of Copenhagen
- DK-2100 Copenhagen
- Denmark
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122
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Burger EM, Andrade SLA, Einsle O. Active sites without restraints: high-resolution analysis of metal cofactors. Curr Opin Struct Biol 2015; 35:32-40. [DOI: 10.1016/j.sbi.2015.07.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 07/24/2015] [Accepted: 07/31/2015] [Indexed: 11/29/2022]
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123
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Identification and characterization of functional homologs of nitrogenase cofactor biosynthesis protein NifB from methanogens. Proc Natl Acad Sci U S A 2015; 112:14829-33. [PMID: 26627238 DOI: 10.1073/pnas.1510409112] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nitrogenase biosynthesis protein NifB catalyzes the radical S-adenosyl-L-methionine (SAM)-dependent insertion of carbide into the M cluster, the cofactor of the molybdenum nitrogenase from Azotobacter vinelandii. Here, we report the identification and characterization of two naturally "truncated" homologs of NifB from Methanosarcina acetivorans (NifB(Ma)) and Methanobacterium thermoautotrophicum (NifB(Mt)), which contain a SAM-binding domain at the N terminus but lack a domain toward the C terminus that shares homology with NifX, an accessory protein in M cluster biosynthesis. NifB(Ma) and NifB(Mt) are monomeric proteins containing a SAM-binding [Fe4S4] cluster (designated the SAM cluster) and a [Fe4S4]-like cluster pair (designated the K cluster) that can be processed into an [Fe8S9] precursor to the M cluster (designated the L cluster). Further, the K clusters in NifB(Ma) and NifB(Mt) can be converted to L clusters upon addition of SAM, which corresponds to their ability to heterologously donate L clusters to the biosynthetic machinery of A. vinelandii for further maturation into the M clusters. Perhaps even more excitingly, NifB(Ma) and NifB(Mt) can catalyze the removal of methyl group from SAM and the abstraction of hydrogen from this methyl group by 5'-deoxyadenosyl radical that initiates the radical-based incorporation of methyl-derived carbide into the M cluster. The successful identification of NifB(Ma) and NifB(Mt) as functional homologs of NifB not only enabled classification of a new subset of radical SAM methyltransferases that specialize in complex metallocluster assembly, but also provided a new tool for further characterization of the distinctive, NifB-catalyzed methyl transfer and conversion to an iron-bound carbide.
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Rees JA, Bjornsson R, Schlesier J, Sippel D, Einsle O, DeBeer S. The Fe-V Cofactor of Vanadium Nitrogenase Contains an Interstitial Carbon Atom. Angew Chem Int Ed Engl 2015; 54:13249-52. [PMID: 26376620 PMCID: PMC4675075 DOI: 10.1002/anie.201505930] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Revised: 08/05/2015] [Indexed: 11/06/2022]
Abstract
The first direct evidence is provided for the presence of an interstitial carbide in the Fe-V cofactor of Azotobacter vinelandii vanadium nitrogenase. As for our identification of the central carbide in the Fe-Mo cofactor, we employed Fe Kβ valence-to-core X-ray emission spectroscopy and density functional theory calculations, and herein report the highly similar spectra of both variants of the cofactor-containing protein. The identification of an analogous carbide, and thus an atomically homologous active site in vanadium nitrogenase, highlights the importance and influence of both the interstitial carbide and the identity of the heteroatom on the electronic structure and catalytic activity of the enzyme.
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Affiliation(s)
- Julian A Rees
- Department of Molecular Theory and Spectroscopy, Max-Planck-Institut für Chemische EnergiekonversionStiftstrasse 34–36, 45470 Mülheim an der Ruhr (Germany) E-mail:
- Department of Chemistry, University of WashingtonBox 351700, Seattle, WA 98195-1700 (USA)
| | - Ragnar Bjornsson
- Department of Molecular Theory and Spectroscopy, Max-Planck-Institut für Chemische EnergiekonversionStiftstrasse 34–36, 45470 Mülheim an der Ruhr (Germany) E-mail:
| | - Julia Schlesier
- Institut für Biochemie and BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-Universität FreiburgAlbertstrasse 21, 79104 Freiburg (Germany)
| | - Daniel Sippel
- Institut für Biochemie and BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-Universität FreiburgAlbertstrasse 21, 79104 Freiburg (Germany)
| | - Oliver Einsle
- Institut für Biochemie and BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-Universität FreiburgAlbertstrasse 21, 79104 Freiburg (Germany)
| | - Serena DeBeer
- Department of Molecular Theory and Spectroscopy, Max-Planck-Institut für Chemische EnergiekonversionStiftstrasse 34–36, 45470 Mülheim an der Ruhr (Germany) E-mail:
- Department of Chemistry and Chemical Biology, Cornell UniversityIthaca, NY 14853 (USA)
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125
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Tanifuji K, Lee CC, Ohki Y, Tatsumi K, Hu Y, Ribbe MW. Combining a Nitrogenase Scaffold and a Synthetic Compound into an Artificial Enzyme. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201507646] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Kazuki Tanifuji
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697‐3900 (USA)
| | - Chi Chung Lee
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697‐3900 (USA)
| | - Yasuhiro Ohki
- Department of Chemistry, Graduate School of Science and Research Center for Materials Science, Nagoya University, Furo‐cho, Chikusa‐ku, Nagoya 464‐8602 (Japan)
| | - Kazuyuki Tatsumi
- Department of Chemistry, Graduate School of Science and Research Center for Materials Science, Nagoya University, Furo‐cho, Chikusa‐ku, Nagoya 464‐8602 (Japan)
| | - Yilin Hu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697‐3900 (USA)
| | - Markus W. Ribbe
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697‐3900 (USA)
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697‐2025 (USA)
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126
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Tanifuji K, Lee CC, Ohki Y, Tatsumi K, Hu Y, Ribbe MW. Combining a Nitrogenase Scaffold and a Synthetic Compound into an Artificial Enzyme. Angew Chem Int Ed Engl 2015; 54:14022-5. [PMID: 26473503 DOI: 10.1002/anie.201507646] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Revised: 09/21/2015] [Indexed: 11/06/2022]
Abstract
Nitrogenase catalyzes substrate reduction at its cofactor center ([(Cit)MoFe7S9C](n-); designated M-cluster). Here, we report the formation of an artificial, nitrogenase-mimicking enzyme upon insertion of a synthetic model complex ([Fe6S9(SEt)2](4-); designated Fe6(RHH)) into the catalytic component of nitrogenase (designated NifDK(apo)). Two Fe6(RHH) clusters were inserted into NifDK(apo), rendering the conformation of the resultant protein (designated NifDK(Fe)) similar to the one upon insertion of native M-clusters. NifDK(Fe) can work together with the reductase component of nitrogenase to reduce C2H2 in an ATP-dependent reaction. It can also act as an enzyme on its own in the presence of Eu(II)DTPA, displaying a strong activity in C2H2 reduction while demonstrating an ability to reduce CN(-) to C1-C3 hydrocarbons in an ATP-independent manner. The successful outcome of this work provides the proof of concept and underlying principles for continued search of novel enzymatic activities based on this approach.
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Affiliation(s)
- Kazuki Tanifuji
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697-3900 (USA)
| | - Chi Chung Lee
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697-3900 (USA)
| | - Yasuhiro Ohki
- Department of Chemistry, Graduate School of Science and Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602 (Japan)
| | - Kazuyuki Tatsumi
- Department of Chemistry, Graduate School of Science and Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602 (Japan)
| | - Yilin Hu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697-3900 (USA).
| | - Markus W Ribbe
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697-3900 (USA). .,Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025 (USA).
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127
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Perche-Letuvée P, Molle T, Forouhar F, Mulliez E, Atta M. Wybutosine biosynthesis: structural and mechanistic overview. RNA Biol 2015; 11:1508-18. [PMID: 25629788 DOI: 10.4161/15476286.2014.992271] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Over the last 10 years, significant progress has been made in understanding the genetics, enzymology and structural components of the wybutosine (yW) biosynthetic pathway. These studies have played a key role in expanding our understanding of yW biosynthesis and have revealed unexpected evolutionary ties, which are presently being unraveled. The enzymes catalyzing the 5 steps of this pathway, from genetically encoded guanosine to wybutosine base, provide an ensemble of amazing reaction mechanisms that are to be discussed in this review article.
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128
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Morsing TJ, Reinholdt A, Sauer SPA, Bendix J. Ligand Sphere Conversions in Terminal Carbide Complexes. Organometallics 2015. [DOI: 10.1021/acs.organomet.5b00803] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Thorbjørn J. Morsing
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 København Ø, Denmark
| | - Anders Reinholdt
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 København Ø, Denmark
| | - Stephan P. A. Sauer
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 København Ø, Denmark
| | - Jesper Bendix
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 København Ø, Denmark
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129
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Costa Pessoa J, Garribba E, Santos MF, Santos-Silva T. Vanadium and proteins: Uptake, transport, structure, activity and function. Coord Chem Rev 2015. [DOI: 10.1016/j.ccr.2015.03.016] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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130
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Čorić I, Mercado BQ, Bill E, Vinyard DJ, Holland PL. Binding of dinitrogen to an iron-sulfur-carbon site. Nature 2015; 526:96-9. [PMID: 26416755 PMCID: PMC4592811 DOI: 10.1038/nature15246] [Citation(s) in RCA: 143] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 07/24/2015] [Indexed: 01/25/2023]
Abstract
Nitrogenases are the enzymes by which certain microorganisms convert atmospheric dinitrogen (N2) to ammonia, thereby providing essential nitrogen atoms for higher organisms. The most common nitrogenases reduce atmospheric N2 at the FeMo cofactor, a sulfur-rich iron-molybdenum cluster (FeMoco). The central iron sites that are coordinated to sulfur and carbon atoms in FeMoco have been proposed to be the substrate binding sites, on the basis of kinetic and spectroscopic studies. In the resting state, the central iron sites each have bonds to three sulfur atoms and one carbon atom. Addition of electrons to the resting state causes the FeMoco to react with N2, but the geometry and bonding environment of N2-bound species remain unknown. Here we describe a synthetic complex with a sulfur-rich coordination sphere that, upon reduction, breaks an Fe-S bond and binds N2. The product is the first synthetic Fe-N2 complex in which iron has bonds to sulfur and carbon atoms, providing a model for N2 coordination in the FeMoco. Our results demonstrate that breaking an Fe-S bond is a chemically reasonable route to N2 binding in the FeMoco, and show structural and spectroscopic details for weakened N2 on a sulfur-rich iron site.
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Affiliation(s)
- Ilija Čorić
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA
| | - Brandon Q Mercado
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA
| | - Eckhard Bill
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - David J Vinyard
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA
| | - Patrick L Holland
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA
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131
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Rees JA, Bjornsson R, Schlesier J, Sippel D, Einsle O, DeBeer S. The Fe–V Cofactor of Vanadium Nitrogenase Contains an Interstitial Carbon Atom. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201505930] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Julian A. Rees
- Department of Molecular Theory and Spectroscopy, Max‐Planck‐Institut für Chemische Energiekonversion, Stiftstrasse 34–36, 45470 Mülheim an der Ruhr (Germany)
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA 98195‐1700 (USA)
| | - Ragnar Bjornsson
- Department of Molecular Theory and Spectroscopy, Max‐Planck‐Institut für Chemische Energiekonversion, Stiftstrasse 34–36, 45470 Mülheim an der Ruhr (Germany)
- Present address: Science Institute, University of Iceland, Dunhaga 3, 107 Reykjavik (Iceland)
| | - Julia Schlesier
- Institut für Biochemie and BIOSS Centre for Biological Signalling Studies, Albert‐Ludwigs‐Universität Freiburg, Albertstrasse 21, 79104 Freiburg (Germany)
| | - Daniel Sippel
- Institut für Biochemie and BIOSS Centre for Biological Signalling Studies, Albert‐Ludwigs‐Universität Freiburg, Albertstrasse 21, 79104 Freiburg (Germany)
| | - Oliver Einsle
- Institut für Biochemie and BIOSS Centre for Biological Signalling Studies, Albert‐Ludwigs‐Universität Freiburg, Albertstrasse 21, 79104 Freiburg (Germany)
| | - Serena DeBeer
- Department of Molecular Theory and Spectroscopy, Max‐Planck‐Institut für Chemische Energiekonversion, Stiftstrasse 34–36, 45470 Mülheim an der Ruhr (Germany)
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853 (USA)
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132
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Refining the pathway of carbide insertion into the nitrogenase M-cluster. Nat Commun 2015; 6:8034. [PMID: 26259825 PMCID: PMC4535184 DOI: 10.1038/ncomms9034] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 07/08/2015] [Indexed: 11/19/2022] Open
Abstract
Carbide insertion plays a pivotal role in the biosynthesis of M-cluster, the cofactor of nitrogenase. Previously, we proposed a carbide insertion pathway involving methyltransfer from SAM to a FeS precursor and hydrogen abstraction from this methyl group that initiates the radical-based precursor maturation. Here we demonstrate that the methyl group is transferred to a precursor-associated sulfur before hydrogen abstraction, thereby refining the initial steps of the carbide insertion pathway. Carbide insertion plays a pivotal role in the biosynthesis of M-cluster, the cofactor of nitrogenase. Here the authors further define the pathway for interstitial carbide atom insertion, showing that the SAM-derived methyl group is transferred to a FeS precursor sulfur before hydrogen abstraction via an SN2-type reaction.
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133
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Abstract
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The iron–molybdenum cofactor of nitrogenase has unprecedented
coordination chemistry, including a high-spin iron cluster called
the iron-molybdenum cofactor (FeMoco). Thus, understanding the mechanism
of nitrogenase challenges coordination chemists to understand the
fundamental N2 chemistry of high-spin iron sites. This
Account summarizes a series of studies in which we have synthesized
a number of new compounds with multiple iron atoms, characterized
them using crystallography and spectroscopy, and studied their reactions
in detail. These studies show that formally iron(I) and iron(0) complexes
with three- and four-coordinate metal atoms have the ability to weaken
and break the triple bond of N2. These reactions occur
at or below room temperature, indicating that they are kinetically
facile. This in turn implies that iron sites in the FeMoco are chemically
reasonable locations for N2 binding and reduction. The careful evaluation of these compounds and their reaction pathways
has taught important lessons about what characteristics make iron
more effective for N2 activation. Cooperation of two iron
atoms can lengthen and weaken the N–N bond, while three working
together enables iron atoms to completely cleave the N–N bond
to nitrides. Alkali metals (typically introduced into the reaction
as part of the reducing agent) are thermodynamically useful because
the alkali metal cations stabilize highly reduced complexes, pull
electron density into the N2 unit, and make reduced nitride
products more stable. Alkali metals can also play a kinetic role,
because cation−π interactions with the supporting ligands
can hold iron atoms near enough to one another to facilitate the cooperation
of multiple iron atoms. Many of these principles may also be relevant
to the iron-catalyzed Haber–Bosch process, at which collections
of iron atoms (often promoted by the addition of alkali metals) break
the N–N bond of N2. The results of these studies
teach more general lessons as well.
They have demonstrated that N2 can be a redox-active ligand,
accepting spin and electron density in complexes of N22–. They have shown the power of cooperation between
multiple transition metals, and also between alkali metals and transition
metals. Finally, alkali metal based cation−π interactions
have the potential to be broadly useful for bringing metals close
together with sufficient flexibility to allow multistep, multielectron
reactions. At the same time, the positive charge on the alkali metal
cation stabilizes charge buildup in intermediates.
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Affiliation(s)
- Sean F. McWilliams
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Patrick L. Holland
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
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134
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Sparr C. Scientific Fireworks to Celebrate the 50th Anniversary of the Bürgenstock Conference. Angew Chem Int Ed Engl 2015; 54:8594-6. [DOI: 10.1002/anie.201504945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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135
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Sparr C. Ein wissenschaftliches Feuerwerk zur Feier von 50 Jahren Bürgenstock-Konferenz. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201504945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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136
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Reinholdt A, Vibenholt JE, Morsing TJ, Schau-Magnussen M, Reeler NEA, Bendix J. Carbide complexes as π-acceptor ligands. Chem Sci 2015; 6:5815-5823. [PMID: 29861908 PMCID: PMC5950194 DOI: 10.1039/c5sc02077h] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 07/06/2015] [Indexed: 11/25/2022] Open
Abstract
A terminal carbide complex binds as a π-acceptor towards electron-rich metal centers, mirroring CO, and provides the first homoleptic, carbide-ligated complex.
The π-accepting character of a terminal carbide complex acting as a ligand is demonstrated experimentally and corroborates earlier theoretical predictions. As a result, coordination of a terminal ruthenium carbide complex to electron-rich metal centres is shown to provide a facile and versatile route to carbide-bridged heterometallic complexes. Synthesis, reactivity, spectroscopic and structural characterization are reported for heterobimetallic systems with auxiliary metals from groups 9–11: Rh(i), Ir(i), Pd(ii), Pt(ii), Ag(i), and Au(i) coordinated by [Ru(C)Cl2(PCy3)2] (RuC). This encompasses the first example of a homoleptic carbide-ligated transition metal complex: [{(Cy3P)2Cl2RuC}2Au]+. Kinetics of substitution on Pt(ii) by RuC ranks the carbide complex as having intermediate nucleophilicity. The 13C-NMR signals from the carbide ligands are significantly more shielded in the bridged heterobimetallic complexes than in the parent terminal carbide complex. Structurally, RuC forms very shorts bonds to the heterometals, which supports the notion of the multiple bonded complex acting as a π-backbonding ligand. Reactions are reported where RuC displaces CO coordinated to Rh(i) and Ir(i). A strong trans influence exerted by RuC indicates it to be a stronger σ-donor than CO. The geometries around the carbide bridges resemble those in complexes of electron-rich metals with carbonyl or bridging nitride-complex-derived ligands, which establishes a link to other strong π-acceptor ligands.
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Affiliation(s)
- Anders Reinholdt
- Department of Chemistry , University of Copenhagen , Universitetsparken 5 , DK-2100 , Denmark . ; Tel: +45 35320101
| | - Johan E Vibenholt
- Department of Chemistry , University of Copenhagen , Universitetsparken 5 , DK-2100 , Denmark . ; Tel: +45 35320101
| | - Thorbjørn J Morsing
- Department of Chemistry , University of Copenhagen , Universitetsparken 5 , DK-2100 , Denmark . ; Tel: +45 35320101
| | - Magnus Schau-Magnussen
- Department of Chemistry , University of Copenhagen , Universitetsparken 5 , DK-2100 , Denmark . ; Tel: +45 35320101
| | - Nini E A Reeler
- Department of Chemistry , University of Copenhagen , Universitetsparken 5 , DK-2100 , Denmark . ; Tel: +45 35320101
| | - Jesper Bendix
- Department of Chemistry , University of Copenhagen , Universitetsparken 5 , DK-2100 , Denmark . ; Tel: +45 35320101
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137
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Kuriyama S, Arashiba K, Nakajima K, Tanaka H, Yoshizawa K, Nishibayashi Y. Nitrogen fixation catalyzed by ferrocene-substituted dinitrogen-bridged dimolybdenum-dinitrogen complexes: unique behavior of ferrocene moiety as redox active site. Chem Sci 2015; 6:3940-3951. [PMID: 29218165 PMCID: PMC5707465 DOI: 10.1039/c5sc00545k] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 04/17/2015] [Indexed: 11/22/2022] Open
Abstract
A series of dinitrogen-bridged dimolybdenum-dinitrogen complexes bearing metallocene-substituted PNP-pincer ligands is synthesized by the reduction of the corresponding monomeric molybdenum-trichloride complexes under 1 atm of molecular dinitrogen. Introduction of ferrocene as a redox-active moiety to the pyridine ring of the PNP-pincer ligand increases the catalytic activity for the formation of ammonia from molecular dinitrogen, up to 45 equiv. of ammonia being formed based on the catalyst (22 equiv. of ammonia based on each molybdenum atom of the catalyst). The time profile for the catalytic reaction reveals that the presence of the ferrocene unit in the catalyst increases the rate of ammonia formation. Electrochemical measurement and theoretical studies indicate that an interaction between the Fe atom of the ferrocene moiety and the Mo atom in the catalyst may play an important role to achieve a high catalytic activity.
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Affiliation(s)
- Shogo Kuriyama
- Institute of Engineering Innovation , School of Engineering , The University of Tokyo , Yayoi, Bunkyo-ku , Tokyo 113-8656 , Japan .
| | - Kazuya Arashiba
- Institute of Engineering Innovation , School of Engineering , The University of Tokyo , Yayoi, Bunkyo-ku , Tokyo 113-8656 , Japan .
| | - Kazunari Nakajima
- Institute of Engineering Innovation , School of Engineering , The University of Tokyo , Yayoi, Bunkyo-ku , Tokyo 113-8656 , Japan .
| | - Hiromasa Tanaka
- Elements Strategy Initiative for Catalysts and Batteries (ESICB) , Kyoto University , Nishikyo-ku , Kyoto 615-8520 , Japan
| | - Kazunari Yoshizawa
- Elements Strategy Initiative for Catalysts and Batteries (ESICB) , Kyoto University , Nishikyo-ku , Kyoto 615-8520 , Japan
- Institute for Materials Chemistry and Engineering and International Research Center for Molecular System , Kyushu University , Nishi-ku , Fukuoka 819-0395 , Japan .
| | - Yoshiaki Nishibayashi
- Institute of Engineering Innovation , School of Engineering , The University of Tokyo , Yayoi, Bunkyo-ku , Tokyo 113-8656 , Japan .
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138
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Nishibayashi Y. Recent progress in transition-metal-catalyzed reduction of molecular dinitrogen under ambient reaction conditions. Inorg Chem 2015; 54:9234-47. [PMID: 26131967 DOI: 10.1021/acs.inorgchem.5b00881] [Citation(s) in RCA: 154] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
This paper describes our recent progress in catalytic nitrogen fixation by using transition-metal-dinitrogen complexes as catalysts. Two reaction systems for the catalytic transformation of molecular dinitrogen into ammonia and its equivalent such as silylamine under ambient reaction conditions have been achieved by the molybdenum-, iron-, and cobalt-dinitrogen complexes as catalysts. Many new findings presented here may provide new access to the development of economical nitrogen fixation in place of the Haber-Bosch process.
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Affiliation(s)
- Yoshiaki Nishibayashi
- Institute of Engineering Innovation, School of Engineering, The University of Tokyo , Yayoi, Bunkyo-ku, Tokyo 113-8656, Japan
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139
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Creutz SE, Peters JC. Diiron bridged-thiolate complexes that bind N2 at the Fe(II)Fe(II), Fe(II)Fe(I), and Fe(I)Fe(I) redox states. J Am Chem Soc 2015; 137:7310-3. [PMID: 26039253 PMCID: PMC4603983 DOI: 10.1021/jacs.5b04738] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
All known nitrogenase cofactors are rich in both sulfur and iron and are presumed capable of binding and reducing N2. Nonetheless, synthetic examples of transition metal model complexes that bind N2 and also feature sulfur donor ligands remain scarce. We report herein an unusual series of low-valent diiron complexes featuring thiolate and dinitrogen ligands. A new binucleating ligand scaffold is introduced that supports an Fe(μ-SAr)Fe diiron subunit that coordinates dinitrogen (N2-Fe(μ-SAr)Fe-N2) across at least three oxidation states (Fe(II)Fe(II), Fe(II)Fe(I), and Fe(I)Fe(I)). The (N2-Fe(μ-SAr)Fe-N2) system undergoes reduction of the bound N2 to produce NH3 (∼50% yield) and can efficiently catalyze the disproportionation of N2H4 to NH3 and N2. The present scaffold also supports dinitrogen binding concomitant with hydride as a co-ligand. Synthetic model complexes of these types are desirable to ultimately constrain hypotheses regarding Fe-mediated nitrogen fixation in synthetic and biological systems.
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Affiliation(s)
- Sidney E. Creutz
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Jonas C. Peters
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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140
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Ermert DM, Gordon JB, Abboud KA, Murray LJ. Nitride-Bridged Triiron Complex and Its Relevance to Dinitrogen Activation. Inorg Chem 2015; 54:9282-9. [DOI: 10.1021/acs.inorgchem.5b00825] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- David M. Ermert
- Department
of Chemistry, Center for Catalysis, University of Florida, Gainesville, Florida 32611, United States
| | - Jesse B. Gordon
- Department
of Chemistry, Center for Catalysis, University of Florida, Gainesville, Florida 32611, United States
| | - Khalil A. Abboud
- Department
of Chemistry, Center for Catalysis, University of Florida, Gainesville, Florida 32611, United States
| | - Leslie J. Murray
- Department
of Chemistry, Center for Catalysis, University of Florida, Gainesville, Florida 32611, United States
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141
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Gee LB, Leontyev I, Stuchebrukhov A, Scott AD, Pelmenschikov V, Cramer SP. Docking and migration of carbon monoxide in nitrogenase: the case for gated pockets from infrared spectroscopy and molecular dynamics. Biochemistry 2015; 54:3314-9. [PMID: 25919807 DOI: 10.1021/acs.biochem.5b00216] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Evidence of a CO docking site near the FeMo cofactor in nitrogenase has been obtained by Fourier transform infrared spectroscopy-monitored low-temperature photolysis. We investigated the possible migration paths for CO from this docking site using molecular dynamics calculations. The simulations support the notion of a gas channel with multiple internal pockets from the active site to the protein exterior. Travel between pockets is gated by the motion of protein residues. Implications for the mechanism of nitrogenase reactions with CO and N2 are discussed.
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Affiliation(s)
- Leland B Gee
- †Department of Chemistry, University of California, Davis, California 95616, United States
| | - Igor Leontyev
- §InterX Inc., Berkeley, California 94710, United States
| | - Alexei Stuchebrukhov
- †Department of Chemistry, University of California, Davis, California 95616, United States
| | - Aubrey D Scott
- †Department of Chemistry, University of California, Davis, California 95616, United States
| | | | - 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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142
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Abstract
The L-cluster is an all-iron homolog of nitrogenase cofactors. Driven by europium(II) diethylenetriaminepentaacetate [Eu(II)-DTPA], the isolated L-cluster is capable of ATP-independent reduction of CO and CN− to C1 to C4 and C1 to C6 hydrocarbons, respectively. Compared to its cofactor homologs, the L-cluster generates considerably more CH4 from the reduction of CO and CN−, which could be explained by the presence of a “free” Fe atom that is “unmasked” by homocitrate as an additional site for methanation. Moreover, the elevated CH4 formation is accompanied by a decrease in the amount of longer hydrocarbons and/or the lengths of the hydrocarbon products, illustrating a competition between CH4 formation/release and C−C coupling/chain extension. These observations suggest the possibility of designing simpler synthetic clusters for hydrocarbon formation while establishing the L-cluster as a platform for mechanistic investigations of CO and CN− reduction without complications originating from the heterometal and homocitrate components. Nitrogenase is a metalloenzyme that is highly complex in structure and uniquely versatile in function. It catalyzes two reactions that parallel two important industrial processes: the reduction of nitrogen to ammonia, which parallels the Haber-Bosch process in ammonia production, and the reduction of carbon monoxide to hydrocarbons, which parallels the Fischer-Tropsch process in fuel production. Thus, the significance of nitrogenase can be appreciated from the perspective of the useful products it generates: (i) ammonia, the “fixed” nitrogen that is essential for the existence of the entire human population; and (ii) hydrocarbons, the “recycled” carbon fuel that could be used to directly address the worldwide energy shortage. This article provides initial insights into the catalytic characteristics of various nitrogenase cofactors in hydrocarbon formation. The reported assay system provides a useful tool for mechanistic investigations of this reaction while suggesting the possibility of designing bioinspired catalysts based on nitrogenase cofactors.
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143
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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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144
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Betz JN, Boswell NW, Fugate CJ, Holliday GL, Akiva E, Scott AG, Babbitt PC, Peters JW, Shepard EM, Broderick JB. [FeFe]-hydrogenase maturation: insights into the role HydE plays in dithiomethylamine biosynthesis. Biochemistry 2015; 54:1807-18. [PMID: 25654171 DOI: 10.1021/bi501205e] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
HydE and HydG are radical S-adenosyl-l-methionine enzymes required for the maturation of [FeFe]-hydrogenase (HydA) and produce the nonprotein organic ligands characteristic of its unique catalytic cluster. The catalytic cluster of HydA (the H-cluster) is a typical [4Fe-4S] cubane bridged to a 2Fe-subcluster that contains two carbon monoxides, three cyanides, and a bridging dithiomethylamine as ligands. While recent studies have shed light on the nature of diatomic ligand biosynthesis by HydG, little information exists on the function of HydE. Herein, we present biochemical, spectroscopic, bioinformatic, and molecular modeling data that together map the active site and provide significant insight into the role of HydE in H-cluster biosynthesis. Electron paramagnetic resonance and UV-visible spectroscopic studies demonstrate that reconstituted HydE binds two [4Fe-4S] clusters and copurifies with S-adenosyl-l-methionine. Incorporation of deuterium from D2O into 5'-deoxyadenosine, the cleavage product of S-adenosyl-l-methionine, coupled with molecular docking experiments suggests that the HydE substrate contains a thiol functional group. This information, along with HydE sequence similarity and genome context networks, has allowed us to redefine the presumed mechanism for HydE away from BioB-like sulfur insertion chemistry; these data collectively suggest that the source of the sulfur atoms in the dithiomethylamine bridge of the H-cluster is likely derived from HydE's thiol containing substrate.
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Affiliation(s)
- Jeremiah N Betz
- Department of Chemistry & Biochemistry, Montana State University , Bozeman, Montana 59717, United States
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145
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Cutsail GE, Telser J, Hoffman BM. Advanced paramagnetic resonance spectroscopies of iron-sulfur proteins: Electron nuclear double resonance (ENDOR) and electron spin echo envelope modulation (ESEEM). BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:1370-94. [PMID: 25686535 DOI: 10.1016/j.bbamcr.2015.01.025] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 01/29/2015] [Accepted: 01/29/2015] [Indexed: 12/20/2022]
Abstract
The advanced electron paramagnetic resonance (EPR) techniques, electron nuclear double resonance (ENDOR) and electron spin echo envelope modulation (ESEEM) spectroscopies, provide unique insights into the structure, coordination chemistry, and biochemical mechanism of nature's widely distributed iron-sulfur cluster (FeS) proteins. This review describes the ENDOR and ESEEM techniques and then provides a series of case studies on their application to a wide variety of FeS proteins including ferredoxins, nitrogenase, and radical SAM enzymes. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.
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Affiliation(s)
- George E Cutsail
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Joshua Telser
- Department of Biological, Chemical and Physical Sciences, Roosevelt University, Chicago, IL 60605, USA
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.
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146
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Lee CC, Hu Y, Ribbe MW. Catalytic reduction of CN-, CO, and CO2 by nitrogenase cofactors in lanthanide-driven reactions. Angew Chem Int Ed Engl 2015; 54:1219-22. [PMID: 25420957 PMCID: PMC4300254 DOI: 10.1002/anie.201410412] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Indexed: 12/19/2022]
Abstract
Nitrogenase cofactors can be extracted into an organic solvent to catalyze the reduction of cyanide (CN(-)), carbon monoxide (CO), and carbon dioxide (CO2) without using adenosine triphosphate (ATP), when samarium(II) iodide (SmI2) and 2,6-lutidinium triflate (Lut-H) are employed as a reductant and a proton source, respectively. Driven by SmI2, the cofactors catalytically reduce CN(-) or CO to C1-C4 hydrocarbons, and CO2 to CO and C1-C3 hydrocarbons. The C-C coupling from CO2 indicates a unique Fischer-Tropsch-like reaction with an atypical carbonaceous substrate, whereas the catalytic turnover of CN(-), CO, and CO2 by isolated cofactors suggests the possibility to develop nitrogenase-based electrocatalysts for the production of hydrocarbons from these carbon-containing compounds.
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Affiliation(s)
| | - Yilin Hu
- Department of Molecular Biology and Biochemistry
| | - Markus W. Ribbe
- Department of Molecular Biology and Biochemistry; Department of Chemistry, University of California, Irvine, Irvine, CA 92697-3900
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147
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Nitrite reduction by molybdoenzymes: a new class of nitric oxide-forming nitrite reductases. J Biol Inorg Chem 2015; 20:403-33. [DOI: 10.1007/s00775-014-1234-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 12/14/2014] [Indexed: 02/07/2023]
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148
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CH Bond Activation of Hydrocarbons Mediated by Rare-Earth Metals and Actinides. ADVANCES IN ORGANOMETALLIC CHEMISTRY 2015. [DOI: 10.1016/bs.adomc.2015.08.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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149
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Hu Y, Ribbe MW. Nitrogenase and homologs. J Biol Inorg Chem 2014; 20:435-45. [PMID: 25491285 DOI: 10.1007/s00775-014-1225-3] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 11/24/2014] [Indexed: 11/24/2022]
Abstract
Nitrogenase catalyzes biological nitrogen fixation, a key step in the global nitrogen cycle. Three homologous nitrogenases have been identified to date, along with several structural and/or functional homologs of this enzyme that are involved in nitrogenase assembly, bacteriochlorophyll biosynthesis and methanogenic process, respectively. In this article, we provide an overview of the structures and functions of nitrogenase and its homologs, which highlights the similarity and disparity of this uniquely versatile group of enzymes.
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Affiliation(s)
- Yilin Hu
- Department of Molecular Biology and Biochemistry, 2230 McGaugh Hall, University of California, Irvine, CA, 92697-3900, USA,
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150
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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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