1
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Wang H, Xiong Y, Wang L, He Y, Chen M, Ding J, Ren N. Structural design of thiadiazole-based donor-acceptor COF/Fe-doped N vacancy g-C 3N x nanosheets for photocatalytic nitrogen fixation under visible light. J Colloid Interface Sci 2024; 662:357-366. [PMID: 38354562 DOI: 10.1016/j.jcis.2024.02.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 01/27/2024] [Accepted: 02/04/2024] [Indexed: 02/16/2024]
Abstract
The rational design of efficient photocatalysts to achieve artificial nitrogen fixation is an urgent challenge. Herein, we combined donor-acceptor covalent organic framework with iron-doped nitrogen vacancy graphitized carbon nitride (D-A COF/Fe-g-C3Nx) for photocatalytic nitrogen fixation. The photocatalyst exhibited good crystallinity, high porosity, and a large specific surface area. Without a sacrificial agent, the optimal 40 % D-A COF/Fe-g-C3Nx exhibited an excellent rate of ammonia production (646 μmol h-1 g-1) at 420 nm, and durable stability after successive cycling. Exhaustive experimental research and theory calculations verified that the D-A unit and Fe doping redistributed the distribution of the charge, which enhanced the visible light utilization and provided chemisorption sites for further polarization. Besides N-vacancies can serve as electron-trapping active sites to promote the directional migration of carriers. The reaction mechanism demonstrated that superoxide radical and hydrogen peroxide were formed by electron and hole, respectively, which promote the reduction of nitrogen to ammonia. This work provides a new idea for the rationalizing design of efficient catalysts for photocatalytic nitrogen fixation under mild conditions.
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Affiliation(s)
- Hui Wang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China.
| | - Yuhan Xiong
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Liang Wang
- General Water of China Co., Ltd, Beijing 100022, China
| | - Yi He
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Meihui Chen
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Jie Ding
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China.
| | - Nanqi Ren
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
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2
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Einsle O. On the Shoulders of Giants-Reaching for Nitrogenase. Molecules 2023; 28:7959. [PMID: 38138449 PMCID: PMC10745432 DOI: 10.3390/molecules28247959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 11/14/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
Only a single enzyme system-nitrogenase-carries out the conversion of atmospheric N2 into bioavailable ammonium, an essential prerequisite for all organismic life. The reduction of this inert substrate at ambient conditions poses unique catalytic challenges that strain our mechanistic understanding even after decades of intense research. Structural biology has added its part to this greater tapestry, and in this review, I provide a personal (and highly biased) summary of the parts of the story to which I had the privilege to contribute. It focuses on the crystallographic analysis of the three isoforms of nitrogenases at high resolution and the binding of ligands and inhibitors to the active-site cofactors of the enzyme. In conjunction with the wealth of available biochemical, biophysical, and spectroscopic data on the protein, this has led us to a mechanistic hypothesis based on an elementary mechanism of repetitive hydride formation and insertion.
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Affiliation(s)
- Oliver Einsle
- Institute of Biochemistry, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104 Freiburg im Breisgau, Germany
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3
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Santos MFA, Pessoa JC. Interaction of Vanadium Complexes with Proteins: Revisiting the Reported Structures in the Protein Data Bank (PDB) since 2015. Molecules 2023; 28:6538. [PMID: 37764313 PMCID: PMC10536487 DOI: 10.3390/molecules28186538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
The structural determination and characterization of molecules, namely proteins and enzymes, is crucial to gaining a better understanding of their role in different chemical and biological processes. The continuous technical developments in the experimental and computational resources of X-ray diffraction (XRD) and, more recently, cryogenic Electron Microscopy (cryo-EM) led to an enormous growth in the number of structures deposited in the Protein Data Bank (PDB). Bioinorganic chemistry arose as a relevant discipline in biology and therapeutics, with a massive number of studies reporting the effects of metal complexes on biological systems, with vanadium complexes being one of the relevant systems addressed. In this review, we focus on the interactions of vanadium compounds (VCs) with proteins. Several types of binding are established between VCs and proteins/enzymes. Considering that the V-species that bind may differ from those initially added, the mentioned structural techniques are pivotal to clarifying the nature and variety of interactions of VCs with proteins and to proposing the mechanisms involved either in enzymatic inhibition or catalysis. As such, we provide an account of the available structural information of VCs bound to proteins obtained by both XRD and/or cryo-EM, mainly exploring the more recent structures, particularly those containing organic-based vanadium complexes.
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Affiliation(s)
- Marino F. A. Santos
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO—Applied Molecular Biosciences Unit, Chemistry Department, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Centro de Química Estrutural, Departamento de Engenharia Química, Institute of Molecular Sciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - João Costa Pessoa
- Centro de Química Estrutural, Departamento de Engenharia Química, Institute of Molecular Sciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
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4
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Martin Del Campo JS, Rigsbee J, Bueno Batista M, Mus F, Rubio LM, Einsle O, Peters JW, Dixon R, Dean DR, Dos Santos PC. Overview of physiological, biochemical, and regulatory aspects of nitrogen fixation in Azotobacter vinelandii. Crit Rev Biochem Mol Biol 2023; 57:492-538. [PMID: 36877487 DOI: 10.1080/10409238.2023.2181309] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
Understanding how Nature accomplishes the reduction of inert nitrogen gas to form metabolically tractable ammonia at ambient temperature and pressure has challenged scientists for more than a century. Such an understanding is a key aspect toward accomplishing the transfer of the genetic determinants of biological nitrogen fixation to crop plants as well as for the development of improved synthetic catalysts based on the biological mechanism. Over the past 30 years, the free-living nitrogen-fixing bacterium Azotobacter vinelandii emerged as a preferred model organism for mechanistic, structural, genetic, and physiological studies aimed at understanding biological nitrogen fixation. This review provides a contemporary overview of these studies and places them within the context of their historical development.
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Affiliation(s)
| | - Jack Rigsbee
- Department of Chemistry, Wake Forest University, Winston-Salem, NC, USA
| | | | - Florence Mus
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
| | - 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/CSIC), Pozuelo de Alarcón, Spain
| | - Oliver Einsle
- Department of Biochemistry, University of Freiburg, Freiburg, Germany
| | - John W Peters
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
| | - Ray Dixon
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK
| | - Dennis R Dean
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA
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5
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Rnf and Fix Have Specific Roles during Aerobic Nitrogen Fixation in Azotobacter vinelandii. Appl Environ Microbiol 2022; 88:e0104922. [PMID: 36000884 PMCID: PMC9469703 DOI: 10.1128/aem.01049-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Biological nitrogen fixation requires large amounts of energy in the form of ATP and low potential electrons to overcome the high activation barrier for cleavage of the dinitrogen triple bond. The model aerobic nitrogen-fixing bacteria, Azotobacter vinelandii, generates low potential electrons in the form of reduced ferredoxin (Fd) and flavodoxin (Fld) using two distinct mechanisms via the enzyme complexes Rnf and Fix. Both Rnf and Fix are expressed during nitrogen fixation, but deleting either rnf1 or fix genes has little effect on diazotrophic growth. However, deleting both rnf1 and fix eliminates the ability to grow diazotrophically. Rnf and Fix both use NADH as a source of electrons, but overcoming the energetics of NADH's endergonic reduction of Fd/Fld is accomplished through different mechanisms. Rnf harnesses free energy from the chemiosmotic potential, whereas Fix uses electron bifurcation to effectively couple the endergonic reduction of Fd/Fld to the exergonic reduction of quinone. Different reaction stoichiometries and condition-specific differential gene expression indicate specific roles for the two reactions. This work's complementary physiological studies and thermodynamic modeling reveal how Rnf and Fix balance redox homeostasis in various conditions. Specifically, the Fix complex is required for efficient growth under low oxygen concentrations, while Rnf is presumed to maintain reduced Fd/Fld production for nitrogenase under standard conditions. This work provides a framework for understanding how the production of low potential electrons sustains robust nitrogen fixation in various conditions. IMPORTANCE The availability of fixed nitrogen is critical for life in many ecosystems, from extreme environments to agriculture. Due to the energy demands of biological nitrogen fixation, organisms must tailor their metabolism during diazotrophic growth to deliver the energy requirements to nitrogenase in the form of ATP and low potential electrons. Therefore, a complete understanding of diazotrophic energy metabolism and redox homeostasis is required to understand the impact on ecological communities or to promote crop growth in agriculture through engineered diazotrophs.
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6
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Structural analysis of the reductase component AnfH of iron-only nitrogenase from Azotobacter vinelandii. J Inorg Biochem 2021; 227:111690. [PMID: 34929539 DOI: 10.1016/j.jinorgbio.2021.111690] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/29/2021] [Accepted: 12/03/2021] [Indexed: 11/20/2022]
Abstract
Biological nitrogen fixation, the conversion of atmospheric dinitrogen into bioavailable ammonium, is exclusively catalyzed by the enzyme nitrogenase that is present in nitrogen-fixing organisms, the diazotrophs. So far, three different nitrogenase variants, encoded in their corresponding, distinct gene clusters, have been found in nature. Each one of these consists of a catalytic dinitrogenase component and a unique, ATP-dependent reductase, the Fe protein. The three variant nitrogenases differ in the composition of the active site and contain either molybdenum, vanadium or only iron in the dinitrogenase component. Here we present the 2.0 Å resolution crystal structure of the ADP-bound reductase component AnfH of the iron-only nitrogenase from the model diazotroph Azotobacter vinelandii. A comparison of this structure with the ones reported for the two other Fe protein homologs NifH and VnfH in the ADP-bound state shows that all are adopting the same conformation. However, cross-reactivity assays with the three nitrogenase homologs revealed AnfH to be compatible with iron-only nitrogenase and to a lesser degree with the vanadium-containing enzyme, but not with molybdenum nitrogenase.
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7
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Pessoa JC, Santos MF, Correia I, Sanna D, Sciortino G, Garribba E. Binding of vanadium ions and complexes to proteins and enzymes in aqueous solution. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214192] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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8
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Odularu AT, Ajibade PA. Challenge of diabetes mellitus and researchers’ contributions to its control. OPEN CHEM 2021. [DOI: 10.1515/chem-2020-0153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
The aim of this review study was to assess the past significant events on diabetes mellitus, transformations that took place over the years in the medical records of treatment, countries involved, and the researchers who brought about the revolutions. This study used the content analysis to report the existence of diabetes mellitus and the treatments provided by researchers to control it. The focus was mainly on three main types of diabetes (type 1, type 2, and type 3 diabetes). Ethical consideration has also helped to boost diabetic studies globally. The research has a history path from pharmaceuticals of organic-based drugs to metal-based drugs with their nanoparticles in addition to the impacts of nanomedicine, biosensors, and telemedicine. Ongoing and future studies in alternative medicine such as vanadium nanoparticles (metal nanoparticles) are promising.
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Affiliation(s)
- Ayodele T. Odularu
- Department of Chemistry, University of Fort Hare , Private Bag X1314 , Alice 5700 , Eastern Cape , South Africa
| | - Peter A. Ajibade
- Department of Chemistry, University of KwaZulu-Natal , Pietermaritzburg Campus , Scottsville 3209 , South Africa
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9
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Rohde M, Laun K, Zebger I, Stripp ST, Einsle O. Two ligand-binding sites in CO-reducing V nitrogenase reveal a general mechanistic principle. SCIENCE ADVANCES 2021; 7:7/22/eabg4474. [PMID: 34049880 PMCID: PMC8163085 DOI: 10.1126/sciadv.abg4474] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 04/14/2021] [Indexed: 06/12/2023]
Abstract
Besides its role in biological nitrogen fixation, vanadium-containing nitrogenase also reduces carbon monoxide (CO) to hydrocarbons, in analogy to the industrial Fischer-Tropsch process. The protein yields 93% of ethylene (C2H4), implying a C-C coupling step that mandates the simultaneous binding of two CO at the active site FeV cofactor. Spectroscopic data indicated multiple CO binding events, but structural analyses of Mo and V nitrogenase only confirmed a single site. Here, we report the structure of a two CO-bound state of V nitrogenase at 1.05 Å resolution, with one μ-bridging and one terminal CO molecule. This additional, specific ligand binding site suggests a mechanistic route for CO reduction and hydrocarbon formation, as well as a second access pathway for protons required during the reaction. Moreover, carbonyls are strong-field ligands that are chemically similar to mechanistically relevant hydrides that may be formed and used in a fully analogous fashion.
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Affiliation(s)
- Michael Rohde
- Institute for Biochemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Konstantin Laun
- Institute of Chemistry, Technical University of Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Ingo Zebger
- Institute of Chemistry, Technical University of Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Sven T Stripp
- Institute of Experimental Physics, Department of Physics, Free University of Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Oliver Einsle
- Institute for Biochemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany.
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10
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Yang ZY, Jimenez-Vicente E, Kallas H, Lukoyanov DA, Yang H, Martin Del Campo JS, Dean DR, Hoffman BM, Seefeldt LC. The electronic structure of FeV-cofactor in vanadium-dependent nitrogenase. Chem Sci 2021; 12:6913-6922. [PMID: 34123320 PMCID: PMC8153082 DOI: 10.1039/d0sc06561g] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/26/2021] [Indexed: 01/01/2023] Open
Abstract
The electronic structure of the active-site metal cofactor (FeV-cofactor) of resting-state V-dependent nitrogenase has been an open question, with earlier studies indicating that it exhibits a broad S = 3/2 EPR signal (Kramers state) having g values of ∼4.3 and 3.8, along with suggestions that it contains metal-ions with valencies [1V3+, 3Fe3+, 4Fe2+]. In the present work, genetic, biochemical, and spectroscopic approaches were combined to reveal that the EPR signals previously assigned to FeV-cofactor do not correlate with active VFe-protein, and thus cannot arise from the resting-state of catalytically relevant FeV-cofactor. It, instead, appears resting-state FeV-cofactor is either diamagnetic, S = 0, or non-Kramers, integer-spin (S = 1, 2 etc.). When VFe-protein is freeze-trapped during high-flux turnover with its natural electron-donating partner Fe protein, conditions which populate reduced states of the FeV-cofactor, a new rhombic S = 1/2 EPR signal from such a reduced state is observed, with g = [2.18, 2.12, 2.09] and showing well-defined 51V (I = 7/2) hyperfine splitting, a iso = 110 MHz. These findings indicate a different assignment for the electronic structure of the resting state of FeV-cofactor: S = 0 (or integer-spin non-Kramers state) with metal-ion valencies, [1V3+, 4Fe3+, 3Fe2+]. Our findings suggest that the V3+ does not change valency throughout the catalytic cycle.
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Affiliation(s)
- Zhi-Yong Yang
- Department of Chemistry and Biochemistry, Utah State University Logan UT 84322 USA +1-435-797-3964
| | | | - Hayden Kallas
- Department of Chemistry and Biochemistry, Utah State University Logan UT 84322 USA +1-435-797-3964
| | - Dmitriy A Lukoyanov
- Department of Chemistry, Northwestern University Evanston IL 60208 USA +1-847-491-3104
| | - Hao Yang
- Department of Chemistry, Northwestern University Evanston IL 60208 USA +1-847-491-3104
| | | | - Dennis R Dean
- Department of Biochemistry, Virginia Tech Blacksburg VA 24061 USA +1-540-231-5895
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University Evanston IL 60208 USA +1-847-491-3104
| | - Lance C Seefeldt
- Department of Chemistry and Biochemistry, Utah State University Logan UT 84322 USA +1-435-797-3964
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11
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Parison K, Gies-Elterlein J, Trncik C, Einsle O. Expression, Isolation, and Characterization of Vanadium Nitrogenase from Azotobacter vinelandii. Methods Mol Biol 2021; 2353:97-121. [PMID: 34292546 DOI: 10.1007/978-1-0716-1605-5_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nitrogenases are the sole enzymes known to mediate biological nitrogen fixation, an essential process for sustaining life on earth. Among the three known variants, molybdenum nitrogenase is the best-studied to date. Recent work on the alternative vanadium nitrogenase provided important insights into the mechanism of nitrogen fixation since this enzyme differs from its molybdenum counterpart in some important aspects. Here, we present a protocol to obtain unmodified vanadium nitrogenase in high yield and purity from the paradigmatic diazotroph Azotobacter vinelandii, including procedures for cell cultivation, purification, and protein characterization.
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Affiliation(s)
- Katharina Parison
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | | | - Christian Trncik
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Oliver Einsle
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.
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12
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Pence N, Lewis N, Alleman AB, Seefeldt LC, Peters JW. Revealing a role for the G subunit in mediating interactions between the nitrogenase component proteins. J Inorg Biochem 2020; 214:111273. [PMID: 33086169 DOI: 10.1016/j.jinorgbio.2020.111273] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 09/16/2020] [Accepted: 10/03/2020] [Indexed: 10/23/2022]
Abstract
Azotobacter vinelandii contains three forms of nitrogenase known as the Mo-, V-, and Fe-nitrogenases. They are all two-component enzyme systems, where the catalytic component, referred to as NifDK, VnfDGK, and AnfDGK, associates with the reductase component, the Fe protein or NifH, VnfH, and AnfH respectively. AnfDGK and VnfDGK have an additional subunit compared to NifDK, termed gamma or AnfG and VnfG, whose role is unknown. The expression of each nitrogenase is tightly regulated by metal availability, however it is known that there is crosstalk between the Mo- and V‑nitrogenases but the Fe‑nitrogenase components cannot support substrate reduction with its Mo‑nitrogenase counterparts. Here, docking models for the nitrogenase complexes were generated in ClusPro 2.0 based on the crystal structure of the Mo‑nitrogenase and refined using the HADDOCK 2.2 refinement interface to identify structural determinants that enable crosstalk between the Mo- and V‑nitrogenase but not the Fe‑nitrogenase. Differing salt bridge interactions were identified at the binding interface of each complex. Specifically, positively charged residues of VnfG enable complementary interactions with NifH and VnfH but not AnfH. Similarly, negatively charged residues of AnfG enable interactions with AnfH but not NifH or VnfH. A role for the G subunit is revealed where VnfG could be mediating crosstalk between the Mo- and V‑nitrogenases while the AnfG subunit on AnfDGK makes interactions with NifH and VnfH unfavorable, reducing competition with NifDK and funneling electrons to the most efficient nitrogenase.
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Affiliation(s)
- Natasha Pence
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, United States of America; Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, United States of America
| | - Nathan Lewis
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, United States of America
| | - Alexander B Alleman
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, United States of America
| | - Lance C Seefeldt
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322, United States of America
| | - John W Peters
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, United States of America.
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13
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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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14
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Affiliation(s)
- Oliver Einsle
- Institute for Biochemistry, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Douglas C. Rees
- Division of Chemistry and Chemical Engineering, Howard Hughes Medical Institute, California Institute of Technology, Pasadena California 91125, United States
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15
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Campos DT, Zuñiga C, Passi A, Del Toro J, Tibocha-Bonilla JD, Zepeda A, Betenbaugh MJ, Zengler K. Modeling of nitrogen fixation and polymer production in the heterotrophic diazotroph Azotobacter vinelandii DJ. Metab Eng Commun 2020; 11:e00132. [PMID: 32551229 PMCID: PMC7292883 DOI: 10.1016/j.mec.2020.e00132] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 05/09/2020] [Accepted: 05/11/2020] [Indexed: 01/28/2023] Open
Abstract
Nitrogen fixation is an important metabolic process carried out by microorganisms, which converts molecular nitrogen into inorganic nitrogenous compounds such as ammonia (NH3). These nitrogenous compounds are crucial for biogeochemical cycles and for the synthesis of essential biomolecules, i.e. nucleic acids, amino acids and proteins. Azotobacter vinelandii is a bacterial non-photosynthetic model organism to study aerobic nitrogen fixation (diazotrophy) and hydrogen production. Moreover, the diazotroph can produce biopolymers like alginate and polyhydroxybutyrate (PHB) that have important industrial applications. However, many metabolic processes such as partitioning of carbon and nitrogen metabolism in A. vinelandii remain unknown to date. Genome-scale metabolic models (M-models) represent reliable tools to unravel and optimize metabolic functions at genome-scale. M-models are mathematical representations that contain information about genes, reactions, metabolites and their associations. M-models can simulate optimal reaction fluxes under a wide variety of conditions using experimentally determined constraints. Here we report on the development of a M-model of the wild type bacterium A. vinelandii DJ (iDT1278) which consists of 2,003 metabolites, 2,469 reactions, and 1,278 genes. We validated the model using high-throughput phenotypic and physiological data, testing 180 carbon sources and 95 nitrogen sources. iDT1278 was able to achieve an accuracy of 89% and 91% for growth with carbon sources and nitrogen source, respectively. This comprehensive M-model will help to comprehend metabolic processes associated with nitrogen fixation, ammonium assimilation, and production of organic nitrogen in an environmentally important microorganism. Genome-scale metabolic model of Azotobacter vinelandii DJ achives over 90% accuracy. iDT1278 is the most comprehensive model to simulate diazotrophy. Determining the most suitable culture conditions to produce polymers A. vinelandii. Constraint-based modeling unravels links among nitrogen fixation and production of organic nitrogen.
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Affiliation(s)
- Diego Tec Campos
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0760, USA.,Facultad de Ingeniería Química, Universidad Autónoma de Yucatán, Mérida, Yucatán, Mexico
| | - Cristal Zuñiga
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0760, USA
| | - Anurag Passi
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0760, USA
| | - John Del Toro
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218, USA
| | - Juan D Tibocha-Bonilla
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, 92093-0412, USA
| | - Alejandro Zepeda
- Facultad de Ingeniería Química, Universidad Autónoma de Yucatán, Mérida, Yucatán, Mexico
| | - Michael J Betenbaugh
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218, USA
| | - Karsten Zengler
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0760, USA.,Department of Bioengineering, University of California, San Diego, La Jolla, CA, 92093-0412, USA.,Center for Microbiome Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0403, USA
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16
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Seefeldt LC, Yang ZY, Lukoyanov DA, Harris DF, Dean DR, Raugei S, Hoffman BM. Reduction of Substrates by Nitrogenases. Chem Rev 2020; 120:5082-5106. [PMID: 32176472 DOI: 10.1021/acs.chemrev.9b00556] [Citation(s) in RCA: 184] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Nitrogenase is the enzyme that catalyzes biological N2 reduction to NH3. This enzyme achieves an impressive rate enhancement over the uncatalyzed reaction. Given the high demand for N2 fixation to support food and chemical production and the heavy reliance of the industrial Haber-Bosch nitrogen fixation reaction on fossil fuels, there is a strong need to elucidate how nitrogenase achieves this difficult reaction under benign conditions as a means of informing the design of next generation synthetic catalysts. This Review summarizes recent progress in addressing how nitrogenase catalyzes the reduction of an array of substrates. New insights into the mechanism of N2 and proton reduction are first considered. This is followed by a summary of recent gains in understanding the reduction of a number of other nitrogenous compounds not considered to be physiological substrates. Progress in understanding the reduction of a wide range of C-based substrates, including CO and CO2, is also discussed, and remaining challenges in understanding nitrogenase substrate reduction are considered.
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Affiliation(s)
- Lance C Seefeldt
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Zhi-Yong Yang
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Dmitriy A Lukoyanov
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Derek F Harris
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Dennis R Dean
- Biochemistry Department, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Simone Raugei
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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17
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Jasniewski AJ, Lee CC, Ribbe MW, Hu Y. Reactivity, Mechanism, and Assembly of the Alternative Nitrogenases. Chem Rev 2020; 120:5107-5157. [PMID: 32129988 DOI: 10.1021/acs.chemrev.9b00704] [Citation(s) in RCA: 107] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Biological nitrogen fixation is catalyzed by the enzyme nitrogenase, which facilitates the cleavage of the relatively inert triple bond of N2. Nitrogenase is most commonly associated with the molybdenum-iron cofactor called FeMoco or the M-cluster, and it has been the subject of extensive structural and spectroscopic characterization over the past 60 years. In the late 1980s and early 1990s, two "alternative nitrogenase" systems were discovered, isolated, and found to incorporate V or Fe in place of Mo. These systems are regulated by separate gene clusters; however, there is a high degree of structural and functional similarity between each nitrogenase. Limited studies with the V- and Fe-nitrogenases initially demonstrated that these enzymes were analogously active as the Mo-nitrogenase, but more recent investigations have found capabilities that are unique to the alternative systems. In this review, we will discuss the reactivity, biosynthetic, and mechanistic proposals for the alternative nitrogenases as well as their electronic and structural properties in comparison to the well-characterized Mo-dependent system. Studies over the past 10 years have been particularly fruitful, though key aspects about V- and Fe-nitrogenases remain unexplored.
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Affiliation(s)
- Andrew J Jasniewski
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, United States
| | - Chi Chung Lee
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, United States
| | - Markus W Ribbe
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, United States.,Department of Chemistry, University of California, Irvine, California 92697-2025, United States
| | - Yilin Hu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, United States
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18
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Luxem KE, Kraepiel AML, Zhang L, Waldbauer JR, Zhang X. Carbon substrate re-orders relative growth of a bacterium using Mo-, V-, or Fe-nitrogenase for nitrogen fixation. Environ Microbiol 2020; 22:1397-1408. [PMID: 32090445 PMCID: PMC7187303 DOI: 10.1111/1462-2920.14955] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 02/07/2020] [Indexed: 01/21/2023]
Abstract
Biological nitrogen fixation is catalyzed by the molybdenum (Mo), vanadium (V) and iron (Fe)‐only nitrogenase metalloenzymes. Studies with purified enzymes have found that the ‘alternative’ V‐ and Fe‐nitrogenases generally reduce N2 more slowly and produce more byproduct H2 than the Mo‐nitrogenase, leading to an assumption that their usage results in slower growth. Here we show that, in the metabolically versatile photoheterotroph Rhodopseudomonas palustris, the type of carbon substrate influences the relative rates of diazotrophic growth based on different nitrogenase isoforms. The V‐nitrogenase supports growth as fast as the Mo‐nitrogenase on acetate but not on the more oxidized substrate succinate. Our data suggest that this is due to insufficient electron flux to the V‐nitrogenase isoform on succinate compared with acetate. Despite slightly faster growth based on the V‐nitrogenase on acetate, the wild‐type strain uses exclusively the Mo‐nitrogenase on both carbon substrates. Notably, the differences in H2:N2 stoichiometry by alternative nitrogenases (~1.5 for V‐nitrogenase, ~4–7 for Fe‐nitrogenase) and Mo‐nitrogenase (~1) measured here are lower than prior in vitro estimates. These results indicate that the metabolic costs of V‐based nitrogen fixation could be less significant for growth than previously assumed, helping explain why alternative nitrogenase genes persist in diverse diazotroph lineages and are broadly distributed in the environment.
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Affiliation(s)
- Katja E Luxem
- Department of Geosciences, Princeton University, Princeton, NJ, 08544, USA
| | - Anne M L Kraepiel
- Princeton Environmental Institute, Princeton University, Princeton, NJ, 08544, USA
| | - Lichun Zhang
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, 60637, USA
| | - Jacob R Waldbauer
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, 60637, USA
| | - Xinning Zhang
- Department of Geosciences, Princeton University, Princeton, NJ, 08544, USA.,Princeton Environmental Institute, Princeton University, Princeton, NJ, 08544, USA
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19
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Harris DF, Lukoyanov DA, Kallas H, Trncik C, Yang ZY, Compton P, Kelleher N, Einsle O, Dean DR, Hoffman BM, Seefeldt LC. Mo-, V-, and Fe-Nitrogenases Use a Universal Eight-Electron Reductive-Elimination Mechanism To Achieve N2 Reduction. Biochemistry 2019; 58:3293-3301. [DOI: 10.1021/acs.biochem.9b00468] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Derek F. Harris
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Dmitriy A. Lukoyanov
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Hayden Kallas
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Christian Trncik
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
| | - Zhi-Yong Yang
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Phil Compton
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Neil Kelleher
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Oliver Einsle
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
| | - Dennis R. Dean
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Brian M. Hoffman
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Lance C. Seefeldt
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
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20
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Abstract
Biological nitrogen fixation, the conversion of dinitrogen (N2) into ammonia (NH3), stands as a particularly challenging chemical process. As the entry point into a bioavailable form of nitrogen, biological nitrogen fixation is a critical step in the global nitrogen cycle. In Nature, only one enzyme, nitrogenase, is competent in performing this reaction. Study of this complex metalloenzyme has revealed a potent substrate reduction system that utilizes some of the most sophisticated metalloclusters known. This chapter discusses the structure and function of nitrogenase, covers methods that have proven useful in the elucidation of enzyme properties, and provides an overview of the three known nitrogenase variants.
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21
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Crystal structure of VnfH, the iron protein component of vanadium nitrogenase. J Biol Inorg Chem 2018; 23:1049-1056. [DOI: 10.1007/s00775-018-1602-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 08/08/2018] [Indexed: 01/08/2023]
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22
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Azotobacter vinelandii Nitrogenase Activity, Hydrogen Production, and Response to Oxygen Exposure. Appl Environ Microbiol 2018; 84:AEM.01208-18. [PMID: 29915110 DOI: 10.1128/aem.01208-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 06/12/2018] [Indexed: 11/20/2022] Open
Abstract
Azotobacter vinelandii selectively utilizes three types of nitrogenase (molybdenum, vanadium, and iron only) to fix N2, with their expression regulated by the presence or absence of different metal cofactors in its environment. Each alternative nitrogenase isoenzyme is predicted to have different electron flux requirements based on in vitro measurements, with the molybdenum nitrogenase requiring the lowest flux and the iron-only nitrogenase requiring the highest. Here, prior characterized strains, derepressed in nitrogenase synthesis and also deficient in uptake hydrogenase, were further modified to generate new mutants lacking the ability to produce poly-β-hydroxybutyrate (PHB). PHB is a storage polymer generated under oxygen-limiting conditions and can represent up to 70% of the cells' dry weight. The absence of such granules facilitated the study of relationships between catalytic biomass and product molar yields across different adaptive respiration conditions. The released hydrogen gas observed during growth, due to the inability of the mutants to recapture hydrogen, allowed for direct monitoring of in vivo nitrogenase activity for each isoenzyme. The data presented here show that increasing oxygen exposure limits equally the in vivo activities of all nitrogenase isoenzymes, while under comparative conditions, the Mo nitrogenase enzyme evolves more hydrogen per unit of biomass than the alternative isoenzymes.IMPORTANCEA. vinelandii has been a focus of intense research for over 100 years. It has been investigated for a variety of functions, including agricultural fertilization and hydrogen production. All of these endeavors are centered around A. vinelandii's ability to fix nitrogen aerobically using three nitrogenase isoenzymes. The majority of research up to this point has targeted in vitro measurements of the molybdenum nitrogenase, and robust data contrasting how oxygen impacts the in vivo activity of each nitrogenase isoenzyme are lacking. This article aims to provide in vivo nitrogenase activity data using a real-time evaluation of hydrogen gas released by derepressed nitrogenase mutants lacking an uptake hydrogenase and PHB accumulation.
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23
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Rohde M, Sippel D, Trncik C, Andrade SLA, Einsle O. The Critical E 4 State of Nitrogenase Catalysis. Biochemistry 2018; 57:5497-5504. [PMID: 29965738 DOI: 10.1021/acs.biochem.8b00509] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The reaction catalyzed by the nitrogenase enzyme involves breaking the stable triple bond of the dinitrogen molecule and is consequently considered among the most challenging reactions in biology. While many aspects regarding its atomic mechanism remain to be elucidated, a kinetic scheme established by David Lowe and Roger Thorneley has remained a gold standard for functional studies of the enzyme for more than 30 years. Recent three-dimensional structures of ligand-bound states of molybdenum- and vanadium-dependent nitrogenases have revealed the actual site of substrate binding on the large active site cofactors of this class of enzymes. The binding mode of an inhibitor and a reaction intermediate further substantiate a hypothesis by Seefeldt, Hoffman, and Dean that the activation of N2 is made possible by a reductive elimination of H2 that leaves the cofactor in a super-reduced state that can bind and reduce the inert N2 molecule. Here we discuss the immediate implications of the structurally observed mode of binding of small molecules to the enzyme with respect to the early stages of the Thorneley-Lowe mechanism of nitrogenase. Four consecutive single-electron reductions give rise to two bridging hydrides at the cluster surface that can recombine to eliminate H2 and enable the reduced cluster to bind its substrate in a bridging mode.
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Affiliation(s)
- Michael Rohde
- Institute for Biochemistry , Albert-Ludwigs-University Freiburg , Albertstrasse 21 , 79104 Freiburg , Germany
| | - Daniel Sippel
- Institute for Biochemistry , Albert-Ludwigs-University Freiburg , Albertstrasse 21 , 79104 Freiburg , Germany
| | - Christian Trncik
- Institute for Biochemistry , Albert-Ludwigs-University Freiburg , Albertstrasse 21 , 79104 Freiburg , Germany
| | - Susana L A Andrade
- Institute for Biochemistry , Albert-Ludwigs-University Freiburg , Albertstrasse 21 , 79104 Freiburg , Germany.,BIOSS Centre for Biological Signalling Studies , Schänzlestrasse 1 , 79104 Freiburg , Germany
| | - Oliver Einsle
- Institute for Biochemistry , Albert-Ludwigs-University Freiburg , Albertstrasse 21 , 79104 Freiburg , Germany.,BIOSS Centre for Biological Signalling Studies , Schänzlestrasse 1 , 79104 Freiburg , Germany
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24
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Sippel D, Rohde M, Netzer J, Trncik C, Gies J, Grunau K, Djurdjevic I, Decamps L, Andrade SLA, Einsle O. A bound reaction intermediate sheds light on the mechanism of nitrogenase. Science 2018; 359:1484-1489. [PMID: 29599235 DOI: 10.1126/science.aar2765] [Citation(s) in RCA: 189] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 01/31/2018] [Indexed: 01/26/2023]
Abstract
Reduction of N2 by nitrogenases occurs at an organometallic iron cofactor that commonly also contains either molybdenum or vanadium. The well-characterized resting state of the cofactor does not bind substrate, so its mode of action remains enigmatic. Carbon monoxide was recently found to replace a bridging sulfide, but the mechanistic relevance was unclear. Here we report the structural analysis of vanadium nitrogenase with a bound intermediate, interpreted as a μ2-bridging, protonated nitrogen that implies the site and mode of substrate binding to the cofactor. Binding results in a flip of amino acid glutamine 176, which hydrogen-bonds the ligand and creates a holding position for the displaced sulfide. The intermediate likely represents state E6 or E7 of the Thorneley-Lowe model and provides clues to the remainder of the catalytic cycle.
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Affiliation(s)
- Daniel Sippel
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104 Freiburg, Germany
| | - Michael Rohde
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104 Freiburg, Germany
| | - Julia Netzer
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104 Freiburg, Germany
| | - Christian Trncik
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104 Freiburg, Germany
| | - Jakob Gies
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104 Freiburg, Germany
| | - Katharina Grunau
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104 Freiburg, Germany
| | - Ivana Djurdjevic
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104 Freiburg, Germany
| | - Laure Decamps
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104 Freiburg, Germany
| | - Susana L A Andrade
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104 Freiburg, Germany.,BIOSS Centre for Biological Signalling Studies, Schänzlestraße 1, 79104 Freiburg, Germany
| | - Oliver Einsle
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104 Freiburg, Germany. .,BIOSS Centre for Biological Signalling Studies, Schänzlestraße 1, 79104 Freiburg, Germany.,Freiburg Institute for Advanced Studies, 79104 Freiburg, Germany
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25
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Cai R, Milton RD, Abdellaoui S, Park T, Patel J, Alkotaini B, Minteer SD. Electroenzymatic C–C Bond Formation from CO2. J Am Chem Soc 2018; 140:5041-5044. [DOI: 10.1021/jacs.8b02319] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Rong Cai
- Department of Chemistry, University of Utah, 315 S 1400 E, Salt Lake City, Utah 84112, United States
| | - Ross D. Milton
- Department of Chemistry, University of Utah, 315 S 1400 E, Salt Lake City, Utah 84112, United States
| | - Sofiene Abdellaoui
- Department of Chemistry, University of Utah, 315 S 1400 E, Salt Lake City, Utah 84112, United States
| | - Terry Park
- Department of Chemistry, University of Utah, 315 S 1400 E, Salt Lake City, Utah 84112, United States
| | - Janki Patel
- Department of Chemistry, University of Utah, 315 S 1400 E, Salt Lake City, Utah 84112, United States
| | - Bassam Alkotaini
- Department of Chemistry, University of Utah, 315 S 1400 E, Salt Lake City, Utah 84112, United States
| | - Shelley D. Minteer
- Department of Chemistry, University of Utah, 315 S 1400 E, Salt Lake City, Utah 84112, United States
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26
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Thakur S, Roy S, Bauzá A, Frontera A, Chattopadhyay S. Estimation of non-covalent C H⋯π, π⋯π (chelate ring) and hydrogen bonding interactions in vanadium(V) Schiff base complexes: Methylene spacer regulated variation in self-assembly. Inorganica Chim Acta 2017. [DOI: 10.1016/j.ica.2017.07.056] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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27
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Sippel D, Einsle O. The structure of vanadium nitrogenase reveals an unusual bridging ligand. Nat Chem Biol 2017; 13:956-960. [PMID: 28692069 PMCID: PMC5563456 DOI: 10.1038/nchembio.2428] [Citation(s) in RCA: 177] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 05/22/2017] [Indexed: 12/28/2022]
Abstract
Nitrogenases catalyze the reduction of N2 gas to ammonium at a complex heterometallic cofactor. Most commonly this is the FeMo cofactor (FeMoco), a [Mo:7Fe:9S:C] cluster whose exact reactivity and substrate binding mode remain unknown. Alternative nitrogenases replace molybdenum with either vanadium or iron and differ in reactivity, prominently in the ability of vanadium nitrogenase to reduce CO to hydrocarbons. Here we report the 1.35 Å structure of vanadium nitrogenase from Azotobacter vinelandii. The 240 kDa protein contains an additional α-helical subunit not present in molybdenum nitrogenase. The FeV cofactor (FeVco) is a [V:7Fe:8S:C] cluster with a homocitrate ligand to vanadium. Unexpectedly, it lacks one sulfide ion compared to FeMoco that is replaced by a bridging ligand, likely a μ-1,3-carbonate. The anion fits into a pocket within the protein that is obstructed in molybdenum nitrogenase, and its different chemical character helps to rationalize the altered chemical properties of this unique N2- and CO-fixing enzyme.
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Affiliation(s)
- Daniel Sippel
- Lehrstuhl Biochemie, Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg Research Institute for Advanced Studies (FRIAS), and BIOSS Centre for Biological Signalling Studies, Freiburg, Germany
| | - Oliver Einsle
- Lehrstuhl Biochemie, Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg Research Institute for Advanced Studies (FRIAS), and BIOSS Centre for Biological Signalling Studies, Freiburg, Germany
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28
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Sickerman NS, Hu Y, Ribbe MW. Activation of CO
2
by Vanadium Nitrogenase. Chem Asian J 2017; 12:1985-1996. [DOI: 10.1002/asia.201700624] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Nathaniel S. Sickerman
- Department of Molecular Biology and Biochemistry University of California, Irvine Irvine CA 92697-3900 USA
| | - 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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29
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Rees JA, Bjornsson R, Kowalska JK, Lima FA, Schlesier J, Sippel D, Weyhermüller T, Einsle O, Kovacs JA, DeBeer S. Comparative electronic structures of nitrogenase FeMoco and FeVco. Dalton Trans 2017; 46:2445-2455. [PMID: 28154874 PMCID: PMC5322470 DOI: 10.1039/c7dt00128b] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 01/25/2017] [Indexed: 12/17/2022]
Abstract
An investigation of the active site cofactors of the molybdenum and vanadium nitrogenases (FeMoco and FeVco) was performed using high-resolution X-ray spectroscopy. Synthetic heterometallic iron-sulfur cluster models and density functional theory calculations complement the study of the MoFe and VFe holoproteins using both non-resonant and resonant X-ray emission spectroscopy. Spectroscopic data show the presence of direct iron-heterometal bonds, which are found to be weaker in FeVco. Furthermore, the interstitial carbide is found to perturb the electronic structures of the cofactors through highly covalent Fe-C bonding. The implications of these conclusions are discussed in light of the differential reactivity of the molybdenum and vanadium nitrogenases towards various substrates. Possible functional roles for both the heterometal and the interstitial carbide are detailed.
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Affiliation(s)
- Julian A Rees
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany. and Department of Chemistry, University of Washington, Box 351700, Seattle, WA 98195-1700, USA.
| | - Ragnar Bjornsson
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany. and Science Institute, University of Iceland, Dunhagi 3, 107 Reykjavik, Iceland
| | - Joanna K Kowalska
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany.
| | - Frederico A Lima
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany. and Centro Nacional de Pesquisa em Energia e Materiais Brazilian Synchrotron Light Laboratory - LNLS Rua Giuseppe Máximo Scolfaro, 10.000 13083-970 Campinas SP, Brazil
| | - Julia Schlesier
- Institute for Biochemistry and BIOSS Centre for Biological Signalling Studies, Albert Ludwigs University Freiburg, Germany.
| | - Daniel Sippel
- Institute for Biochemistry and BIOSS Centre for Biological Signalling Studies, Albert Ludwigs University Freiburg, Germany.
| | - Thomas Weyhermüller
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany.
| | - Oliver Einsle
- Institute for Biochemistry and BIOSS Centre for Biological Signalling Studies, Albert Ludwigs University Freiburg, Germany.
| | - Julie A Kovacs
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA 98195-1700, USA.
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany. and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
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