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Willard D, Arellano JJ, Underdahl M, Lee TM, Ramaswamy AS, Fumes G, Kliman A, Wong EY, Owens CP. Mutational Analysis of the Nitrogenase Carbon Monoxide Protective Protein CowN Reveals That a Conserved C-Terminal Glutamic Acid Residue Is Necessary for Its Activity. Biochemistry 2024; 63:152-158. [PMID: 38091601 PMCID: PMC10765410 DOI: 10.1021/acs.biochem.3c00421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 11/21/2023] [Accepted: 11/27/2023] [Indexed: 01/03/2024]
Abstract
Nitrogenase is the only enzyme that catalyzes the reduction of nitrogen gas into ammonia. Nitrogenase is tightly inhibited by the environmental gas carbon monoxide (CO). Many nitrogen fixing bacteria protect nitrogenase from CO inhibition using the protective protein CowN. This work demonstrates that a conserved glutamic acid residue near the C-terminus of Gluconacetobacter diazotrophicus CowN is necessary for its function. Mutation of the glutamic acid residue abolishes both CowN's protection against CO inhibition and the ability of CowN to bind to nitrogenase. In contrast, a conserved C-terminal cysteine residue is not important for CO protection by CowN. Overall, this work uncovers structural features in CowN that are required for its function and provides new insights into its nitrogenase binding and CO protection mechanism.
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Affiliation(s)
- Dustin
L. Willard
- Department of Chemistry and
Biochemistry, Schmid College, Chapman University, Orange, California 92866, United States
| | - Joshuah J. Arellano
- Department of Chemistry and
Biochemistry, Schmid College, Chapman University, Orange, California 92866, United States
| | - Mitch Underdahl
- Department of Chemistry and
Biochemistry, Schmid College, Chapman University, Orange, California 92866, United States
| | - Terrence M. Lee
- Department of Chemistry and
Biochemistry, Schmid College, Chapman University, Orange, California 92866, United States
| | - Avinash S. Ramaswamy
- Department of Chemistry and
Biochemistry, Schmid College, Chapman University, Orange, California 92866, United States
| | - Gabriella Fumes
- Department of Chemistry and
Biochemistry, Schmid College, Chapman University, Orange, California 92866, United States
| | - Agatha Kliman
- Department of Chemistry and
Biochemistry, Schmid College, Chapman University, Orange, California 92866, United States
| | - Emily Y. Wong
- Department of Chemistry and
Biochemistry, Schmid College, Chapman University, Orange, California 92866, United States
| | - Cedric P. Owens
- Department of Chemistry and
Biochemistry, Schmid College, Chapman University, Orange, California 92866, United States
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Quantum Mechanical Calculations of Redox Potentials of the Metal Clusters in Nitrogenase. MOLECULES (BASEL, SWITZERLAND) 2022; 28:molecules28010065. [PMID: 36615260 PMCID: PMC9822455 DOI: 10.3390/molecules28010065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/14/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
We have calculated redox potentials of the two metal clusters in Mo-nitrogenase with quantum mechanical (QM) calculations. We employ an approach calibrated for iron-sulfur clusters with 1-4 Fe ions, involving QM-cluster calculations in continuum solvent and large QM systems (400-500 atoms), based on structures from combined QM and molecular mechanics (QM/MM) geometry optimisations. Calculations on the P-cluster show that we can reproduce the experimental redox potentials within 0.33 V. This is similar to the accuracy obtained for the smaller clusters, although two of the redox reactions involve also proton transfer. The calculated P1+/PN redox potential is nearly the same independently of whether P1+ is protonated or deprotonated, explaining why redox titrations do not show any pH dependence. For the FeMo cluster, the calculations clearly show that the formal oxidation state of the cluster in the resting E0 state is MoIIIFe3IIFe4III , in agreement with previous experimental studies and QM calculations. Moreover, the redox potentials of the first five E0-E4 states are nearly constant, as is expected if the electrons are delivered by the same site (the P-cluster). However, the redox potentials are insensitive to the formal oxidation states of the Fe ion (i.e., whether the added protons bind to sulfide or Fe ions). Finally, we show that the later (E4-E8) states of the reaction mechanism have redox potential that are more positive (i.e., more exothermic) than that of the E0/E1 couple.
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Medina MS, Bretzing KO, Aviles RA, Chong KM, Espinoza A, Garcia CNG, Katz BB, Kharwa RN, Hernandez A, Lee JL, Lee TM, Lo Verde C, Strul MW, Wong EY, Owens CP. CowN sustains nitrogenase turnover in the presence of the inhibitor carbon monoxide. J Biol Chem 2021; 296:100501. [PMID: 33667548 PMCID: PMC8047169 DOI: 10.1016/j.jbc.2021.100501] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 01/28/2021] [Accepted: 03/01/2021] [Indexed: 11/28/2022] Open
Abstract
Nitrogenase is the only enzyme capable of catalyzing nitrogen fixation, the reduction of dinitrogen gas (N2) to ammonia (NH3). Nitrogenase is tightly inhibited by the environmental gas carbon monoxide (CO). Nitrogen-fixing bacteria rely on the protein CowN to grow in the presence of CO. However, the mechanism by which CowN operates is unknown. Here, we present the biochemical characterization of CowN and examine how CowN protects nitrogenase from CO. We determine that CowN interacts directly with nitrogenase and that CowN protection observes hyperbolic kinetics with respect to CowN concentration. At a CO concentration of 0.001 atm, CowN restores nearly full nitrogenase activity. Our results further indicate that CowN's protection mechanism involves decreasing the binding affinity of CO to nitrogenase's active site approximately tenfold without interrupting substrate turnover. Taken together, our work suggests CowN is an important auxiliary protein in nitrogen fixation that engenders CO tolerance to nitrogenase.
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Affiliation(s)
- Michael S Medina
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Kevin O Bretzing
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Richard A Aviles
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Kiersten M Chong
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Alejandro Espinoza
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Chloe Nicole G Garcia
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Benjamin B Katz
- Department of Chemistry, University of California, Irvine, Irvine, California, USA
| | - Ruchita N Kharwa
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Andrea Hernandez
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Justin L Lee
- Department of Chemistry, University of California, Irvine, Irvine, California, USA
| | - Terrence M Lee
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Christine Lo Verde
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Max W Strul
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Emily Y Wong
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Cedric P Owens
- Schmid College of Science and Technology, Chapman University, Orange, California, USA.
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Abstract
Nitrogenase is the only enzyme capable of reducing N2 to NH3. This challenging reaction requires the coordinated transfer of multiple electrons from the reductase, Fe-protein, to the catalytic component, MoFe-protein, in an ATP-dependent fashion. In the last two decades, there have been significant advances in our understanding of how nitrogenase orchestrates electron transfer (ET) from the Fe-protein to the catalytic site of MoFe-protein and how energy from ATP hydrolysis transduces the ET processes. In this review, we summarize these advances, with focus on the structural and thermodynamic redox properties of nitrogenase component proteins and their complexes, as well as on new insights regarding the mechanism of ET reactions during catalysis and how they are coupled to ATP hydrolysis. We also discuss recently developed chemical, photochemical, and electrochemical methods for uncoupling substrate reduction from ATP hydrolysis, which may provide new avenues for studying the catalytic mechanism of nitrogenase.
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Affiliation(s)
- Hannah L Rutledge
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - F Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
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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: 177] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Nitrogenase is the enzyme that catalyzes biological N2 reduction to NH3. This enzyme achieves an impressive rate enhancement over the uncatalyzed reaction. Given the high demand for N2 fixation to support food and chemical production and the heavy reliance of the industrial Haber-Bosch nitrogen fixation reaction on fossil fuels, there is a strong need to elucidate how nitrogenase achieves this difficult reaction under benign conditions as a means of informing the design of next generation synthetic catalysts. This Review summarizes recent progress in addressing how nitrogenase catalyzes the reduction of an array of substrates. New insights into the mechanism of N2 and proton reduction are first considered. This is followed by a summary of recent gains in understanding the reduction of a number of other nitrogenous compounds not considered to be physiological substrates. Progress in understanding the reduction of a wide range of C-based substrates, including CO and CO2, is also discussed, and remaining challenges in understanding nitrogenase substrate reduction are considered.
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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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Harris AW, Harguindey A, Patalano RE, Roy S, Yehezkeli O, Goodwin AP, Cha JN. Investigating Protein–Nanocrystal Interactions for Photodriven Activity. ACS APPLIED BIO MATERIALS 2020; 3:1026-1035. [DOI: 10.1021/acsabm.9b01025] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
| | | | | | | | - Omer Yehezkeli
- Biotechnology and Food Engineering, Technion—Israel Institute of Technology, Haifa 32000, Israel
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Cao L, Börner MC, Bergmann J, Caldararu O, Ryde U. Geometry and Electronic Structure of the P-Cluster in Nitrogenase Studied by Combined Quantum Mechanical and Molecular Mechanical Calculations and Quantum Refinement. Inorg Chem 2019; 58:9672-9690. [DOI: 10.1021/acs.inorgchem.9b00400] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Lili Cao
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Melanie C. Börner
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
- Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, 48149 Münster, Germany
| | - Justin Bergmann
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Octav Caldararu
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
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Conformationally Gated Electron Transfer in Nitrogenase. Isolation, Purification, and Characterization of Nitrogenase From Gluconacetobacter diazotrophicus. Methods Enzymol 2017. [PMID: 29746246 DOI: 10.1016/bs.mie.2017.09.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Nitrogenase is a complex, bacterial enzyme that catalyzes the ATP-dependent reduction of dinitrogen (N2) to ammonia (NH3). In its most prevalent form, it consists of two proteins, the catalytic molybdenum-iron protein (MoFeP) and its specific reductase, the iron protein (FeP). A defining feature of nitrogenase is that electron and proton transfer processes linked to substrate reduction are synchronized by conformational changes driven by ATP-dependent FeP-MoFeP interactions. Yet, despite extensive crystallographic, spectroscopic, and biochemical information on nitrogenase, the structural basis of the ATP-dependent synchronization mechanism is not understood in detail. In this chapter, we summarize some of our efforts toward obtaining such an understanding. Experimental investigations of the structure-function relationships in nitrogenase are challenged by the fact that it cannot be readily expressed heterologously in nondiazotrophic bacteria, and the purification protocols for nitrogenase are only known for a small number of diazotrophic organisms. Here, we present methods for purifying and characterizing nitrogenase from a new model organism, Gluconacetobacter diazotrophicus. We also describe procedures for observing redox-dependent conformational changes in G. diazotrophicus nitrogenase by X-ray crystallography and electron paramagnetic resonance spectroscopy, which have provided new insights into the redox-dependent conformational gating processes in nitrogenase.
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Dizicheh ZB, Halloran N, Asma W, Ghirlanda G. De Novo Design of Iron–Sulfur Proteins. Methods Enzymol 2017; 595:33-53. [DOI: 10.1016/bs.mie.2017.07.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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