Home entertainment Structural basis for the conformational protection of nitrogenase from O2

Structural basis for the conformational protection of nitrogenase from O2

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  • Chalkley, M. J., Drover, M. W. & Peters, J. C. Catalytic N2-to-NH3 (or -N2H4) conversion by well-defined molecular coordination complexes. Chem. Rev. 120, 5582–5636 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Rohr, B. A., Singh, A. R. & Nørskov, J. K. A theoretical explanation of the effect of oxygen poisoning on industrial Haber–Bosch catalysts. J. Catal. 372, 33–38 (2019).

    Article 
    CAS 

    Google Scholar 

  • Gallon, J. R. The oxygen sensitivity of nitrogenase: a problem for biochemists and micro-organisms. Trends Biochem. Sci. 6, 19–23 (1981).

    Article 
    CAS 
    MATH 

    Google Scholar 

  • Robson, R. L. & Postgate, J. R. Oxygen and hydrogen in biological nitrogen fixation. Annu. Rev. Microbiol. 34, 183–207 (1980).

    Article 
    CAS 
    PubMed 
    MATH 

    Google Scholar 

  • Wittenberg, J. B., Bergersen, F. J., Appleby, C. A. & Turner, G. L. Facilitated oxygen diffusion: the role of leghemoglobin in nitrogen fixation by bacteroids isolated from soybean root nodules. J. Biol. Chem. 249, 4057–4066 (1974).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Poole, R. K. & Hill, S. Respiratory protection of nitrogenase activity in Azotobacter vinelandii—roles of the terminal oxidases. Biosci. Rep. 17, 303–317 (1997).

    Article 
    CAS 
    PubMed 
    MATH 

    Google Scholar 

  • Postgate, J. R. Biological nitrogen fixation: fundamentals. Phil. Trans. R. Soc. Lond. B Biol. Sci. 296, 375–385 (1982).

    Article 
    ADS 
    CAS 

    Google Scholar 

  • Takimoto, R. et al. A critical role of an oxygen-responsive gene for aerobic nitrogenase activity in Azotobacter vinelandii and its application to Escherichia coli. Sci. Rep. 12, 4182 (2022).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 
    MATH 

    Google Scholar 

  • Dalton, H. & Postgate, J. Effect of oxygen on growth of Azotobacter chroococcum in batch and continuous cultures. J. Gen. Microbiol. 54, 463–473 (1968).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Shethna, Y., DerVartanian, D. & Beinert, H. Non heme (iron-sulfur) proteins of Azotobacter vinelandii. Biochem. Biophys. Res. Commun. 31, 862–868 (1968).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Robson, R. Characterization of an oxygen-stable nitrogenase complex isolated from Azotobacter chroococcum. Biochem. J. 181, 569–575 (1979).

    Article 
    CAS 
    PubMed 
    PubMed Central 
    MATH 

    Google Scholar 

  • Scherings, G., Haaker, H., Wassink, H. & Veeger, C. On the formation of an oxygen‐tolerant three-component nitrogenase complex from Azotobacter vinelandii. Eur. J. Biochem. 135, 591–599 (1983).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Hoffman, B. M., Lukoyanov, D., Yang, Z.-Y., Dean, D. R. & Seefeldt, L. C. Mechanism of nitrogen fixation by nitrogenase: the next stage. Chem. Rev. 114, 4041–4062 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Fowler, D. et al. The global nitrogen cycle in the twenty-first century. Phil. Trans. R. Soc. Lond. B Biol. Sci. 368, 20130164 (2013).

    Article 
    MATH 

    Google Scholar 

  • Seefeldt, L. C., Hoffman, B. M. & Dean, D. R. Mechanism of Mo-dependent nitrogenase. Annu. Rev. Biochem. 78, 701–722 (2009).

    Article 
    CAS 
    PubMed 
    PubMed Central 
    MATH 

    Google Scholar 

  • Einsle, O. & Rees, D. C. Structural enzymology of nitrogenase enzymes. Chem. Rev. 120, 4969–5004 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 
    MATH 

    Google Scholar 

  • Spatzal, T. et al. Evidence for interstitial carbon in nitrogenase FeMo cofactor. Science 334, 940–940 (2011).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 
    MATH 

    Google Scholar 

  • Lancaster, K. M. et al. X-ray emission spectroscopy evidences a central carbon in the nitrogenase iron-molybdenum cofactor. Science 334, 974–977 (2011).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 
    MATH 

    Google Scholar 

  • Georgiadis, M. et al. Crystallographic structure of the nitrogenase iron protein from Azotobacter vinelandii. Science 257, 1653–1659 (1992).

    Article 
    ADS 
    CAS 
    PubMed 
    MATH 

    Google Scholar 

  • Rutledge, H. L. & Tezcan, F. A. Electron transfer in nitrogenase. Chem. Rev. 120, 5158–5193 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 
    MATH 

    Google Scholar 

  • Seefeldt, L. C. et al. Reduction of substrates by nitrogenases. Chem. Rev. 120, 5082–5106 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 
    MATH 

    Google Scholar 

  • Yates, M. G. & Planque, K. Nitrogenase from Azotobacter chroococcum: purification and properties of the component proteins. Eur. J. Biochem. 60, 467–476 (1975).

    Article 
    CAS 
    PubMed 
    MATH 

    Google Scholar 

  • Eady, R., Smith, B., Cook, K. & Postgate, J. Nitrogenase of Klebsiella pneumoniae. Purification and properties of the component proteins. Biochem. J. 128, 655–675 (1972).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Wong, P. P. & Burris, R. Nature of oxygen inhibition of nitrogenase from Azotobacter vinelandii. Proc. Natl Acad. Sci. USA 69, 672–675 (1972).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 
    MATH 

    Google Scholar 

  • Bulen, W., Burns, R. & LeComte, J. Nitrogen fixation: hydrosulfite as electron donor with cell-free preparations of Azotobacter vinelandii and Rhodospirillum rubrum. Proc. Natl Acad. Sci. USA 53, 532–539 (1965).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 
    MATH 

    Google Scholar 

  • Kelly, M. Some properties of purified nitrogenase of Azotobacter chroococcum. Biochim. Biophys. Acta Enzymol. 171, 9–22 (1969).

    Article 
    CAS 
    MATH 

    Google Scholar 

  • Haaker, H. & Veeger, C. Involvement of the cytoplasmic membrane in nitrogen fixation by Azotobacter vinelandii. Eur. J. Biochem. 77, 1–10 (1977).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Yates, M. Effect of non-haem iron proteins and cytochrome C from Azotobacter upon the activity and oxygen sensitivity of Azobacter nitrogenase. FEBS Lett. 8, 281–285 (1970).

    Article 
    CAS 
    PubMed 
    MATH 

    Google Scholar 

  • Maier, R. & Moshiri, F. Role of the Azotobacter vinelandii nitrogenase-protective Shethna protein in preventing oxygen-mediated cell death. J. Bacteriol. 182, 3854–3857 (2000).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Lery, L. M., Bitar, M., Costa, M. G., Rössle, S. C. & Bisch, P. M. Unraveling the molecular mechanisms of nitrogenase conformational protection against oxygen in diazotrophic bacteria. BMC Genom. 11, S7 (2010).

    Article 
    CAS 

    Google Scholar 

  • Schlesier, J., Rohde, M., Gerhardt, S. & Einsle, O. A conformational switch triggers nitrogenase protection from oxygen damage by Shethna protein II (FeSII). J. Am. Chem. Soc. 138, 239–247 (2016).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Wang, Z., Burns, A. & Watt, G. Complex formation and oxygen sensitivity of Azotobacter vinelandii nitrogenase and its component proteins. Biochemistry 24, 214–221 (1985).

    Article 
    CAS 
    PubMed 
    MATH 

    Google Scholar 

  • Veeger, C. et al. in Nitrogen Fixation Vol. 1 (eds Newton, W. E. & Orme-Johnson, W. H.) 111–137 (University Park Press, 1980).

  • Kabasakal, B. V. et al. The crystal structure of Shethna protein II (FeSII) from Azotobacter vinelandii suggests a domain swap. Acta Crystallogr. D Struct. Biol. 80, 599–604 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Rutledge, H. L., Cook, B. D., Nguyen, H. P. M., Herzik, M. A. & Tezcan, F. A. Structures of the nitrogenase complex prepared under catalytic turnover conditions. Science 377, 865–869 (2022).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Cook, B. D. et al. Preparation of oxygen-sensitive proteins for high-resolution cryoEM structure determination using (an)aerobic blot-free vitrification. Preprint at bioRxiv https://doi.org/10.1101/2024.07.19.604374 (2024).

  • Tezcan, F. A. et al. Nitrogenase complexes: multiple docking sites for a nucleotide switch protein. Science 309, 1377–1380 (2005).

    Article 
    ADS 
    CAS 
    PubMed 
    MATH 

    Google Scholar 

  • Lou, J. et al. Mutagenesis studies of the FeSII protein of Azotobacter vinelandii: roles of histidine and lysine residues in the protection of nitrogenase from oxygen damage. Biochemistry 38, 5563–5571 (1999).

    Article 
    CAS 
    PubMed 
    MATH 

    Google Scholar 

  • Dey, A. et al. Solvent tuning of electrochemical potentials in the active sites of HiPIP versus ferredoxin. Science 318, 1464–1468 (2007).

    Article 
    ADS 
    CAS 
    PubMed 
    MATH 

    Google Scholar 

  • Lanzilotta, W. N. & Seefeldt, L. C. Changes in the midpoint potentials of the nitrogenase metal centers as a result of iron protein molybdenum-iron protein complex formation. Biochemistry 36, 12976–12983 (1997).

    Article 
    CAS 
    PubMed 
    MATH 

    Google Scholar 

  • Moshiri, F., Crouse, B. R., Johnson, M. K. & Maier, R. J. The “nitrogenase-protective” FeSII protein of Azotobacter vinelandii: overexpression, characterization, and crystallization. Biochemistry 34, 12973–12982 (1995).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Alleman, A. B. & Peters, J. W. Mechanisms for generating low potential electrons across the metabolic diversity of nitrogen-fixing bacteria. Appl. Env. Microbiol. 89, e00378–00323 (2023).

    Article 
    ADS 
    MATH 

    Google Scholar 

  • Ribbe, M. W., Hu, Y., Hodgson, K. O. & Hedman, B. Biosynthesis of nitrogenase metalloclusters. Chem. Rev. 114, 4063–4080 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Rubio, L. M. & Ludden, P. W. Biosynthesis of the iron-molybdenum cofactor of nitrogenase. Annu. Rev. Microbiol. 62, 93–111 (2008).

    Article 
    CAS 
    PubMed 
    MATH 

    Google Scholar 

  • Berman-Frank, I., Lundgren, P. & Falkowski, P. Nitrogen fixation and photosynthetic oxygen evolution in cyanobacteria. Res. Microbiol. 154, 157–164 (2003).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Santi, C., Bogusz, D. & Franche, C. Biological nitrogen fixation in non-legume plants. Ann. Bot. 111, 743–767 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Ryu, M.-H. et al. Control of nitrogen fixation in bacteria that associate with cereals. Nat. Microbiol. 5, 314–330 (2020).

    Article 
    CAS 
    PubMed 
    MATH 

    Google Scholar 

  • Quechol, R. et al. Heterologous synthesis of the complex homometallic cores of nitrogenase P- and M-clusters in Escherichia coli. Proc. Natl Acad. Sci. USA 120, e2314788120 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Gibson, D. G. et al. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat. Methods 6, 343–345 (2009).

    Article 
    CAS 
    PubMed 
    MATH 

    Google Scholar 

  • Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Jamali, K. et al. Automated model building and protein identification in cryo-EM maps. Nature 628, 450–457 (2024).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 
    MATH 

    Google Scholar 

  • Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486–501 (2010).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 
    MATH 

    Google Scholar 

  • Liebschner, D. et al. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Crystallogr. D Struct. Biol. 75, 861–877 (2019).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 
    MATH 

    Google Scholar 

  • Wojdyr, M. Fityk: a general-purpose peak fitting program. J. Appl. Crystallogr. 43, 1126–1128 (2010).

    Article 
    ADS 
    CAS 
    MATH 

    Google Scholar 

  • Schuck, P. Size-distribution analysis of macromolecules by sedimentation velocity ultracentrifugation and lamm equation modeling. Biophys. J. 78, 1606–1619 (2000).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 
    MATH 

    Google Scholar 

  • Stoll, S. & Schweiger, A. EasySpin, a comprehensive software package for spectral simulation and analysis in EPR. J. Magn. Reson. 178, 42–55 (2006).

    Article 
    ADS 
    CAS 
    PubMed 
    MATH 

    Google Scholar 

  • Manalastas-Cantos, K. et al. ATSAS 3.0: expanded functionality and new tools for small-angle scattering data analysis. J. Appl. Crystallogr. 54, 343–355 (2021).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Svergun, D., Barberato, C. & Koch, M. H. J. CRYSOL—a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates. J. Appl. Crystallogr. 28, 768–773 (1995).

    Article 
    ADS 
    CAS 

    Google Scholar 

  • Pettersen, E. F. et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).

    Article 
    CAS 
    PubMed 
    MATH 

    Google Scholar 

  • Honorato, R. V. et al. The HADDOCK2.4 web server for integrative modeling of biomolecular complexes. Nat. Protoc. 19, 3219–3241 (2024).

    Article 
    CAS 
    PubMed 
    MATH 

    Google Scholar 

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