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Crystal structure of nitric oxide reductase from denitrifying fungus Fusarium oxysporum

Abstract

Structures of nitric oxide reductase (NOR) in the ferric resting and the ferrous CO states have been solved at 2.0 Å resolution. These structures provide significant new insights into how NO is reduced in biological systems. The haem distal pocket is open to solvent, implicating this region as a possible NADH binding site. In combination with mutagenesis results, a hydrogen-bonding network from the water molecule adjacent to the iron ligand to the protein surface of the distal pocket through the hydroxyl group of Ser 286 and the carboxyl group of Asp 393 can be assigned to a pathway for proton delivery during the NO reduction reaction.

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References

  1. Culotta, E. & Koshland, D.E. Jr. NO news is good news. Science 258, 1862–1865 (1992).

    Article  CAS  Google Scholar 

  2. Stamler, J.S., Singel, D.S., Loscalzo, J. Biochemistry of nitric oxide and its redox-activated forms. Science 258, 1898–1902 (1992).

    Article  CAS  Google Scholar 

  3. Coyne, M.S., Arunakumari, A.A., Averill, R.A., Tiedje, J.M. Immunological identification and distribution of dissimilatory heme cd1 and nonheme copper nitrite reductases in denitrifying bacteria. Appl. Environ. Microbiol. 55, 2924–2931 (1989).

    CAS  PubMed  PubMed Central  Google Scholar 

  4. Ferguson, S.J. Denitrification: a question of the control and organization of electron and ion transport. Trends Biochem. Sci. 12, 354–357 (1987).

    Article  CAS  Google Scholar 

  5. Knowles, R. Denitrification. Microbiol. Rev. 46, 43–70 (1982).

    CAS  PubMed  PubMed Central  Google Scholar 

  6. Carr, G.J. & Ferguson, S.J. The nitric oxide reductase of Paracoccus denitrificans. Biochem. J. 269, 423–429 (1990).

    Article  CAS  Google Scholar 

  7. Turk, T. & Hollocher, T.C. Oxidation of dithiothreitol during turnover of nitric oxide reductase: evidence for generation of nitroxyl with the enzyme from Paracoccus denitrificans. Biochem. Biophys. Res. Commun. 183, 983–988 (1992).

    Article  CAS  Google Scholar 

  8. Kastrau, D.H.W., Heiss, B., Kroneck, P.M.H., Zumft, W.G. Nitric oxide reductase from Pseudomonas stutzeri, a novel cytochrome be complex, Phospholipid requirement, electron paramagnetic resonance and redox properties. Eur. J. Biochem. 222, 293–303 (1994).

    Article  CAS  Google Scholar 

  9. Shoun, H., Suyama, W., Yasui, T. Soluble, nitrate/nitrite-inducible cytochrome P450 of the fungus Fusarium oxysporum. FEBS Lett. 244, 11–14 (1989).

    Article  CAS  Google Scholar 

  10. Shoun, H. & Tanimoto, T. Denitrification by the fungus Fusarium oxysporum and involvement of cytochrome P450 in the respiratory nitrite reduction. J. Biol. Chem. 266, 11078–11082 (1991).

    CAS  PubMed  Google Scholar 

  11. Nakahara, K., Tanimoto, T., Hatano, K., Usuda, K., Shoun, H. Cytochrome P450 55A1 (P450dNIR) acts as nitric oxide reductase employing NADH as the direct electron donor. J. Biol. Chem. 268, 8350–8355 (1993).

    CAS  PubMed  Google Scholar 

  12. Kizawa, H., Tomura, D., Oda, M., Fukamizu, A., Hoshino, T., Gotoh, O., Yasui, T., Shoun, H. Nucleotide sequence of the unique nitrate/nitrite-inducible cytochrome P450 cDNA from Fusarium oxysporum. J. Biol. Chem. 266, 10632–10637 (1991).

    CAS  PubMed  Google Scholar 

  13. Shiro, Y., Fujii, M., lizuka, T., Adachi, S., Tsukamoto, K., Nakahara, K., Shoun, H. Spectroscopic and kinetic studies on reaction of cytochrome P450nor with nitric oxide. J. Biol. Chem. 270, 1617–1623 (1995).

    Article  CAS  Google Scholar 

  14. Poulos, T.L., Finzel, B.C., Howard, A. J. High-resolution crystal structure of cytochrome P450cam. J. Mol. Biol. 195, 687–700 (1987).

    Article  CAS  Google Scholar 

  15. Raag, R. & Poulos, T.L. Crystal structure of the carbon monoxide-substrate-cytochrome P450cam ternary complex. Biochemistry 28, 7586–7592 (1989).

    Article  CAS  Google Scholar 

  16. Ravichandran, K.G., Boddupalli, S.S., Hasemann, C.A., Peterson, J.A., Deisenhofer, J. Crystal structure of hemoprotein domain of P450BM3, a prototype for microsomal P450's. Science 261, 731–736 (1993).

    Article  CAS  Google Scholar 

  17. Hasemann, C.A., Ravichandran, K.G., Peterson, J.A., Deisenhofer, J. Crystal structure and refinement of cytochrome P450terp at 2.3 Å resolution. J. Mol. Biol. 236, 1169–1185 (1994).

    Article  CAS  Google Scholar 

  18. Cupp-Vickery, J.R. & Poulos, T.L. Structure of cytochrome P450eryF involved in erythromycin biosynthesis. Nature Struct. Biol. 2, 144–153 (1995).

    Article  CAS  Google Scholar 

  19. Cupp-Vickery, J.R., Han, O., Hutchinson, C.R., Poulos, T. L. Substrate-assisted catalysis in cytochrome P450eryF. Nature Struct. Biol. 3, 632–637 (1996).

    Article  CAS  Google Scholar 

  20. Collaborative computing project No. 4 The CCP4 suite: programs for protein crystallography. Acta crystallogr. D50, 760–763 (1994).

  21. Laskowski, R.A., MacArthur, M.W., Moss, D.S., Thronton, J.M. PROCHECK: a program to check the stereochemical quality of protein structure. J. Appl. Crystallogr. 26, 283–291 (1993).

    Article  CAS  Google Scholar 

  22. Poulos, T.L., Cupp-Vickery, J., Li, H. Cytochrome P450. structure, mechanism, and biochemistry (2nd Ed.). (ed. Ortiz de Montellano, P. R.) 125–150 (Plenum Press, New York; 1995).

    Google Scholar 

  23. Peterson, J.A. & Graham-Lorence, S.E. Cytochrome P450. structure, mechanism, and biochemistry (2nd Ed.). (ed, Ortiz de Montellano, P. R.) 151–180 (Plenum Press, New York; 1995).

    Google Scholar 

  24. Hasemann, C.A., Ravichandran, K.G., Boddupalli, S.S., Peterson, J.A., Deisenhofer, J. Structure and function of cytochrome P450: a comparative analysis of three crystal structures. Structure 3, 41–62 (1995).

    Article  CAS  Google Scholar 

  25. Shiro, Y., Kato, M., lizuka, T., Nakahara, K., Shoun, H. Kinetics and thermodynamics of CO binding to cytochrome P450nor. Biochemistry 33, 8673–8677 (1994).

    Article  CAS  Google Scholar 

  26. Shiro, Y., Fujii, M., Isogai, Y., Adachi, S., lizuka, T., Obayashi, E., Makino, R., Nakahara, R., Shoun, H. Iron-ligand structure and iron redox property of nitric oxide reductase cytochrome P450nor from Fusarium oxysporum: relevance to Its NO reduction activity. Biochemistry 34, 9052–9058 (1995).

    Article  CAS  Google Scholar 

  27. Usuda, K., Toritsuka, N., Matsuo, Y., Kim, D.-H., Shoun, H. Denitrification by the fungus Cylindrocarpon tonkinense: anaerobic cell growth and two isozyme forms of cytochrome P450nor. Appl. Environ. Microbiol. 61, 883–889 (1995).

    CAS  PubMed  PubMed Central  Google Scholar 

  28. Toritsuka, N., Shoun, H., Singh, U.P., Park, S.-Y., Iizuka, T., Shiro, Y. Functional and structural comparison of nitric oxide reductases from denitrifying Cylindrocarpon tonkinense and Fusarium oxysporum. Biochim. Biophys. Acta 1338, 93–99 (1997).

    Article  CAS  Google Scholar 

  29. Imai, M., Shimada, H., Watanabe, Y., Matsushima-Hibiya, Y., Makino, R., Koga, H., Horiuchi, T., Ishimura, Y. Uncoupling of the cytochrome P-450cam monooxygenase reaction by a single mutation, threonine-252 to alanine or valine: A possible role of the hydroxy amino acid in oxygen activation. Proc. Natl. Acad. Sci. USA 86, 7823–7827 (1989).

    Article  CAS  Google Scholar 

  30. Raag, R., Martinis, S.A., Sligar, S.G., Poulos, T.L. Crystal structure of the cytochrome P- 450cam active site mutant Thr252Ala. Biochemistry 30, 11420–11429 (1991).

    Article  CAS  Google Scholar 

  31. Gerber, N.C. & Sligar, S.G. Catalytic mechanism of cytochrome P450: evidence for a distal charge relay. J. Am. Chem. Soc. 114, 8742–8743 (1992).

    Article  CAS  Google Scholar 

  32. Gerber, N.C. & Sligar, S.G. A role for Asp-251 in cytochrome P450cam oxygen activation. J. Biol. Chem. 269, 4260–4266 (1994).

    CAS  PubMed  Google Scholar 

  33. Yeom, H., Sligar, S.G., Li, H., Poulos, T.L., Fulco, A.J. The role of Thr268 in oxygen activation of cytochrome P450BM3. Biochemistry 34, 14733–14740 (1995).

    Article  CAS  Google Scholar 

  34. Harris, D.L. & Loew, G.H.J. Investigation of the proton-assisted pathway to formation of the catalytically active, ferryl species of P450s by molecular dynamics studies of P450eryF. J. Am. Chem. Soc. 118, 6377–6387 (1996).

    Article  CAS  Google Scholar 

  35. Park, S.-Y., Shimizu, H., Adachi, S.-i., Shiro, Y., Iizuka, T., Nakagawa, A., Tanaka, I., Shoun, H., Hori, H. Crystallization, Preliminary Diffraction and Electron Paramagnetic Resonance Studies of a Single Crystal of Cytochrome P450nor. FEBS Lett. 412, 346–350 (1997).

    Article  Google Scholar 

  36. Sakabe, N. A focusing weissenberg camera with multi-layer-line screens for macromolecular crystallography. J. Appl. Crystallogr. 16, 542–547 (1983).

    Article  CAS  Google Scholar 

  37. Otwinowski, Z. Oscillation data reduction program. In Data collection and processing (L. Sawyer, N. Isaace & S. Bailey, eds) 56–62 (SERC Daresbury Laboratory, Warrington, UK; 1993).

    Google Scholar 

  38. Abrahams, J.P., Leliew, A.G.W., Lutter, R., Walker, J.E. Structure at 2.8 Å resolution of F1-ATPase fom bovine heart mitochondria. Nature 370, 621–628 (1994).

    Article  CAS  Google Scholar 

  39. Jones, T.A., Zou, J.Y., Cowan, S.W., Kjeldgaard, M. Improved method for building protein models in electron density maps and location of errors in these models. Acta Crystallogr. A47, 110–119 (1991).

    Article  CAS  Google Scholar 

  40. Brünger, A.T. X-PLOR, a system for X-ay crystallography and NMR. Version 3.1 (Yale University Press, New Haven, Connecticut; 1992).

    Google Scholar 

  41. Kraulis, P.J. MOLSCRIPT: a program to protuce both de tailed and schematic plots of protein structures. J. Appl. Crystallogr. 24, 946–950 (1991).

    Article  Google Scholar 

  42. Evans, S.V. SETOR: hardware lighted three-dimentional solid model representations of macromolecules. J. Mol. Graphics 11, 134–1338 (1993).

    Article  CAS  Google Scholar 

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Correspondence to Yoshitsugu Shiro.

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Park, SY., Shimizu, H., Adachi, Si. et al. Crystal structure of nitric oxide reductase from denitrifying fungus Fusarium oxysporum. Nat Struct Mol Biol 4, 827–832 (1997). https://doi.org/10.1038/nsb1097-827

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  • DOI: https://doi.org/10.1038/nsb1097-827

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