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Crystal structure of a bacterial non-haem iron hydroxylase that catalyses the biological oxidation of methane

Nature volume 366, pages 537–543 (1993)Cite this article

Abstract

The 2.2 Å crystal structure of the 251K α2β2γ2 dimeric hydroxylase protein of methane mono-oxygenase from Methylococcus capsulatus (Bath) reveals the geometry of the catalytic di-iron core. The two iron atoms are bridged by exogenous hydroxide and acetate ligands and further coordinated by four glutamate residues, two histidine residues and a water molecule. The dinuclear iron centre lies in a hydrophobic active-site cavity for binding methane. An extended canyon runs between αβ pairs, which have many long α-helices, for possible docking of the reductase and coupling proteins required for catalysis.

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References

  1. Higgins, I. J., Best, D. J. & Hammond, R. C. Nature 286, 561–564 (1980).

    ADS  CAS  Article  Google Scholar 

  2. Pearman, G. I. & Fraser, P. J. Nature 332, 489–190 (1988).

    ADS  Article  Google Scholar 

  3. Colby, J. & Dalton, H. Biochem. J. 171, 461–468 (1978).

    CAS  Article  Google Scholar 

  4. Woodland, M. P., Patil, D. S., Cammack, R. & Dalton, H. Biochim, biophys. Acta 873, 237–242 (1986).

    CAS  Article  Google Scholar 

  5. Fox, B. G., Surerus, K. K., Münck, E. & Lipscomb, J. D. J. biol. Chem. 263, 10553–10556 (1988).

    CAS  PubMed  Google Scholar 

  6. DeWitt, J. G. et al. J. Am. chem. Soc. 113, 9219–9235 (1991).

    CAS  Article  Google Scholar 

  7. Que, L. Jr & True, A. E. Prog. inorg. Chem. 38, 97–200 (1990).

    CAS  Google Scholar 

  8. Vincent, J. B., Olivier-Lilley, G. L. & Averill, B. A. Chem. Rev. 90, 1447–1467 (1990).

    CAS  Article  Google Scholar 

  9. Kurtz, D. M. Jr & Pickril, B. C. Biochem. biophys. Res. Commun. 181, 337–341 (1991).

    CAS  Article  Google Scholar 

  10. Fox, B. G., Shanklin, J., Somerville, C. & Münck, E. Proc. natn. Acad. Sci. U.S.A. 90, 2486–2490 (1993).

    ADS  CAS  Article  Google Scholar 

  11. Lund, J. & Dalton, H. Eur. J. Biochem. 147, 291–296 (1985).

    CAS  Article  Google Scholar 

  12. Green, J. & Dalton, H. J. biol. Chem. 260, 15795–15801 (1985).

    CAS  PubMed  Google Scholar 

  13. Colby, J., Stirling, D. I. & Dalton, H. Biochem. J. 165, 395–402 (1977).

    CAS  Article  Google Scholar 

  14. Lindstrom, J. E. et al. Appl. environ. Microbiol. 57, 2514–2522 (1991).

    CAS  PubMed  PubMed Central  Google Scholar 

  15. Pritchard, P. H. & Costa, C. F. Environ. Sci. Technol. 25, 372–379 (1991).

    ADS  CAS  Article  Google Scholar 

  16. Green, J. & Dalton, H. J. biol. Chem. 264, 17698–17703 (1989).

    CAS  PubMed  Google Scholar 

  17. Fox, B. G., Borneman, J. G., Wackett, L. P. & Lipscomb, J. D. Biochemistry 29, 6419–6427 (1990).

    CAS  Article  Google Scholar 

  18. Periana, R. A. et al. Science 259, 340–343 (1993).

    ADS  CAS  Article  Google Scholar 

  19. Ericson, A. et al. J. Am. chem. Soc. 110, 2330–2332 (1988).

    CAS  Article  Google Scholar 

  20. DeRose, V., Liu, K. E., Lippard, S. J. & Hoffman, B. J. Am. chem. Soc. 115, 6440–6441 (1993).

    CAS  Article  Google Scholar 

  21. Fox, B. G. et al. J. Am. chem. Soc. 115, 3688–3701 (1993).

    CAS  Article  Google Scholar 

  22. Thomann, H. et al. J. Am. chem. Soc. 115, 8881–8882 (1993).

    CAS  Article  Google Scholar 

  23. Stainthorpe, A. C., Lees, V., Salmond, G. P. C., Dalton, H. & Murrell, J. C. Gene 91, 27–34 (1990).

    CAS  Article  Google Scholar 

  24. Nordlund, P., Dalton, H. & Eklund, H. FEBS Lett. 307, 257–262 (1992).

    CAS  Article  Google Scholar 

  25. Nordlund, P., Sjöberg, B.-M. & Eklund, H. Nature 345, 593–598 (1990).

    ADS  CAS  Article  Google Scholar 

  26. Nordlund, P. & Eklund, H. J. molec. Biol. 232, 123–164 (1993).

    CAS  Article  Google Scholar 

  27. Prior, S. D. & Dalton, H. FEMS Microbiol. Lett. 29, 105–109 (1985).

    CAS  Article  Google Scholar 

  28. Fox, B. G., Froland, W. A., Dege, J. E. & Lipscomb, J. D. J. biol. Chem. 264, 10023–10033 (1989).

    CAS  PubMed  Google Scholar 

  29. Atta, M., Fontecave, M., Wilkins, P. C. & Dalton, H. Eur. J. Biochem. 217, 217–223 (1993).

    CAS  Article  Google Scholar 

  30. Hamman, S. et al. Biochem. biophys. Res. Commun. 195, 594–599 (1993).

    CAS  Article  Google Scholar 

  31. Andersson, K. K., Elgren, T. E., Que, L. Jr & Lipscomb, J. D. J. Am. chem. Soc. 114, 8711–8713 (1992).

    CAS  Article  Google Scholar 

  32. Priestley, N. D. et al. J. Am. chem. Soc. 114, 7561–7562 (1992).

    CAS  Article  Google Scholar 

  33. Liu, K. E., Johnson, C. C., Newcomb, M. & Lippard, S. J. J. Am. chem. Soc. 115, 939–947 (1993).

    CAS  Article  Google Scholar 

  34. Rardin, R. L., Tolman, W. B. & Lippard, S. J. New. J. Chem. 15, 417–430 (1991).

    CAS  Google Scholar 

  35. Poulos, T. L., Finzel, B. C. & Howard, A. J. J. molec. Biol. 195, 687–700 (1987).

    CAS  Article  Google Scholar 

  36. Raag, R., Martinis, S. A., Sligar, S. G. & Poulos, T. L. Biochemistry 30, 11420–11429 (1991).

    CAS  Article  Google Scholar 

  37. Poulos, T. L., Finzel, B. C., Gunsalus, I. C., Wagner, G. C. & Kraut, J. J. biol. Chem. 260, 16122–16130 (1985).

    CAS  PubMed  Google Scholar 

  38. Liu, K. E. & Lippard, S. J. J. biol. Chem. 266, 12836–12839 (1991).

    CAS  PubMed  Google Scholar 

  39. Fox, B. G., Liu, Y., Dege, J. E. & Lipscomb, J. D. J. biol. Chem. 266, 540–550 (1991).

    CAS  PubMed  Google Scholar 

  40. Froland, W. A., Andersson, K. K., Lee, S.-K., Liu, Y. & Lipscomb, J. D. J. biol. Chem. 267, 17588–17597 (1992).

    CAS  PubMed  Google Scholar 

  41. Liu, K. E., Feig, A. L., Goldberg, D. P., Watton, S. P. & Lippard, S. J. in The Activation of Dioxygen and Homogeneous Catalytic Oxidation (eds Barton, D. H. R., Martell, A. E. & Sawyer, D.) (Plenum, New York, 1993).

    Google Scholar 

  42. Jiang, Y., Wilkins, P. C. & Dalton, H. Biochem. biophys. Acta 1163, 105–112 (1993).

    CAS  PubMed  Google Scholar 

  43. Nordlund, I., Powlowski, J. & Shingler, V. J. Sact. 172, 6826–6833 (1990).

    CAS  Google Scholar 

  44. Yen, K. M. et al. J. Bact. 173, 5315–5327 (1991).

    CAS  Article  Google Scholar 

  45. Rosenzweig, A. C., Frederick, C. A. & Lippard, S. J. J. molec. Biol. 227, 283–285 (1992).

    Article  Google Scholar 

  46. Knight, S. thesis, Swedish Univ. Agric. Sci., 1989.

  47. Terwillinger, T. C. & Eisenberg, D. Acta crystallogr. A39, 813–817 (1983).

    Article  Google Scholar 

  48. Otwinowski, Z. MLPHARE, CCP4 Proc. 80–88 (Daresbury Lab., Warrington, UK, 1991).

    Google Scholar 

  49. Wang, B. C. Meth. Enzym. 115, 90–112 (1985).

    CAS  Article  Google Scholar 

  50. Jones, T. A. in Molecular Replacements (eds Dodson, E.J.) 91–105 (SERC, Daresbury, UK, 1992).

    Google Scholar 

  51. Rould, M. A., Perona, J. J. & Steitz, T. A. Acta crystallogr. A48, 751–756 (1992).

    CAS  Article  Google Scholar 

  52. Nordlund, P. thesis, Swedish Univ. Agric. Sci., 1990.

  53. Jones, T. A. & Thirup, S. EMBO J. 5, 829–822 (1985).

    Google Scholar 

  54. Jones, T. A., Bergdoll, M. & Kjeldgaard, M. in Crystallographic Computing and Modeling Methods in Molecular Design (eds Bugg, C. & Ealick, S.) (Springer, New York, 1989).

    Google Scholar 

  55. Stainthorpe, A. C., Murrell, J. C., Salmond, G. P. C., Dalton, H. & Lees, V. Arch. Microbiol. 152, 154–159 (1989).

    CAS  Article  Google Scholar 

  56. Brünger, T. A., Kuriyan, J. & Karplus, M. Science 235, 458–460 (1987).

    ADS  Article  Google Scholar 

  57. Kraulis, P. J. appl. Crystallogr. 24, 946–950 (1991).

    Article  Google Scholar 

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Affiliations

  1. Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, USA

    Amy C. Rosenzweig & Stephen J. Lippard

  2. Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Dana Farber Cancer Institute, Boston, Massachusetts, 02115, USA

    Christin A. Frederick

  3. Department of Molecular Biology, Stockholm University, S-10691, Stockholm, Sweden

    P& auml;r Nordlund

Authors
  1. Amy C. Rosenzweig
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  2. Christin A. Frederick
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  3. Stephen J. Lippard
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  4. P& auml;r Nordlund
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Rosenzweig, A., Frederick, C., Lippard, S. et al. Crystal structure of a bacterial non-haem iron hydroxylase that catalyses the biological oxidation of methane. Nature 366, 537–543 (1993). https://doi.org/10.1038/366537a0

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