The catalytic pathway of cytochrome P450cam at atomic resolution

Science

Volumn 287, Issue 5458, 2000, Pages 1615-1622

  Schlichting, Ilme ^a   Berendzen, Joel ^b   Chu, Kelvin ^b,g   Stock, Ann M ^c   Maves, Shelley A ^d   Benson, David E ^d   Sweet, Robert M ^e   Ringe, Dagmar ^f   Petsko, Gregory A ^f   Sligar, Stephen G ^a,d  

^a MAX PLANCK INSTITUTE OF MOLECULAR PHYSIOLOGY   (Germany)

^b LOS ALAMOS NATIONAL LABORATORY   (United States)

^c RUTGERS UNIVERSITY   (United States)

^d UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^e BROOKHAVEN NATIONAL LABORATORY   (United States)

^f BRANDEIS UNIVERSITY   (United States)

^g University of Vermont   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CAMPHOR; CAMPHOR 5 MONOOXYGENASE; HYDROCARBON; OXYGEN; PROTON; WATER;

ARTICLE; CATALYST; CRYSTALLOGRAPHY; ELECTRON; ENZYME ACTIVITY; ENZYME STRUCTURE; ENZYME SUBSTRATE COMPLEX; ENZYMOLOGY; HIGH TEMPERATURE; HYDROPHILICITY; HYDROXYLATION; PRIORITY JOURNAL; PSEUDOMONAS PUTIDA; RADIOLYSIS; WATER STRUCTURE;

CAMPHOR; CAMPHOR 5-MONOOXYGENASE; CATALYSIS; CRYSTALLIZATION; CRYSTALLOGRAPHY, X-RAY; ELECTRONS; FERRIC COMPOUNDS; FERROUS COMPOUNDS; HYDROGEN BONDING; HYDROXYLATION; LIGANDS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; OXYGEN; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTONS; PSEUDOMONAS PUTIDA; WATER;

DRYOBALANOPS; PSEUDOMONAS; PSEUDOMONAS PUTIDA;

EID: 0034088779     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.287.5458.1615     Document Type: Article

References (68)

1. For a comprehensive review of all aspects of P450, see P. R. Ortiz de Montellano, Ed., Cytochrome P450: Structure, Mechanism and Biochemistry (Plenum, New York, ed. 2, 1995).
2. F. P. Guengerich, J. Biol. Chem. 266, 10019 (1991); T. D. Porter and M. J. Coon, J. Biol. Chem. 266, 13469 (1991); J. H. Capdevila, J. R. Falck, R. W. Estabrook, FASEB J. 6, 731 (1992); M. Kubota et al., J. Biochem. 110, 232 (1991).
3. F. P. Guengerich, J. Biol. Chem. 266, 10019 (1991); T. D. Porter and M. J. Coon, J. Biol. Chem. 266, 13469 (1991); J. H. Capdevila, J. R. Falck, R. W. Estabrook, FASEB J. 6, 731 (1992); M. Kubota et al., J. Biochem. 110, 232 (1991).
4. F. P. Guengerich, J. Biol. Chem. 266, 10019 (1991); T. D. Porter and M. J. Coon, J. Biol. Chem. 266, 13469 (1991); J. H. Capdevila, J. R. Falck, R. W. Estabrook, FASEB J. 6, 731 (1992); M. Kubota et al., J. Biochem. 110, 232 (1991).
5. F. P. Guengerich, J. Biol. Chem. 266, 10019 (1991); T. D. Porter and M. J. Coon, J. Biol. Chem. 266, 13469 (1991); J. H. Capdevila, J. R. Falck, R. W. Estabrook, FASEB J. 6, 731 (1992); M. Kubota et al., J. Biochem. 110, 232 (1991).
6. J. Hedegaard and I. C. Gunsalus, J. Biol. Chem. 240, 4038 (1965); A. Tyson, J. D. Lipscomb, I. C. Gunsalus, J. Biol. Chem. 247, 5777 (1972); S. G. Sligar and I. C. Gunsalus, Proc. Natl. Acad Sci. U.S.A. 73, 1078 (1976); E. J. Mueller, P. J. Loida, S. G. Sligar, in Cytochrome P450: Structure, Mechanism and Biochemistry, P. R. Ortiz de Montellano, Ed. (Plenum, New York, ed. 2, 1995), pp. 83-124.
7. J. Hedegaard and I. C. Gunsalus, J. Biol. Chem. 240, 4038 (1965); A. Tyson, J. D. Lipscomb, I. C. Gunsalus, J. Biol. Chem. 247, 5777 (1972); S. G. Sligar and I. C. Gunsalus, Proc. Natl. Acad Sci. U.S.A. 73, 1078 (1976); E. J. Mueller, P. J. Loida, S. G. Sligar, in Cytochrome P450: Structure, Mechanism and Biochemistry, P. R. Ortiz de Montellano, Ed. (Plenum, New York, ed. 2, 1995), pp. 83-124.
8. J. Hedegaard and I. C. Gunsalus, J. Biol. Chem. 240, 4038 (1965); A. Tyson, J. D. Lipscomb, I. C. Gunsalus, J. Biol. Chem. 247, 5777 (1972); S. G. Sligar and I. C. Gunsalus, Proc. Natl. Acad Sci. U.S.A. 73, 1078 (1976); E. J. Mueller, P. J. Loida, S. G. Sligar, in Cytochrome P450: Structure, Mechanism and Biochemistry, P. R. Ortiz de Montellano, Ed. (Plenum, New York, ed. 2, 1995), pp. 83-124.
9. J. Hedegaard and I. C. Gunsalus, J. Biol. Chem. 240, 4038 (1965); A. Tyson, J. D. Lipscomb, I. C. Gunsalus, J. Biol. Chem. 247, 5777 (1972); S. G. Sligar and I. C. Gunsalus, Proc. Natl. Acad Sci. U.S.A. 73, 1078 (1976); E. J. Mueller, P. J. Loida, S. G. Sligar, in Cytochrome P450: Structure, Mechanism and Biochemistry, P. R. Ortiz de Montellano, Ed. (Plenum, New York, ed. 2, 1995), pp. 83-124.
10. + site is close to a neighboring molecule in the lattice. In general, for the experiments reported here, similar electron density features are seen in molecules 1 and 2, but mixtures seem to be present in molecule 2 that could not be modeled satisfactorily. It is possible that the two molecules represent slightly different stages of the reaction or different mixtures of species.
11. + site is close to a neighboring molecule in the lattice. In general, for the experiments reported here, similar electron density features are seen in molecules 1 and 2, but mixtures seem to be present in molecule 2 that could not be modeled satisfactorily. It is possible that the two molecules represent slightly different stages of the reaction or different mixtures of species.
12. + site is close to a neighboring molecule in the lattice. In general, for the experiments reported here, similar electron density features are seen in molecules 1 and 2, but mixtures seem to be present in molecule 2 that could not be modeled satisfactorily. It is possible that the two molecules represent slightly different stages of the reaction or different mixtures of species.
13. + site is close to a neighboring molecule in the lattice. In general, for the experiments reported here, similar electron density features are seen in molecules 1 and 2, but mixtures seem to be present in molecule 2 that could not be modeled satisfactorily. It is possible that the two molecules represent slightly different stages of the reaction or different mixtures of species.
14. R. Raag and T. L. Poulos, Biochemistry 28, 7585 (1989).
15. There are many examples; one is the difference between oxy- and carbonmonoxy-myoglobin. See the lively discussion in S. Borman, Chem. Eng. News 77, 31 (1999).
16. The number of model compounds that have been synthesized and characterized is too great to permit referencing even a representative sample. For a recent review, see J. T. Groves and Y. Han, in Cytochrome P450: Structure, Mechanism and Biochemistry, P. R. Ortiz de Montellano, Ed. (Plenum, New York, ed. 2, 1995), pp. 3-48.
17. R. E. White and M. J. Coon, Annu. Rev. Biochem. 49, 315 (1980); V. P. Miller et al., J. Biol. Chem. 267, 8936 (1992); W. R. Patterson et al., Biochemistry 34, 4342 (1995).
18. R. E. White and M. J. Coon, Annu. Rev. Biochem. 49, 315 (1980); V. P. Miller et al., J. Biol. Chem. 267, 8936 (1992); W. R. Patterson et al., Biochemistry 34, 4342 (1995).
19. R. E. White and M. J. Coon, Annu. Rev. Biochem. 49, 315 (1980); V. P. Miller et al., J. Biol. Chem. 267, 8936 (1992); W. R. Patterson et al., Biochemistry 34, 4342 (1995).
20. S. G. Sligar, J. D. Lipscomb, P. C. Debrunner, I. C. Gunsalus, Biochem. Biophys. Res. Commun. 61, 290 (1974); C. B. Brewer and J. A. Peterson, Arch. Biochem. Biophys. 249, 515 (1986).
21. S. G. Sligar, J. D. Lipscomb, P. C. Debrunner, I. C. Gunsalus, Biochem. Biophys. Res. Commun. 61, 290 (1974); C. B. Brewer and J. A. Peterson, Arch. Biochem. Biophys. 249, 515 (1986).
22. B. L. Stoddard, Pharmacol. Ther. 70, 215 (1996).
23. I. Schlichting and R. S. Goody, Methods Enzymol. 277, 467 (1997).
24. D. Ringe et al., Philos. Trans. R. Soc. London Ser. A 340, 243 (1992).
25. J. Hajdu and I. Anderson, Annu. Rev. Biophys. Biomol. Struct. 22, 467 (1993).
26. C. A. Petsko, Philos. Trans. R. Soc. London Ser. A Math. Phys. Sci. 340, 323 (1992).
27. J. D. Lipscomb, S. G. Sligar, M. J. Namtvedt, I. C. Gunsalus, J. Biol. Chem. 251, 1116 (1976).
28. B. Chance, P. Angiolillo, E. K. Yang, L. Powers, FEBS Lett. 112, 178 (1980); J. G. De Witt et al., J. Am. Chem. Soc. 113, 9219 (1991); R. Watanabe, N. Usami, K. Kobayashi, Int. J. Radiat. Biol. 68, 113 (1995); Y. Lindquist, W. J. Huang, G. Schneider, J. Shanklin, EMBO J. 15, 4081 (1996); M. Erikson, A. Jordan, H. Eklund, Biochemistry 37, 13349 (1998); E. R. Stadtman, Annu. Rev. Biochem. 62, 797 (1993).
29. B. Chance, P. Angiolillo, E. K. Yang, L. Powers, FEBS Lett. 112, 178 (1980); J. G. De Witt et al., J. Am. Chem. Soc. 113, 9219 (1991); R. Watanabe, N. Usami, K. Kobayashi, Int. J. Radiat. Biol. 68, 113 (1995); Y. Lindquist, W. J. Huang, G. Schneider, J. Shanklin, EMBO J. 15, 4081 (1996); M. Erikson, A. Jordan, H. Eklund, Biochemistry 37, 13349 (1998); E. R. Stadtman, Annu. Rev. Biochem. 62, 797 (1993).
30. B. Chance, P. Angiolillo, E. K. Yang, L. Powers, FEBS Lett. 112, 178 (1980); J. G. De Witt et al., J. Am. Chem. Soc. 113, 9219 (1991); R. Watanabe, N. Usami, K. Kobayashi, Int. J. Radiat. Biol. 68, 113 (1995); Y. Lindquist, W. J. Huang, G. Schneider, J. Shanklin, EMBO J. 15, 4081 (1996); M. Erikson, A. Jordan, H. Eklund, Biochemistry 37, 13349 (1998); E. R. Stadtman, Annu. Rev. Biochem. 62, 797 (1993).
31. B. Chance, P. Angiolillo, E. K. Yang, L. Powers, FEBS Lett. 112, 178 (1980); J. G. De Witt et al., J. Am. Chem. Soc. 113, 9219 (1991); R. Watanabe, N. Usami, K. Kobayashi, Int. J. Radiat. Biol. 68, 113 (1995); Y. Lindquist, W. J. Huang, G. Schneider, J. Shanklin, EMBO J. 15, 4081 (1996); M. Erikson, A. Jordan, H. Eklund, Biochemistry 37, 13349 (1998); E. R. Stadtman, Annu. Rev. Biochem. 62, 797 (1993).
32. B. Chance, P. Angiolillo, E. K. Yang, L. Powers, FEBS Lett. 112, 178 (1980); J. G. De Witt et al., J. Am. Chem. Soc. 113, 9219 (1991); R. Watanabe, N. Usami, K. Kobayashi, Int. J. Radiat. Biol. 68, 113 (1995); Y. Lindquist, W. J. Huang, G. Schneider, J. Shanklin, EMBO J. 15, 4081 (1996); M. Erikson, A. Jordan, H. Eklund, Biochemistry 37, 13349 (1998); E. R. Stadtman, Annu. Rev. Biochem. 62, 797 (1993).
33. B. Chance, P. Angiolillo, E. K. Yang, L. Powers, FEBS Lett. 112, 178 (1980); J. G. De Witt et al., J. Am. Chem. Soc. 113, 9219 (1991); R. Watanabe, N. Usami, K. Kobayashi, Int. J. Radiat. Biol. 68, 113 (1995); Y. Lindquist, W. J. Huang, G. Schneider, J. Shanklin, EMBO J. 15, 4081 (1996); M. Erikson, A. Jordan, H. Eklund, Biochemistry 37, 13349 (1998); E. R. Stadtman, Annu. Rev. Biochem. 62, 797 (1993).
34. K. Kobayashi et al., Biochim. Biophys. Acta 1037, 297 (1990); R. Davydov et al., FEBS Lett. 295, 113 (1991).
35. K. Kobayashi et al., Biochim. Biophys. Acta 1037, 297 (1990); R. Davydov et al., FEBS Lett. 295, 113 (1991).
36. M. Sharrock et al., Biochim. Biophys. Acta 420, 8 (1976); M. J. Honeychurch, A. O. Hill, L. L. Wong, FEBS Lett. 451, 351 (1999).
37. M. Sharrock et al., Biochim. Biophys. Acta 420, 8 (1976); M. J. Honeychurch, A. O. Hill, L. L. Wong, FEBS Lett. 451, 351 (1999).
38. J. Contzen and C. Jung, Biochemistry 38, 16253 (1999).
39. J. H. Dawson et al., J. Am. Chem. Soc. 108, 8114 (1986); D. Harris, G. Loew, L. Waskell, J. Am. Chem. Soc. 120, 4308 (1998).
40. J. H. Dawson et al., J. Am. Chem. Soc. 108, 8114 (1986); D. Harris, G. Loew, L. Waskell, J. Am. Chem. Soc. 120, 4308 (1998).
41. V. Fülöp et al., Structure 2, 201 (1994); S. L. Edwards, H. X. Nguyen, R. C. Hamlin, J. Kraut, Biochemistry 26, 1503 (1987); P. Gouet et al., Nature Struct. Biol. 3, 951 (1996).
42. V. Fülöp et al., Structure 2, 201 (1994); S. L. Edwards, H. X. Nguyen, R. C. Hamlin, J. Kraut, Biochemistry 26, 1503 (1987); P. Gouet et al., Nature Struct. Biol. 3, 951 (1996).
43. V. Fülöp et al., Structure 2, 201 (1994); S. L. Edwards, H. X. Nguyen, R. C. Hamlin, J. Kraut, Biochemistry 26, 1503 (1987); P. Gouet et al., Nature Struct. Biol. 3, 951 (1996).
44. J. T. Groves and G. A. McClusky, Biochem. Biophys. Res. Commun. 81, 154 (1978); J. T. Groves and D. V. Subramanian, J. Am. Chem. Soc. 106, 2177 (1984).
45. J. T. Groves and G. A. McClusky, Biochem. Biophys. Res. Commun. 81, 154 (1978); J. T. Groves and D. V. Subramanian, J. Am. Chem. Soc. 106, 2177 (1984).
46. H. Li, S. Narasimhulu, L. M. Havran, J. D. Winkler, T. L. Poulos, J. Am. Chem. Soc. 117, 6297 (1995).
47. I. Schlichting et al., data not shown.
48. M. Vidakovic, S. G. Sugar, H. Li, T. L. Poulos, Biochemistry 37, 9211 (1998).
49. H. Shimada, R. Makino, M. Unno, T. Horiuchi, Y. Ishimura, in Cytochrome P450. 8th International Conference, M. C. Lechner and J. Libbey, Eds. (Eurotext, Paris, 1994), pp. 299-306.
50. N. C. Gerber and S. G. Sligar, J. Biol. Chem. 269, 4260 (1994); J. Aikens and S. G. Sligar, J. Am. Chem. Soc. 116, 1143 (1994); S. A. Martinis, W. M. Atkins, P. S. Stayton, S. G. Sligar, J. Am. Chem. Soc. 111, 9252 (1989).
51. N. C. Gerber and S. G. Sligar, J. Biol. Chem. 269, 4260 (1994); J. Aikens and S. G. Sligar, J. Am. Chem. Soc. 116, 1143 (1994); S. A. Martinis, W. M. Atkins, P. S. Stayton, S. G. Sligar, J. Am. Chem. Soc. 111, 9252 (1989).
52. N. C. Gerber and S. G. Sligar, J. Biol. Chem. 269, 4260 (1994); J. Aikens and S. G. Sligar, J. Am. Chem. Soc. 116, 1143 (1994); S. A. Martinis, W. M. Atkins, P. S. Stayton, S. G. Sligar, J. Am. Chem. Soc. 111, 9252 (1989).
53. P. J. Loida and S. G. Sligar, Biochemistry 32, 11530 (1993).
54. D. L. Harris and G. H. Loew, J. Am. Chem. Soc. 118, 6377 (1996).
55. D. E. Benson, K. S. Suslick, S. G. Sligar, Biochemistry 36, 5104 (1997).
56. Y. Kimata, S. Tsukada, T. Iwamoto, K. Harii, Biochem. Biophys. Res. Commun. 208, 96 (1995).
57. R. Raag, S. A. Martinis, S. G. Sligar, T. L. Poulos, Biochemistry 30, 11420 (1991).
58. M. Newcomb et al., J. Am. Chem. Soc. in press.
59. R. M. Esnouf, J. Mol. Graphics 15, 133 (1997).
60. E. A. Meritt and M. E. P. Murphy, Acta Crystallogr. Sect. D 50, 869 (1994).
61. N. C. Gerber and S. G. Sligar, J. Am. Chem. Soc. 114, 8742 (1992).
62. T. L. Poulos, M. Perez, G. C. Wagner, J. Biol. Chem. 257, 10427 (1982).
63. W. Kabsch, J. Appl. Crystallogr. 26, 795 (1993).
64. J. Navaza, Acta Crystallogr. Sect. A 50, 157 (1994).
65. A. T. Brünger, X-PLOR: A System for Crystallography and NMR, version 3.1 (Yale Univ. Press, New Haven, CT, 1992).
66. A. T. Brünger et al., Acta Crystallogr. Sect. D 54, 905 (1998).
67. T. A. Jones, S. Cowan, J. Y. Zou, M. Kjeldgaard, Acta Crystallogr. Sect. A 47, 110 (1991).
68. The literature of cytochrome P450 is so vast, and so many people have made important contributions, that it is impossible in the space allowed to give even a representative set of references. We have tried to cite review articles whenever possible to provide links to the original papers. We apologize to those we have been unable to include. We gratefully acknowledge G. Holtermann for designing the pressure cell; M. Davies, N. C. Gerber, E. J. Mueller, and M. Vidakovic for supplying us with protein; C. Jung, G. Rosenbaum, and K. Scheffzek for discussions; and R. S. Goody, K. C. Holmes, and W. Kabsch for continuous support and encouragement. P. Ortiz de Montellano and J. A. Peterson provided useful advice. The referees made a number of very helpful suggestions that greatly improved the manuscript. We thank the Alexander von Humboldt Stiftung, the Human Frontiers Science Project, and the Richard und Anne Liese Leyendecker Stiftung for generous support and acknowledge the European Community biotech grant BIO2-CT942060 to I.S., NIH grants GM31756 and GM33775 to S.G.S, and GM26788 to G.A.P. and D.R. Beamline X12C is supported by the U.S. Department of Energy Offices of Health and Environmental Research and of Basic Energy Sciences, NIH, and NSF. The coordinates have been submitted to the PDB: 1d26, 1d24, 1d28, and 1d29 for the ferric, reduced, oxy, and oxyferryl complex, respectively.