Structural changes caused by radiation-induced reduction and radiolysis: The effect of X-ray absorbed dose in a fungal multicopper oxidase

Acta Crystallographica Section D: Biological Crystallography

Volumn 68, Issue 5, 2012, Pages 564-577

  De La Mora, Eugenio ^a   Lovett, Janet E ^b,c,d   Blanford, Christopher F ^b,e   Garman, Elspeth F ^f   Valderrama, Brenda ^a   Rudino Pinera, Enrique ^a  

^a INSTITUTO DE BIOTECNOLOGÍA   (Mexico)

^b UNIVERSITY OF OXFORD   (United Kingdom)

^c UNIVERSITY OF OXFORD   (United Kingdom)

^d UNIVERSITY OF EDINBURGH   (United Kingdom)

^e UNIVERSITY OF MANCHESTER   (United Kingdom)

^f UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

bioelectrocatalysis; blue multicopper oxidases; copper reduction; dioxygen; fungal laccases; MicroPIXE; O arrange=stagger 2 reduction; protein electrochemistry; radiation damage; radiolysis; X ray induced reduction

Indexed keywords

COPPER; LACCASE; OXYGEN;

ARTICLE; BASIDIOMYCETES; CHEMICAL STRUCTURE; CHEMISTRY; CRYSTALLIZATION; ELECTRON SPIN RESONANCE; ENZYME ACTIVE SITE; ENZYMOLOGY; OXIDATION REDUCTION REACTION; PROTEIN CONFORMATION; RADIATION EXPOSURE; ULTRAVIOLET SPECTROPHOTOMETRY; X RAY; X RAY CRYSTALLOGRAPHY;

BASIDIOMYCOTA; CATALYTIC DOMAIN; COPPER; CRYSTALLIZATION; CRYSTALLOGRAPHY, X-RAY; ELECTRON SPIN RESONANCE SPECTROSCOPY; LACCASE; MODELS, MOLECULAR; OXIDATION-REDUCTION; OXYGEN; PROTEIN CONFORMATION; SPECTROPHOTOMETRY, ULTRAVIOLET; X-RAYS;

CORIOLOPSIS GALLICA; LYCAENINAE;

EID: 84860310355     PISSN: 09074449     EISSN: 13990047     Source Type: Journal    
DOI: 10.1107/S0907444912005343     Document Type: Article

References (85)

1. Adams, P. D. et al. (2010). Acta Cryst. D66, 213-221.
2. Augustine, A. J., Quintanar, L., Stoj, C. S., Kosman, D. J. & Solomon, E. I. (2007). J. Am. Chem. Soc. 129, 13118-13126.
3. Benson, D. A., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J. & Sayers, E. W. (2011). Nucleic Acids Res. 39, D32-D37.
4. Bento, I., Martins, L. O., Lopes, G. G., Carrondo, M. A. & Lindley, P. F. (2005). Dalton Trans., pp. 3507-3513.
5. Bento, I., Silva, C. S., Chen, Z., Martins, L. O., Lindley, P. F. & Soares, C. M. (2010). BMC Struct. Biol. 10, 28.
6. Berglund, G. I., Carlsson, G. H., Smith, A. T., Szöke, H., Henriksen, A. & Hajdu, J. (2002). Nature (London), 417, 463-468.
7. Bertrand, T., Jolivalt, C., Briozzo, P., Caminade, E., Joly, N., Madzak, C. & Mougin, C. (2002). Biochemistry, 41, 7325-7333.
8. Blanford, C. F., Heath, R. S. & Armstrong, F. A. (2007). Chem. Commun., pp. 1710-1712.
9. Bordoli, L., Kiefer, F., Arnold, K., Benkert, P., Battey, J. & Schwede, T. (2009). Nature Protoc. 4, 1-13.
10. Bradford, M. M. (1976). Anal. Biochem. 72, 248-254.
11. Buning, C., Canters, G. W., Comba, P., Dennison, C., Jeuken, L., Melter, M. & Sanders-Loehr, J. (2000). J. Am. Chem. Soc. 122, 204-211.
12. Burmeister, W. P. (2000). Acta Cryst. D56, 328-341.
13. Canters, G.W., Kolczak, U., Armstrong, F., Jeuken, L. J., Camba, R. & Sola, M. (2000). Faraday Discuss. 115, 205-220.
14. Chen, Z., Durão, P., Silva, C. S., Pereira, M. M., Todorovic, S., Hildebrandt, P., Bento, I., Lindley, P. F. & Martins, L. O. (2010). Dalton Trans. 39, 2875-2882.
15. Cole, J. L., Clark, P. A. & Solomon, E. I. (1990). J. Am. Chem. Soc. 112, 9534-9548.
16. Cracknell, J. A., Vincent, K. A. & Armstrong, F. A. (2008). Chem. Rev. 108, 2439-2461.
17. Dos Santos, L., Climent, V., Blanford, C. F. & Armstrong, F. A. (2010). Phys. Chem. Chem. Phys. 12, 13962-13974.
18. Ducros, V., Brzozowski, A. M., Wilson, K. S., Brown, S. H., Ostergaard, P., Schneider, P., Yaver, D. S., Pedersen, A. H. & Davies, G. J. (1998). Nature Struct. Biol. 5, 310-316.
19. Ducros, V., Brzozowski, A. M., Wilson, K. S., Østergaard, P., Schneider, P., Svendson, A. & Davies, G. J. (2001). Acta Cryst. D57, 333-336.
20. Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. (2010). Acta Cryst. D66, 486-501.
21. Enguita, F. J., Marcal, D., Martins, L. O., Grenha, R., Henriques, A. O., Lindley, P. F. & Carrondo, M. A. (2004). J. Biol. Chem. 279, 23472-23476.
22. Evans, P. (2006). Acta Cryst. D62, 72-82.
23. Felsenfeld, G. (1960). Arch. Biochem. Biophys. 87, 247-251.
24. Ferraroni, M., Myasoedova, N. M., Schmatchenko, V., Leontievsky, A. A., Golovleva, L. A., Scozzafava, A. & Briganti, F. (2007). BMC Struct. Biol. 7, 60.
25. Fourmond, V., Hoke, K., Heering, H. A., Baffert, C., Leroux, F., Bertrand, P. & Léger, C. (2009). Bioelectrochemistry, 76, 141-147.
26. Garavaglia, S., Cambria, M. T., Miglio, M., Ragusa, S., Iacobazzi, V., Palmieri, F., D'Ambrosio, C., Scaloni, A. & Rizzi, M. (2004). J. Mol. Biol. 342, 1519-1531.
27. Garman, E. (1999). Structure, 7, R291-R299.
28. Garman, E. F. (2010). Acta Cryst. D66, 339-351.
29. Garman, E. F. & Grime, G. W. (2005). Prog. Biophys. Mol. Biol. 89, 173-205.
30. Grime, G. W., Dawson, M., Marsh, M., McArthur, I. C. & Watt, F. (1991). Nucl. Instrum. Methods Phys. Res. B, 54, 52-63.
31. Guss, J. M., Harrowell, P. R., Murata, M., Norris, V. A. & Freeman, H. C. (1986). J. Mol. Biol. 192, 361-387.
32. Hakulinen, N., Andberg, M., Kallio, J., Koivula, A., Kruus, K. & Rouvinen, J. (2008). J. Struct. Biol. 162, 29-39.
33. Hakulinen, N., Kruus, K., Koivula, A. & Rouvinen, J. (2006). Biochem. Biophys. Res. Commun. 350, 929-934.
34. Hall, J. F., Kanbi, L. D., Strange, R. W. & Hasnain, S. S. (1999). Biochemistry, 38, 12675-12680.
35. Hanna, P. M., Tamilarasan, R. & McMillin, D. R. (1988). Biochem. J. 256, 1001-1004.
36. Hersleth, H. P. & Andersson, K. K. (2010). Biochim. Biophys. Acta, 1814, 785-796.
37. Hwang, H. J. & Lu, Y. (2004). Proc. Natl Acad. Sci. USA, 101, 12842-12847.
38. Iwaki, M., Kataoka, K., Kajino, T., Sugiyama, R., Morishita, H. & Sakurai, T. (2010). FEBS Lett. 584, 4027-4031.
39. Johansson, S. A. E., Campbell, J. L. & Malmqvist, K. G. (1995). Particle-Induced X-ray Emission Spectrometry (PIXE). New York: John Wiley & Sons.
40. Kallio, J. P., Auer, S., Jänis, J., Andberg, M., Kruus, K., Rouvinen, J., Koivula, A. & Hakulinen, N. (2009). J. Mol. Biol. 392, 895-909.
41. Kallio, J. P., Gasparetti, C., Andberg, M., Boer, H., Koivula, A., Kruus, K., Rouvinen, J. & Hakulinen, N. (2011). FEBS J. 278, 2283-2295.
42. Kau, L. S., Spira-Solomon, D. J., Penner-Hahn, J. E., Hodgson, K. O. & Solomon, E. I. (1987). J. Am. Chem. Soc. 109, 6433-6442.
43. Komori, H., Miyazaki, K. & Higuchi, Y. (2009). FEBS Lett. 583, 1189-1195.
44. Kosman, D. J. (2010). J. Biol. Inorg. Chem. 15, 15-28.
45. Kunamneni, A., Plou, F. J., Ballesteros, A. & Alcalde, M. (2008). Recent Pat. Biotechnol. 2, 10-24.
46. Larkin, M. A., Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H., Valentin, F., Wallace, I. M., Wilm, A., Lopez, R., Thompson, J. D., Gibson, T. J. & Higgins, D. G. (2007). Bioinformatics, 23, 2947-2948.
47. Laskowski, R. A., MacArthur, M. W., Moss, D. S. & Thornton, J. M. (1993). J. Appl. Cryst. 26, 283-291.
48. Leslie, A. G. W. (2006). Acta Cryst. D62, 48-57.
49. Lewis, N. S. & Nocera, D. G. (2006). Proc. Natl Acad. Sci. USA, 103, 15729-15735.
50. Lyashenko, A. V. et al. (2006). Acta Cryst. F62, 954-957.
51. Macedo, S., Pechlaner, M., Schmid, W., Weik, M., Sato, K., Dennison, C. & Djinović-Carugo, K. (2009). J. Synchrotron Rad. 16, 191-204.
52. Machonkin, T. E., Quintanar, L., Palmer, A. E., Hassett, R., Severance, S., Kosman, D. J. & Solomon, E. I. (2001). J. Am. Chem. Soc. 123, 5507-5517.
53. Matera, I., Gullotto, A., Tilli, S., Ferraroni, M., Scozzafava, A. & Briganti, F. (2008). Inorg. Chim. Acta, 361, 4129-4137.
54. McGeehan, J., Ravelli, R. B. G., Murray, J. W., Owen, R. L., Cipriani, F.,McSweeney, S.,Weik, M. & Garman, E. F. (2009). J. Synchrotron Rad. 16, 163-172.
55. Meharenna, Y. T., Doukov, T., Li, H., Soltis, S. M. & Poulos, T. L. (2010). Biochemistry, 49, 2984-2986.
56. Messerschmidt, A., Luecke, H. & Huber, R. (1993). J. Mol. Biol. 230, 997-1014.
57. Murray, J.W., Garman, E. F. & Ravelli, R. B. G. (2004). J. Appl. Cryst. 37, 513-522.
58. Murshudov, G. N., Skubák, P., Lebedev, A. A., Pannu, N. S., Steiner, R. A., Nicholls, R. A., Winn, M. D., Long, F. & Vagin, A. A. (2011). Acta Cryst. D67, 355-367.
59. Nave, C. & Garman, E. F. (2005). J. Synchrotron Rad. 12, 257-260.
60. Oliéric, V., Ennifar, E., Meents, A., Fleurant, M., Besnard, C., Pattison, P., Schiltz, M., Schulze-Briese, C. & Dumas, P. (2007). Acta Cryst. D63, 759-768.
61. Olsson, M. H. M., Søndergaard, C. R., Rostkowski, M. & Jensen, J. H. (2011). J. Chem. Theory Comput. 7, 525-537.
62. O'Neill, P., Stevens, D. L. & Garman, E. (2002). J. Synchrotron Rad. 9, 329-332.
63. Owen, R. L., Holton, J. M., Schulze-Briese, C. & Garman, E. F. (2009). J. Synchrotron Rad. 16, 143-151.
64. Paithankar, K. S., Owen, R. L. & Garman, E. F. (2009). J. Synchrotron Rad. 16, 152-162.
65. Paulus, U. A., Wokaun, A., Scherer, G. G., Schmidt, T. J., Stamenkovic, V., Radmilovic, V., Markovic, N. M. & Ross, P. N. (2002). J. Phys. Chem. B, 106, 4181-4191.
66. Pickard, M. A., Roman, R., Tinoco, R. & Vazquez-Duhalt, R. (1999). Appl. Environ. Microb. 65, 3805-3809.
67. Piontek, K., Antorini,M. & Choinowski, T. (2002). J. Biol. Chem. 277, 37663-37669.
68. Polyakov, K.M., Fedorova, T. V., Stepanova, E. V., Cherkashin, E. A., Kurzeev, S. A., Strokopytov, B. V., Lamzin, V. S. & Koroleva, O. V. (2009). Acta Cryst. D65, 611-617.
69. Quintanar, L., Stoj, C., Wang, T.-P., Kosman, D. J. & Solomon, E. I. (2005). Biochemistry, 44, 6081-6091.
70. Ravel, B. & Newville, M. (2005). J. Synchrotron Rad. 12, 537-541.
71. Ravelli, R. B. G. & Garman, E. F. (2006). Curr. Opin. Struct. Biol. 16, 624-629.
72. Ravelli, R. B. G. & McSweeney, S. M. (2000). Structure, 8, 315-328.
73. Remenyi, R., Jeuken, L. J., Comba, P. & Canters, G.W. (2001). J. Biol. Inorg. Chem. 6, 23-26.
74. Sakurai, T. (2006). FEBS Lett. 580, 1729-1732.
75. Sakurai, T., Suzuki, S. & Chikira, M. (1990). J. Biochem. 107, 37-42.
76. Solomon, E. I., Sundaram, U. M. & Machonkin, T. E. (1996). Chem. Rev. 96, 2563-2606.
77. Stoll, S. & Schweiger, A. (2006). J. Magn. Reson. 178, 42-55.
78. Taylor, A. B., Stoj, C. S., Ziegler, L., Kosman, D. J. & Hart, P. J. (2005). Proc. Natl Acad. Sci. USA, 102, 15459-15464.
79. Tye, J. W., Hall, M. B. & Darensbourg, M. Y. (2005). Proc. Natl Acad. Sci. USA, 102, 16911-16912.
80. Vagin, A. & Teplyakov, A. (2010). Acta Cryst. D66, 22-25.
81. Vaguine, A. A., Richelle, J. & Wodak, S. J. (1999). Acta Cryst. D55, 191-205.
82. Vakoufari, E., Wilson, K. S. & Petratos, K. (1994). FEBS Lett. 347, 203-206.
83. Weik, M., Ravelli, R. B. G., Kryger, G., McSweeney, S., Raves, M. L., Harel, M., Gros, P., Silman, I., Kroon, J. & Sussman, J. L. (2000). Proc. Natl Acad. Sci. USA, 97, 623-628.
84. Winn, M. D. et al. (2011). Acta Cryst. D67, 235-242.
85. Zhu, Z., Cunane, L. M., Chen, Z., Durley, R. C., Mathews, F. S. & Davidson, V. L. (1998). Biochemistry, 37, 17128-17136.