Crystal structure and biophysical properties of Bacillus subtilis BdbD. An oxidizing thiol:disulfide oxidoreductase containing a novel metal site

Journal of Biological Chemistry

Volumn 284, Issue 35, 2009, Pages 23719-23733

  Crow, Allister ^a   Lewin, Allison ^a   Hecht, Oliver ^a   Möller, Mirja Carlsson ^b   Moore, Geoffrey R ^a   Hederstedt, Lars ^b   Le Brun, Nick E ^a  

^a UNIVERSITY OF EAST ANGLIA   (United Kingdom)

^b LUND UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVE SITE; BACILLUS SUBTILIS; BIOPHYSICAL PROPERTIES; CONFORMATIONAL CHANGE; CYTOPLASMIC MEMBRANE; DISULFIDE BONDS; DISULFIDE OXIDOREDUCTASE; ELECTRON EXCHANGE; INTER-DOMAIN; MEMBRANE ANCHORS; METAL SITES; N-TERMINALS; NORMAL HYDROGEN ELECTRODES; REDUCTION POTENTIAL; SUBTILIS; THIOREDOXINS;

AMINES; BACTERIOLOGY; CALCIUM; CELL MEMBRANES; ENZYMES; ESCHERICHIA COLI; HYDROGEN; PROTEINS;

CRYSTAL STRUCTURE;

CALCIUM ION; CYSTEINE; OXIDOREDUCTASE; PEPTIDE; PROTEIN; THIOL; THIOL DISULFIDE OXIDOREDUCTASE; UNCLASSIFIED DRUG;

ARTICLE; BACILLUS SUBTILIS; CELL MEMBRANE; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; CRYSTAL STRUCTURE; DISULFIDE BOND; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME SUBSTRATE; NONHUMAN; OXIDATION; PH ELECTRODE; PKA; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; BINDING SITES; CALCIUM; CRYSTALLIZATION; MOLECULAR CONFORMATION; MOLECULAR SEQUENCE DATA; OXIDATION-REDUCTION; PROTEIN BINDING; PROTEIN DISULFIDE REDUCTASE (GLUTATHIONE); PROTEIN STRUCTURE, TERTIARY; SEQUENCE HOMOLOGY, AMINO ACID;

BACILLUS SUBTILIS; ESCHERICHIA COLI;

EID: 69949125089     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M109.005785     Document Type: Article

References (75)

1. Dailey, F. E., and Berg, H. C. (1993) Proc. Natl. Acad. Sci. U.S.A. 90, 1043-1047
2. Yamanaka, H., Kameyama, M., Baba, T., Fujii, Y., and Okamoto, K. (1994) J. Bacteriol. 176, 2906-2913
3. Yu, J., Webb, H., and Hirst, T. R. (1992) Mol. Microbiol. 6, 1949-1958
4. Heras, B., Shouldice, S. R., Totsika, M., Scanlon, M. J., Schembri, M. A., and Martin, J. L. (2009) Nat. Rev. Microbiol. 7, 215-225
5. Aslund, F., and Beckwith, J. (1999) J. Bacteriol. 181, 1375-1379
6. Martin, J. L. (1995) Structure 3, 245-250
7. Bardwell, J. C., McGovern, K., and Beckwith, J. (1991) Cell 67, 581-589
8. Martin, J. L., Bardwell, J. C., and Kuriyan, J. (1993) Nature 365, 464-468
9. Wunderlich, M., and Glockshuber, R. (1993) Protein Sci. 2, 717-726
10. Zapun, A., Bardwell, J. C., and Creighton, T. E. (1993) Biochemistry 32, 5083-5092
11. Nelson, J. W., and Creighton, T. E. (1994) Biochemistry 33, 5974-5983
12. Bardwell, J. C., Lee, J. O., Jander, G., Martin, N., Belin, D., and Beckwith, J. (1993) Proc. Natl. Acad. Sci. U.S.A. 90, 1038-1042
13. Bader, M., Muse, W., Ballou, D. P., Gassner, C., and Bardwell, J. C. (1999) Cell 98, 217-227
14. Kadokura, H., Bader, M., Tian, H., Bardwell, J. C., and Beckwith, J. (2000) Proc. Natl. Acad. Sci. U.S.A. 97, 10884-10889
15. Dutton, R. J., Boyd, D., Berkmen, M., and Beckwith, J. (2008) Proc. Natl. Acad. Sci. U.S.A. 105, 11933-11938
16. Heras, B., Kurz, M., Jarrott, R., Shouldice, S. R., Frei, P., Robin, G., Cemazar, M., Thöny-Meyer, L., Glockshuber, R., and Martin, J. L. (2008) J. Biol. Chem. 283, 4261-4271
17. Goulding, C. W., Apostol, M. I., Gleiter, S., Parseghian, A., Bardwell, J., Gennaro, M., and Eisenberg, D. (2004) J. Biol. Chem. 279, 3516-3524
18. Kouwen, T. R., van der Goot, A., Dorenbos, R., Winter, T., Antelmann, H., Plaisier, M. C., Quax, W. J., van Dijl, J. M., and Dubois, J. Y. (2007) Mol. Microbiol. 64, 984-999
19. Meima, R., Eschevins, C., Fillinger, S., Bolhuis, A., Hamoen, L. W., Dorenbos, R., Quax, W. J., van Dijl, J. M., Provvedi, R., Chen, I., Dubnau, D., and Bron, S. (2002) J. Biol. Chem. 277, 6994-7001
20. Erlendsson, L. S., and Hederstedt, L. (2002) J. Bacteriol. 184, 1423-1429
21. Erlendsson, L. S., Acheson, R. M., Hederstedt, L., and Le Brun, N. E. (2003) J. Biol. Chem. 278, 17852-17858
22. Erlendsson, L. S., Möller, M., and Hederstedt, L. (2004) J. Bacteriol. 186, 6230-6238
23. Crow, A., Liu, Y., Möller, M. C., Le Brun, N. E., and Hederstedt, L. (2009) J. Biol. Chem. 284, 10056-10066
24. Schägger, H., and von Jagow, G. (1987) Anal. Biochem. 166, 368-379
25. Pace, C. N., Vajdos, F., Fee, L., Grimsley, G., and Gray, T. (1995) Protein Sci. 4, 2411-2423
26. Leslie, A. G. (2006) Acta Crystallogr. D Biol. Crystallogr. 62, 48-57
27. Evans, P. (2006) Acta Crystallogr. D Biol. Crystallogr. 62, 72-82
28. Potterton, L., McNicholas, S., Krissinel, E., Gruber, J., Cowtan, K., Emsley, P., Murshudov, G. N., Cohen, S., Perrakis, A., and Noble, M. (2004) Acta Crystallogr. D Biol. Crystallogr. 60, 2288-2294
29. Morris, R. J., Perrakis, A., and Lamzin, V. S. (2003) Methods Enzymol. 374, 229-244
30. Emsley, P., and Cowtan, K. (2004) Acta Crystallogr. D Biol. Crystallogr. 60, 2126-2132
31. Murshudov, G. N., Vagin, A. A., and Dodson, E. J. (1997) Acta Crystallogr. D Biol. Crystallogr. 53, 240-255
32. Laskowski, R. A., Macarthur, M. W., Moss, D. S., and Thornton, J. M. (1993) J. Appl. Crystallogr. 26, 283-291
33. Kleywegt, G. J., and Jones, T. A. (1996) Acta Crystallogr. D Biol. Crystallogr. 52, 826-828
34. Kleywegt, G. J. (2007) Acta Crystallogr. D Biol. Crystallogr. 63, 94-100
35. Chau, M. H., and Nelson, J. W. (1991) FEBS Lett. 291, 296-298
36. Lewin, A., Crow, A., Hodson, C. T., Hederstedt, L., and Le Brun, N. E. (2008) Biochem. J. 414, 81-91
37. Delaglio, F., Grzesiek, S., Vuister, G. W., Zhu, G., Pfeifer, J., and Bax, A. (1995) J. Biomol. NMR 6, 277-293
38. Lewin, A., Crow, A., Oubrie, A., and Le Brun, N. E. (2006) J. Biol. Chem. 281, 35467-35477
39. Monika, E. M., Goldman, B. S., Beckman, D. L., and Kranz, R. G. (1997) J. Mol. Biol. 271, 679-692
40. Käll, L., Krogh, A., and Sonnhammer, E. L. (2004) J. Mol. Biol. 338, 1027-1036
41. Inaba, K., Murakami, S., Suzuki, M., Nakagawa, A., Yamashita, E., Okada, K., and Ito, K. (2006) Cell 127, 789-801
42. Guddat, L. W., Bardwell, J. C., and Martin, J. L. (1998) Structure 6, 757-767
43. Chivers, P. T., Prehoda, K. E., and Raines, R. T. (1997) Biochemistry 36, 4061-4066
44. Grauschopf, U., Winther, J. R., Korber, P., Zander, T., Dallinger, P., and Bardwell, J. C. A. (1995) Cell 83, 947-955
45. Moutevelis, E., and Warwicker, J. (2004) Protein Sci. 13, 2744-2752
46. Ren, G., Stephan, D., Xu, Z., Zheng, Y., Tang, D., Harrison, R. S., Kurz, M., Jarrott, R., Shouldice, S. R., Hiniker, A., Martin, J. L., Heras, B., and Bardwell, J. C. (2009) J. Biol. Chem. 284, 10150-10159
47. Stirnimann, C. U., Rozhkova, A., Grauschopf, U., Grütter, M. G., Glockshuber, R., and Capitani, G. (2005) Structure 13, 985-993
48. Qin, J., Clore, G. M., Kennedy, W. M., Huth, J. R., and Gronenborn, A. M. (1995) Structure 3, 289-297
49. Qin, J., Clore, G. M., Kennedy, W. P., Kuszewski, J., and Gronenborn, A. M. (1996) Structure 4, 613-620
50. Kadokura, H., Tian, H., Zander, T., Bardwell, J. C., and Beckwith, J. (2004) Science 303, 534-537
51. Chivers, P. T., and Raines, R. T. (1997) Biochemistry 36, 15810-15816
52. Crow, A., Acheson, R. M., Le Brun, N. E., and Oubrie, A. (2004) J. Biol. Chem. 279, 23654-23660
53. Harding, M. M. (2006) Acta Crystallogr. D Biol. Crystallogr. 62, 678-682
54. Dominguez, D. C. (2004) Mol. Microbiol. 54, 291-297
55. Norris, V., Grant, S., Freestone, P., Canvin, J., Sheikh, F. N., Toth, I., Trinei, M., Modha, K., and Norman, R. I. (1996) J. Bacteriol. 178, 3677-3682
56. Rigden, D. J., Jedrzejas, M. J., Moroz, O. V., and Galperin, M. Y. (2003) Trends Microbiol. 11, 295-297
57. Rigden, D. J., Jedrzejas, M. J., and Galperin, M. Y. (2003) FEMS Microbiol. Lett. 221, 103-110
58. Welch, R. A. (2001) Curr. Top. Microbiol. Immunol. 257, 85-111
59. Bauche, C., Chenal, A., Knapp, O., Bodenreider, C., Benz, R., Chaffotte, A., and Ladant, D. (2006) J. Biol. Chem. 281, 16914-16926
60. Meier, R., Drepper, T., Svensson, V., Jaeger, K. E., and Baumann, U. (2007) J. Biol. Chem. 282, 31477-31483
61. Mitchell, E., Houles, C., Sudakevitz, D., Wimmerova, M., Gautier, C., Pérez, S., Wu, A. M., Gilboa-Garber, N., and Imberty, A. (2002) Nat. Struct. Biol. 9, 918-921
62. Wilson, J. J., Matsushita, O., Okabe, A., and Sakon, J. (2003) EMBO J. 22, 1743-1752
63. Fülöp, V., Ridout, C. J., Greenwood, C., and Hajdu, J. (1995) Structure 3, 1225-1233
64. Piotukh, K., Kosslick, D., Zimmermann, J., Krause, E., and Freund, C. (2007) Free Radic. Biol. Med. 43, 1263-1270
65. Huber-Wunderlich, M., and Glockshuber, R. (1998) Fold. Des. 3, 161-171
66. Aslund, F., Berndt, K. D., and Holmgren, A. (1997) J. Biol. Chem. 272, 30780-30786
67. Zapun, A., Missiakas, D., Raina, S., and Creighton, T. E. (1995) Biochemistry 34, 5075-5089
68. Siedler, F., Rudolph-Böhner, S., Doi, M., Musiol, H. J., and Moroder, L. (1993) Biochemistry 32, 7488-7495
69. Charbonnier, J. B., Belin, P., Moutiez, M., Stura, E. A., and Quéméneur, E. (1999) Protein Sci. 8, 96-105
70. Lillig, C. H., Berndt, C., and Holmgren, A. (2008) Biochim. Biophys. Acta 1780, 1304-1317
71. Lillig, C. H., Berndt, C., Vergnolle, O., Lönn, M. E., Hudemann, C., Bill, E., and Holmgren, A. (2005) Proc. Natl. Acad. Sci. U.S.A. 102, 8168-8173
72. Pettigrew, G. W., Echalier, A., and Pauleta, S. R. (2006) J. Inorg. Biochem. 100, 551-567
73. DeLano, W. L. (2002) The PyMOL Molecular Graphics System, DeLano Scientific, San Carlos, CA
74. Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994) Nucleic Acids Res. 22, 4673-4680
75. Nicholas, K. B., Nicholas, H. B., Jr., and Deerfield, D. W., 2nd (1997) EMBNEW. News 4, 14