Structural and dynamic features of the MutT protein in the recognition of nucleotides with the mutagenic 8-oxoguanine base

Journal of Biological Chemistry

Volumn 285, Issue 1, 2010, Pages 444-452

  Nakamura, Teruya ^a   Meshitsuka, Sachiko ^b   Kitagawa, Seiju ^b   Abe, Nanase ^b   Yamada, Junichi ^b   Ishino, Tetsuya ^b   Nakano, Hiroaki ^b   Tsuzuki, Teruhisa ^c   Doi, Takefumi ^b   Kobayashi, Yuji ^b   Fujii, Satoshi ^d   Sejiguchi, Mutsuo ^e   Yamagata, Yuriko ^a  

^a KUMAMOTO UNIVERSITY   (Japan)

^b OSAKA UNIVERSITY   (Japan)

^c KYUSHU UNIVERSITY   (Japan)

^d UNIVERSITY OF SHIZUOKA   (Japan)

^e FUKUOKA DENTAL COLLEGE   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEXATION; ESCHERICHIA COLI; LIGANDS; NUCLEOTIDES;

8-OXOGUANINE; BINARY COMPLEXES; CONFORMATIONAL CHANGE; DYNAMIC FEATURES; GUANINE NUCLEOTIDES; LIGAND-FREE; STRUCTURAL BASIS; SUBSTRATE SPECIFICITY;

HYDROGEN BONDS;

8 HYDROXYGUANINE; BACTERIAL PROTEIN; NUCLEOTIDE; PROTEIN MUTT; UNCLASSIFIED DRUG;

ARTICLE; BINDING AFFINITY; CONTROLLED STUDY; CRYSTAL STRUCTURE; CRYSTALLIZATION; ENZYME SPECIFICITY; ESCHERICHIA COLI; GENE SEQUENCE; HYDROGEN BOND; MOLECULAR DYNAMICS; MUTAGENESIS; NONHUMAN; NUCLEOTIDE SEQUENCE; OXIDATION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN EXPRESSION; PROTEIN PURIFICATION; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT;

ESCHERICHIA COLI;

EID: 73649095513     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M109.066373     Document Type: Article

References (72)

1. Maki, H., and Sekiguchi, M. (1992) Nature 355, 273-275
2. Taddei, F., Hayakawa, H., Bouton, M., Cirinesi, A., Matic, I., Sekiguchi, M., and Radman, M. (1997) Science 278, 128-130
3. Au, K. G., Cabrera, M., Miller, J. H., and Modrich, P. (1988) Proc. Natl. Acad. Sci. U.S.A. 85, 9163-9166
4. Cabrera, M., Nghiem, Y., and Miller, J. H. (1988) J. Bacteriol. 170, 5405-5407
5. Michaels, M. L., Cruz, C., Grollman, A. P., and Miller, J. H. (1992) Proc. Natl. Acad. Sci. U.S.A. 89, 7022-7025
6. Tchou, J., Kasai, H., Shibutani, S., Chung, M. H., Laval, J., Grollman, A. P., and Nishimura, S. (1991) Proc. Natl. Acad. Sci. U.S.A. 88, 4690-4694
7. Ito, R., Hayakawa, H., Sekiguchi, M., and Ishibashi, T. (2005) Biochemistry 44, 6670-6674
8. Fujikawa, K., Kamiya, H., Yakushiji, H., Fujii, Y., Nakabeppu, Y., and Kasai, H. (1999) J. Biol. Chem. 274, 18201-18205
9. Fujikawa, K., Kamiya, H., Yakushiji, H., Nakabeppu, Y., and Kasai, H. (2001) Nucleic Acids Res. 29, 449-454
10. Mishima, M., Sakai, Y., Itoh, N., Kamiya, H., Furuichi, M., Takahashi, M., Yamagata, Y., Iwai, S., Nakabeppu, Y., and Shirakawa, M. (2004) J. Biol. Chem. 279, 33806-33815
11. Tchou, J., Bodepudi, V., Shibutani, S., Antoshechkin, I., Miller, J., Grollman, A. P., and Johnson, F. (1994) J. Biol. Chem. 269, 15318-15324
12. Hatahet, Z., Kow, Y. W., Purmal, A. A., Cunningham, R. P., and Wallace, S. S. (1994) J. Biol. Chem. 269, 18814-18820
13. Fromme, J. C., and Verdine, G. L. (2003) J. Biol. Chem. 278, 51543-51548
14. Porello, S. L., Leyes, A. E., and David, S. S. (1998) Biochemistry 37, 14756-14764
15. Bruner, S. D., Norman, D. P., and Verdine, G. L. (2000) Nature 403, 859-866
16. Fromme, J. C., Banerjee, A., Huang, S. J., and Verdine, G. L. (2004) Nature 427, 652-656
17. Bessman, M. J., Frick, D. N., and O'Handley, S. F. (1996) J. Biol. Chem. 271, 25059-25062
18. Abeygunawardana, C., Weber, D. J., Gittis, A. G., Frick, D. N., Lin, J., Miller, A. F., Bessman, M. J., and Mildvan, A. S. (1995) Biochemistry 34, 14997-15005
19. Massiah, M. A., Saraswat, V., Azurmendi, H. F., and Mildvan, A. S. (2003) Biochemistry 42, 10140-10154
20. Doublié, S. (1997) Methods Enzymol. 276, 523-530
21. LeMaster, D. M., and Richards, F. M. (1985) Biochemistry 24, 7263-7268
22. Nakamura, T., Kitaguchi, Y., Miyazawa, M., Kamiya, H., Toma, S., Ikemizu, S., Shirakawa, M., Nakabeppu, Y., and Yamagata, Y. (2006) Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 62, 1283-1285
23. Akiyama, M., Maki, H., Sekiguchi, M., and Horiuchi, T. (1989) Proc. Natl. Acad. Sci. U.S.A. 86, 3949-3952
24. Nakamura, T., Doi, T., Sekiguchi, M., and Yamagata, Y. (2004) Acta Crystallogr. D Biol. Crystallogr. 60, 1641-1643
25. Rossmann, M. G., and van Beek, C. G. (1999) Acta Crystallogr. D Biol. Crystallogr. 55, 1631-1640
26. Otwinowski, Z., and Minor, W. (1997) Methods Enzymol. 276, 307-326
27. Matthews, B. W. (1968) J. Mol. Biol. 33, 491-497
28. Terwilliger, T. C., and Berendzen, J. (1999) Acta Crystallogr. D Biol. Crystallogr. 55, 849-861
29. Collaborative Computational Project, Number 4. (1994) Acta Crystallogr. D Biol. Crystallogr. 50, 760-763
30. Cowtan, K. (1994) Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography 31, 34-38
31. Cambillau, C., Horjales, E., and Jones, T. A. (1984) J. Mol. Graph. 2, 53-54
32. Jones, T. A., Zou, J. Y., Cowan, S. W., and Kjeldgaard, M. (1991) Acta Crystallogr. Sect. A 47, 110-119
33. Brünger, A. T. (1992) A System for X-Ray Crystallography and NMR, Yale University Press, New Haven, CT
34. Brünger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J. S., Kuszewski, J., Nilges, M., Pannu, N. S., Read, R. J., Rice, L. M., Simonson, T., and Warren, G. L. (1998) Acta Crystallogr. D Biol. Crystallogr. 54, 905-921
35. Navaza, J. (1994) Acta Crystallogr. Sect. A 50, 157-163
36. Laskowski, R. A., MacArthur, M. W., Moss, D. S., and Thornton, J. M. (1993) J. Appl. Crystallogr. 26, 283-291
37. Kabsch, W. (1976) Acta Crystallogr. Sect. A 32, 922-923
38. DeLano, W. L. (2002) The PyMOL Molecular Graphics System, DeLano Scientific LLC, San Carlos, CA
39. Gabelli, S. B., Bianchet, M. A., Xu, W., Dunn, C. A., Niu, Z. D., Amzel, L. M., and Bessman, M. J. (2007) Structure 15, 1014-1022
40. Messing, S. A., Gabelli, S. B., Liu, Q., Celesnik, H., Belasco, J. G., Piñeiro, S. A., and Amzel, L. M. (2009) Structure 17, 472-481
41. Holm, L., Kääriäinen, S., Rosenström, P., and Schenkel, A. (2008) Bioinformatics 24, 2780-2781
42. Bhatnagar, S. K., Bullions, L. C., and Bessman, M. J. (1991) J. Biol. Chem. 266, 9050-9054
43. Saenger, W. (1984) Principles of Nucleic Acid Structure, Springer-Verlag, New York
44. Steyert, S. R., Messing, S. A., Amzel, L. M., Gabelli, S. B., and Piñeiro, S. A. (2008) J. Bacteriol. 190, 8215-8219
45. Saraswat, V., Massiah, M. A., Lopez, G., Amzel, L. M., and Mildvan, A. S. (2002) Biochemistry 41, 15566-15577
46. Saraswat, V., Azurmendi, H. F., and Mildvan, A. S. (2004) Biochemistry 43, 3404-3414
47. Funahashi, J., Takano, K., Yamagata, Y., and Yutani, K. (2002) J. Biol. Chem. 277, 21792-21800
48. Takano, K., Yamagata, Y., Funahashi, J., Hioki, Y., Kuramitsu, S., and Yutani, K. (1999) Biochemistry 38, 12698-12708
49. Kouchakdjian, M., Bodepudi, V., Shibutani, S., Eisenberg, M., Johnson, F., Grollman, A. P., and Patel, D. J. (1991) Biochemistry 30, 1403-1412
50. Uesugi, S., Yano, J., Yano, E., and Ikehara, M. (1977) J. Am. Chem. Soc. 99, 2313-2323
51. Kamiya, H., Murata-Kamiya, N., Iida, E., and Harashima, H. (2001) Biochem. Biophys. Res. Commun. 288, 499-502
52. Xu, W., Jones, C. R., Dunn, C. A., and Bessman, M. J. (2004) J. Bacteriol. 186, 8380-8384
53. Wang, S., Mura, C., Sawaya, M. R., Cascio, D., and Eisenberg, D. (2002) Acta Crystallogr. D Biol. Crystallogr. 58, 571-578
54. Gabelli, S. B., Bianchet, M. A., Bessman, M. J., and Amzel, L. M. (2001) Nat. Struct. Biol. 8, 467-472
55. Bailey, S., Sedelnikova, S. E., Blackburn, G. M., Abdelghany, H. M., Baker, P. J., McLennan, A. G., and Rafferty, J. B. (2002) Structure 10, 589-600
56. Kang, L. W., Gabelli, S. B., Bianchet, M. A., Xu, W. L., Bessman, M. J., and Amzel, L. M. (2003) J. Bacteriol. 185, 4110-4118
57. Kang, L. W., Gabelli, S. B., Cunningham, J. E., O'Handley, S. F., and Amzel, L. M. (2003) Structure 11, 1015-1023
58. Shen, B. W., Perraud, A. L., Scharenberg, A., and Stoddard, B. L. (2003) J. Mol. Biol. 332, 385-398
59. Gabelli, S. B., Bianchet, M. A., Azurmendi, H. F., Xia, Z., Sarawat, V., Mildvan, A. S., and Amzel, L. M. (2004) Structure 12, 927-935
60. Ranatunga, W., Hill, E. E., Mooster, J. L., Holbrook, E. L., Schulze-Gahmen, U., Xu, W., Bessman, M. J., Brenner, S. E., and Holbrook, S. R. (2004) J. Mol. Biol. 339, 103-116
61. Yoshiba, S., Ooga, T., Nakagawa, N., Shibata, T., Inoue, Y., Yokoyama, S., Kuramitsu, S., and Masui, R. (2004) J. Biol. Chem. 279, 37163-37174
62. She, M., Decker, C. J., Chen, N., Tumati, S., Parker, R., and Song, H. (2006) Nat. Struct. Mol. Biol. 13, 63-70
63. Zha, M., Zhong, C., Peng, Y., Hu, H., and Ding, J. (2006) J. Mol. Biol. 364, 1021-1033
64. Scarsdale, J. N., Peculis, B. A., and Wright, H. T. (2006) Structure 14, 331-343
65. Wakamatsu, T., Nakagawa, N., Kuramitsu, S., and Masui, R. (2008) J. Bacteriol. 190, 1108-1117
66. Gabelli, S. B., Bianchet, M. A., Ohnishi, Y., Ichikawa, Y., Bessman, M. J., and Amzel, L. M. (2002) Biochemistry 41, 9279-9285
67. Zha, M., Guo, Q., Zhang, Y., Yu, B., Ou, Y., Zhong, C., and Ding, J. (2008) J. Mol. Biol. 379, 568-578
68. Frick, D. N., Weber, D. J., Gillespie, J. R., Bessman, M. J., and Mildvan, A. S. (1994) J. Biol. Chem. 269, 1794-1803
69. Shimokawa, H., Fujii, Y., Furuichi, M., Sekiguchi, M., and Nakabeppu, Y. (2000) Nucleic Acids Res. 28, 3240-3249
70. Harris, T. K., Wu, G., Massiah, M. A., and Mildvan, A. S. (2000) Biochemistry 39, 1655-1674
71. Mildvan, A. S., Xia, Z., Azurmendi, H. F., Saraswat, V., Legler, P. M., Massiah, M. A., Gabelli, S. B., Bianchet, M. A., Kang, L. W., and Amzel, L. M. (2005) Arch. Biochem. Biophys. 433, 129-143
72. Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994) Nucleic Acids Res. 22, 4673-4680