Unique features of the structure and interactions of mycobacterial uracil-DNA glycosylase: Structure of a complex of the Mycobacterium tuberculosis enzyme in comparison with those from other sources

Acta Crystallographica Section D: Biological Crystallography

Volumn 64, Issue 5, 2008, Pages 551-560

  Kaushal, Prem Singh ^a   Talawar, Ramappa K ^a   Krishna, P D V ^a   Varshney, Umesh ^a   Vijayan, M ^a  

^a INDIAN INSTITUTE OF SCIENCE   (India)

Author keywords

Myctobacterium tuberculosis; Uracil DNA glycosylase

Indexed keywords

BACTERIAL PROTEIN; DNA; URACIL DNA GLYCOSIDASE;

AMINO ACID SEQUENCE; ANIMAL; ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; COMPARATIVE STUDY; ENZYMOLOGY; GENETICS; HUMAN; METABOLISM; MOLECULAR GENETICS; MYCOBACTERIUM TUBERCULOSIS; PROTEIN BINDING; PROTEIN SECONDARY STRUCTURE; SEQUENCE HOMOLOGY;

AMINO ACID SEQUENCE; ANIMALS; BACTERIAL PROTEINS; BINDING SITES; DNA; HUMANS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MYCOBACTERIUM TUBERCULOSIS; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY; SEQUENCE HOMOLOGY, AMINO ACID; URACIL-DNA GLYCOSIDASE;

CORYNEBACTERINEAE; MYCOBACTERIUM; MYCOBACTERIUM TUBERCULOSIS;

EID: 43249128071     PISSN: 09074449     EISSN: 13990047     Source Type: Journal    
DOI: 10.1107/S090744490800512X     Document Type: Article

References (70)

1. Acharya, N., Kumar, P. & Varshney, U. (2003). Microbiology, 149, 1647-1658.
2. Acharya, N., Roy, S. & Varshney, U. (2002). J. Mol Biol. 321, 579-590.
3. Acharya, N., Talawar, R. K., Purnapatre, K. & Varshney, U. (2004). Biochem. Biophys. Res. Commun. 320, 893-899.
4. Baker, N. A., Sept, D., Joseph, S., Holst, M. J. & McCammon, J. A. (2001). Proc. Natl Acad. Sci. USA, 98, 10037-10041.
5. Bennett, S. E., Schimerlik, M. I. & Mosbaugh, D. W. (1993). J. Biol. Chem. 268, 26879-26885.
6. Bianchet, M. A., Seiple, L. A., Jiang, Y. L., Ichikawa, Y., Amzel, L. M. & Stivers, J. T. (2003). Biochemistry, 42, 12455-12460.
7. Blaisdell, P. & Warner, H. (1983). J. Biol. Chem. 258, 1603-1609.
8. 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. & Warren, G. L. (1998). Acta Cryst. D54, 905-921.
9. Cohen, G. E. (1997). J. Appl. Cryst. 30, 1160-1161.
10. Collaborative Computational Project, Number 4 (1994). Acta Cryst. D50, 760-763.
11. Cone, R., Bonura, T. & Friedberg, E. C. (1980). J. Biol. Chem. 255, 10354-10358.
12. Das, S., Kumar, P., Bhor, V., Surolia, A. & Vijayan, M. (2006). Acta Cryst. D62, 628-638.
13. Datta, S., Krishna, R., Ganesh, N., Chandra, N. R., Muniyappa, K. & Vijayan, M. (2003). J. Bacteriol. 185, 4280-4284.
14. Datta, S., Prabu, M. M., Vaze, M. B., Ganesh, N., Chandra, N. R., Muniyappa, K. & Vijayan, M. (2000). Nucleic Acids Res. 28, 4964-4973.
15. DeLano, W. L. (2002). PyMOL Molecular Visualization System. http://www.pymol.org.
16. Dinner, A. R., Blackburn, G. M. & Karplus, M. (2001). Nature (London), 413, 752-755.
17. Emsley, P. & Cowtan, K. (2004). Acta Cryst. D60, 2126-2132.
18. Focher, F., Verri, A., Spadari, S., Manservigi, R., Gambino, J. & Wright, G. E. (1993). Biochem. J. 292, 883-889.
19. Geoui, T., Buisson, M., Tarbouriech, N. & Burmeister, W. P. (2007). J. Mol. Biol. 366, 117-131.
20. Gille, C. & Frommel, C. (2001). Bioinformatics, 17, 377-378.
21. Hubbard, S. J. & Thronton, J. M. (1993). NACCESS Computer Program. Department of Biochemistry and Molecular Biology, University College, London.
22. Jiang, Y. L., Krosky, D. J., Seiple, L. & Stivers, J. T. (2005). J. Am. Chem. Soc. 127, 17412-17420.
23. Kraulis, P. J. (1991). J. Appl. Cryst. 24, 946-950.
24. Krishna, R., Manjunath, G. P., Kumar, P., Surolia, A., Chandra, N. R., Muniyappa, K. & Vijayan, M. (2006). Nucleic Acids Res. 34, 2186-2195.
25. Krishna, R., Prabu, J. R., Manjunath, G. P., Datta, S., Chandra, N. R., Muniyappa, K. & Vijayan, M. (2007). J. Mol. Biol. 367, 1130-1144.
26. Krokan, H. & Wittwer, C. U. (1981). Nucleic Acids Res. 11, 2599-2613.
27. Kubota, Y., Nash, R. A., Klungland, A., Schar, P., Barnes, D. E. & Lindahl, T. (1996). EMBO J. 15, 6662-6670.
28. Laskowski, R. A., MacArthur, M. W., Moss, D. S. & Thornton, J. M. (1993). J. Appl. Cryst. 26, 283-291.
29. Leiros, I., Moe, E., Lanes, O., Smalås, A. O. & Willassen, N. P. (2003). Acta Cryst. D59, 1357-1365.
30. Leiros, I., Moe, E., Smala° s, A. O. & McSweeney, S. (2005). Acta Cryst. D61, 1049-1056.
31. Lindahl, T. (1974). Proc. Natl Acad. Sci. USA, 71, 3649-3653.
32. Lindahl, T. & Nyberg, B. (1974). Biochemistry, 13, 3405-3410.
33. McDonald, I. K. & Thornton, J. M. (1994). J. Mol. Biol. 238, 777-793.
34. Matthews, B. W. (1968). J. Mol. Biol. 33, 491-497.
35. Merritt, E. A. & Bacon, D. J. (1997). Methods Enzymol. 277, 505-524.
36. Moe, E., Leiros, I., Riise, E. K., Olufsen, M., Lanes, O., Smalas, A. & Willassen, N. P. (2004). J. Mol. Biol. 343, 1221-1230.
37. Mol, C. D., Arvai, A. S., Sanderson, R. J., Slupphaug, G., Kavli, B., Krokan, H. E., Mosbaugh, D. W. & Tainer, J. A. (1995). Cell, 82, 701-708.
38. Mol, C. D., Arvai, A. S., Slupphaug, G., Kavli, B., Alseth, I., Krokan, H. E. & Tainer, J. A. (1995). Cell, 80, 869-878.
39. Mrabet, N. T. et al. (1992). Biochemistry, 31, 2239-2253.
40. Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255.
41. Navaza, J. (1994). Acta Cryst. A50, 157-163.
42. Nicholl, I. D., Nealon, K. & Kenny, M. K. (1997). Biochemistry, 36, 7557-7566.
43. Olufsen, M., Brandsdal, B. O. & Smalas, A. O. (2007). J. Mol. Graph. Model. 26, 124-134.
44. Olufsen, M., Smalas, A. O., Moe, E. & Brandsdal, B. O. (2005). J. Biol. Chem. 280, 18042-18048.
45. Parikh, S. S., Mol, C. D., Slupphaug, G., Bharati, S., Krokan, H. E. & Tainer, J. A. (1998). EMBO J. 17, 5214-5226.
46. Parikh, S. S., Mol, C. D. & Tainer, J. A. (1997). Structure, 5, 1543-1550.
47. Parikh, S. S., Walcher, G., Jones, G. D., Slupphaug, G., Krokan, H. E., Blackburn, G. M. & Tainer, J. A. (2000). Proc. Natl Acad. Sci. USA, 97, 5083-5088.
48. Purnapatre, K. & Varshney, U. (1998). Eur. J. Biochem. 256, 580-858.
49. Putnam, C. D., Shroyer, M. J., Lundquist, A. J., Mol, C. D., Arvai, A. S., Mosbaugh, D. W. & Tainer, J. A. (1999). J. Mol. Biol. 287, 331-346.
50. Ravishankar, R., Bidya Sagar, M., Roy, S., Purnapatre, K., Handa, P., Varshney, U. & Vijayan, M. (1998). Nucleic Acids Res. 26, 4880-4887.
51. Roy, S., Gupta, S., Das, S., Sekar, K., Chatterji, D. & Vijayan, M. (2004). J. Mol. Biol. 339, 1103-1113.
52. Roy, S., Saraswathi, R., Chatterji, D. & Vijayan, M. (2008). J. Mol. Biol. 375, 948-959.
53. Saikrishnan, K., Bidya Sagar, M., Ravishankar, R., Roy, S., Purnapatre, K., Handa, P., Varshney, U. & Vijayan, M. (2002). Acta Cryst. D58, 1269-1276.
54. Saikrishnan, K., Jeyakanthan, J., Venkatesh, J., Acharya, N., Sekar, K., Varshney, U. & Vijayan, M. (2003). J. Mol. Biol. 331, 385-393.
55. Saikrishnan, K., Kalapala, S. K., Varshney, U. & Vijayan, M. (2005). J. Mol. Biol. 345, 29-38.
56. Saikrishnan, K., Manjunath, G. P., Singh, P., Jeyakanthan, J., Dauter, Z., Sekar, K., Muniyappa, K. & Vijayan, M. (2005). Acta Cryst. D61, 1140-1148.
57. Sassetti, C. M. & Rubin, E. J. (2003). Proc. Natl Acad. Sci. USA, 100, 12989-12994.
58. Savva, R., McAuley-Hecht, K., Brown, T. & Pearl, L. (1995). Nature (London), 373, 487-493.
59. Savva, R. & Pearl, L. H. (1995). Nature Struct. Biol. 2, 752-757.
60. Selvaraj, M., Roy, S., Singh, N. S., Sangeetha, R., Varshney, U. & Vijayan, M. (2007). J. Mol. Biol. 372, 186-193.
61. Singh, P., Talawar, R. K., Krishna, P. D. V., Varshney, U. & Vijayan, M. (2006). Acta Cryst. F62, 1231-1234.
62. Slupphaug, G., Mol, C. D., Kavli, B., Arvai, A. S., Krokan, H. E. & Tainer, J. A. (1996). Nature (London), 384, 87-92.
63. Srinath, T., Bharti, S. K. & Varshney, U. (2007). DNA Repair, 6, 1517-1528.
64. Storoni, L. C., McCoy, A. J. & Read, R. J. (2004). Acta Cryst. D60, 432-438.
65. Tye, B. K. & Lehman, I. R. (1977). J. Mol. Biol. 117, 293-306.
66. Warner, H. R., Johnson, L. K. & Snustad, D. P. (1980). J. Virol. 33, 535-538.
67. Wang, Z. & Mosbaugh, D. W. (1988). J. Bacteriol. 170, 1082-1091.
68. Werner, R. M., Jiang, Y. L., Gordley, R. G., Jagadeesh, G. J., Ladner, J. E., Xiao, G., Tordova, M., Gilliland, G. L. & Stivers, J. T. (2000). Biochemistry, 39, 12585-12594.
69. Winn, M. D., Murshdov, G. N. & Papiz, M. Z. (2003). Methods Enzymol. 374, 300-321.
70. Xiao, G., Tordova, M., Jagadeesh, J., Drohat, A. C., Stivers, J. T. & Gilliland, G. L. (1999). Proteins, 35, 13-24.