Structures of Burkholderia thailandensis nucleoside kinase: Implications for the catalytic mechanism and nucleoside selectivity

Acta Crystallographica Section D: Biological Crystallography

Volumn 67, Issue 11, 2011, Pages 945-956

  Yasutake, Yoshiaki ^a   Ota, Hiroko ^b   Hino, Emisa ^b   Sakasegawa, Shin Ichi ^b   Tamura, Tomohiro ^a,c  

^a NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^b ASAHI KASEI PHARMA CORPORATION   (Japan)

^c HOKKAIDO UNIVERSITY   (Japan)

Author keywords

adenosine kinase; conformational dynamics; mizoribine; nucleoside kinases; phosphofructokinase family

Indexed keywords

ADENOSINE TRIPHOSPHATE; BACTERIAL PROTEIN; IMMUNOSUPPRESSIVE AGENT; MAGNESIUM; MIZORIBINE; NUCLEOSIDE PHOSPHOTRANSFERASE; PHOSPHOTRANSFERASE; RIBONUCLEOSIDE;

ARTICLE; AUTOIMMUNE DISEASE; BURKHOLDERIA; CHEMISTRY; CRYSTALLIZATION; ENZYME SPECIFICITY; ENZYMOLOGY; GENETICS; GRAFT REJECTION; HUMAN; METABOLISM; MUTATION; PROTEIN CONFORMATION; SITE DIRECTED MUTAGENESIS;

ADENOSINE TRIPHOSPHATE; AUTOIMMUNE DISEASES; BACTERIAL PROTEINS; BURKHOLDERIA; CRYSTALLIZATION; GRAFT REJECTION; HUMANS; IMMUNOSUPPRESSIVE AGENTS; MAGNESIUM; MUTAGENESIS, SITE-DIRECTED; MUTATION; PHOSPHOTRANSFERASES; PROTEIN CONFORMATION; RIBONUCLEOSIDES; SUBSTRATE SPECIFICITY;

BURKHOLDERIA THAILANDENSIS; NEGIBACTERIA;

EID: 80955159978     PISSN: 09074449     EISSN: 13990047     Source Type: Journal    
DOI: 10.1107/S0907444911038777     Document Type: Article

References (45)

1. Abe, Y., Tsuji, Y., Hisano, M., Nakada, M., Miura, K., Watanabe, S., Odajima, Y. & Iikura, Y. (2004). Pediatr. Int. 46, 597-600.
2. Arnfors, L., Hansen, T., Schönheit, P., Ladenstein, R. & Meining, W. (2006). Acta Cryst. D62, 1085-1097.
3. Battye, T. G. G., Kontogiannis, L., Johnson, O., Powell, H. R. & Leslie, A. G. W. (2011). Acta Cryst. D67, 271-281.
4. Cabrera, R., Babul, J. & Guixé, V. (2010). Arch. Biochem. Biophys. 502, 23-30.
5. Chua, T. K., Seetharaman, J., Kasprzak, J. M., Ng, C., Patel, B. K., Love, C., Bujnicki, J. M. & Sivaraman, J. (2010). J. Struct. Biol. 171, 397-401.
6. Dauter, Z., Dauter, M. & Rajashankar, K. R. (2000). Acta Cryst. D56, 232-237.
7. DeLano, W. L. (2002). PyMOL. http://www.pymol.org.
8. Emsley, P. & Cowtan, K. (2004). Acta Cryst. D60, 2126-2132.
9. Hansen, T., Arnfors, L., Ladenstein, R. & Schönheit, P. (2007). Extremophiles, 11, 105-114.
10. Hayward, S. & Berendsen, H. J. (1998). Proteins, 30, 144-154.
11. Heinig, M. & Frishman, D. (2004). Nucleic Acids Res. 32, W500-W502.
12. Hemsley, A., Arnheim, N., Toney, M. D., Cortopassi, G. & Galas, D. J. (1989). Nucleic Acids Res. 17, 6545-6551.
13. Hiramitsu, T., Ota, H., Watarai, Y., Achiha, M., Fukami, H., Sakasegawa, S., Hino, E., Yamaguchi, T., Ueda, S., Kagimoto, Y., Tamura, T. & Uchida, K. (2011). J. Biosci. Bioeng. 112, 205-207.
14. Holm, L. & Park, J. (2000). Bioinformatics, 16, 566-567.
15. Kleywegt, G. J. (1999). Acta Cryst. D55, 1878-1884.
16. Koyama, H. & Tsuji, M. (1983). Biochem. Pharmacol. 32, 3547-3553.
17. Kusumi, T., Tsuda, M., Katsunuma, T. & Yamamura, M. (1989). Cell Biochem. Funct. 7, 201-204.
18. Laskowski, R. A., MacArthur, M. W., Moss, D. S. & Thornton, J. M. (1993). J. Appl. Cryst. 26, 283-291.
19. Long, M. C., Escuyer, V. & Parker, W. B. (2003). J. Bacteriol. 185, 6548-6555.
20. Maj, M. C., Singh, B. & Gupta, R. S. (2002). Biochemistry, 41, 4059-4069.
21. Mathews, I. I., Erion, M. D. & Ealick, S. E. (1998). Biochemistry, 37, 15607-15620.
22. McCoy, A. J., Grosse-Kunstleve, R. W., Adams, P. D., Winn, M. D., Storoni, L. C. & Read, R. J. (2007). J. Appl. Cryst. 40, 658-674.
23. Miallau, L., Hunter, W. N., McSweeney, S. M. & Leonard, G. A. (2007). J. Biol. Chem. 282, 19948-19957.
24. Miller, R. L., Adamczyk, D. L., Miller, W. H., Koszalka, G. W., Rideout, J. L., Beacham, L. M. III., Chao, E. Y., Haggerty, J. J., Krenitsky, T. A. & Elion, G. B. (1979). J. Biol. Chem. 254, 2346-2352.
25. Mitani, Y., Meng, X., Kamagata, Y. & Tamura, T. (2005). J. Bacteriol. 187, 2582-2591.
26. Mizuno, K., Tsujino, M., Takada, M., Hayashi, M. & Atsumi, K. (1974). J. Antibiot. 27, 775-782.
27. 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.
28. Nakashima, N. & Tamura, T. (2004). Biotechnol. Bioeng. 86, 136-148.
29. Ota, H., Sakasegawa, S., Yasuda, Y., Imamura, S. & Tamura, T. (2008). FEBS J. 275, 5865-5872.
30. Ota, H., Yasuda, Y., Sakasegawa, S., Imamura, S. & Tamura, T. (2008). J. Biosci. Bioeng. 106, 511-514.
31. Otwinowski, Z. & Minor, W. (1997). Methods Enzymol. 276, 307-326.
32. Padilla, J. E. & Yeates, T. O. (2003). Acta Cryst. D59, 1124-1130.
33. Reddy, M. C., Palaninathan, S. K., Shetty, N. D., Owen, J. L., Watson, M. D. & Sacchettini, J. C. (2007). J. Biol. Chem. 282, 27334-27342.
34. Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.
35. Sigrell, J. A., Cameron, A. D., Jones, T. A. & Mowbray, S. L. (1998). Structure, 6, 183-193.
36. Sigrell, J. A., Cameron, A. D. & Mowbray, S. L. (1999). J. Mol. Biol. 290, 1009-1018.
37. Stypinski, D., Obaidi, M., Combs, M., Weber, M., Stewart, A. J. & Ishikawa, H. (2007). Br. J. Clin. Pharmacol. 63, 459-468.
38. Terwilliger, T. C. (2000). Acta Cryst. D56, 965-972.
39. Terwilliger, T. C. & Berendzen, J. (1999). Acta Cryst. D55, 849-861.
40. Thompson, J. D., Higgins, D. G. & Gibson, T. J. (1994). Nucleic Acids Res. 22, 4673-4680.
41. Winn, M. D. et al. (2011). Acta Cryst. D67, 235-242.
42. Wu, L.-F., Reizer, A., Reizer, J., Cai, B., Tomich, J. M. & Saier, M. H. (1991). J. Bacteriol. 173, 3117-3127.
43. Yeates, T. O. (1997). Methods Enzymol. 276, 344-358.
44. Yokota, S. (2002). Pediatr. Int. 44, 196-198.
45. Zhang, Y., Dougherty, M., Downs, D. M. & Ealick, S. E. (2004). Structure, 12, 1809-1821.