Structure of a backtracked state reveals conformational changes similar to the state following nucleotide incorporation in human norovirus polymerase

Acta Crystallographica Section D: Biological Crystallography

Volumn 70, Issue 12, 2014, Pages 3099-3109

  Zamyatkin, Dmitry ^a   Rao, Chandni ^a   Hoffarth, Elesha ^a   Jurca, Gabriela ^a   Rho, Hayeong ^a   Parra, Francisco ^b   Grochulski, Pawel ^c   Ng, Kenneth Kai Sing ^a  

^a UNIVERSITY OF CALGARY   (Canada)

^b DEPARTAMENTO DE BIOQUÍMICA Y BIOLOGÍA MOLECULAR   (Spain)

^c CANADIAN LIGHT SOURCE INC   (Canada)

Author keywords

human norovirus polymerase

Indexed keywords

NOROVIRUS;

NUCLEOTIDE; RNA DIRECTED RNA POLYMERASE;

CALICIVIRUS INFECTION; CHEMICAL STRUCTURE; CHEMISTRY; ENZYME ACTIVE SITE; ENZYMOLOGY; HUMAN; METABOLISM; NOROVIRUS; PROTEIN CONFORMATION; VIROLOGY; X RAY CRYSTALLOGRAPHY;

CALICIVIRIDAE INFECTIONS; CATALYTIC DOMAIN; CRYSTALLOGRAPHY, X-RAY; HUMANS; MODELS, MOLECULAR; NOROVIRUS; NUCLEOTIDES; PROTEIN CONFORMATION; RNA REPLICASE;

EID: 84916918593     PISSN: 09074449     EISSN: 13990047     Source Type: Journal    
DOI: 10.1107/S1399004714021518     Document Type: Article

References (51)

1. Alam, I., Lee, J.-H., Cho, K. J., Han, K. R., Yang, J. M., Chung, M. S. and Kim, K. H. (2012). Virology, 426, 143-151.
2. Arnold, J. J. and Cameron, C. E. (2004). Biochemistry, 43, 5126-5137.
3. Beard, W. A. and Wilson, S. H. (2006). Chem. Rev. 106, 361-382.
4. Blanton, L. H., Adams, S. M., Beard, R. S., Wei, G., Bulens, S. N., Widdowson, M. A., Glass, R. I. and Monroe, S. S. (2006). J. Infect. Dis. 193, 413-421.
5. Caillet-Saguy, C., Lim, S. P., Shi, P.-Y., Lescar, J. and Bressanelli, S. (2014). Antiviral Res. 105, 8-16.
6. Cameron, C. E., Moustafa, I. M. and Arnold, J. J. (2009). Curr. Opin. Struct. Biol. 19, 768-774.
7. Castro, C., Smidansky, E. D., Arnold, J. J., Maksimchuk, K. R., Moustafa, I., Uchida, A., Götte, M., Konigsberg, W. and Cameron, C. E. (2009). Nature Struct. Mol. Biol. 16, 212-218.
8. Chen, V. B., Arendall, W. B., Headd, J. J., Keedy, D. A., Immormino, R. M., Kapral, G. J., Murray, L. W., Richardson, J. S. and Richardson, D. C. (2010). Acta Cryst. D66, 12-21.
9. Cheung, A. C. M. and Cramer, P. (2011). Nature (London), 471, 249-253.Choi, K. H. (2012). Adv. Exp. Med. Biol. 726, 267-304.
10. DeLano, W. L. (2002). PyMOL. http://www.pymol.org.
11. Diederichs, K. and Karplus, P. A. (1997). Nature Struct. Biol. 4, 269-275.
12. Doublié, S., Sawaya, M. R. and Ellenberger, T. (1999). Structure, 7, R31-R35.
13. Eltahla, A. A., Lim, K. L., Eden, J.-S., Kelly, A. G., Mackenzie, J. M. and White, P. A. (2014). Antimicrob. Agents Chemother. 58, 3115-3123.
14. Emsley, P. and Cowtan, K. (2004). Acta Cryst. D60, 2126-2132.
15. Ferrer-Orta, C., Arias, A., Escarmís, C. and Verdaguer, N. (2006). Curr. Opin. Struct. Biol. 16, 27-34.
16. Ferrer-Orta, C., Arias, A., Perez-Luque, R., Escarmís, C., Domingo, E. and Verdaguer, N. (2004). J. Biol. Chem. 279, 47212-47221.
17. Ferrer-Orta, C., Arias, A., Pérez-Luque, R., Escarmís, C., Domingo, E. and Verdaguer, N. (2007). Proc. Natl Acad. Sci. USA, 104, 9463-9468.
18. Fullerton, S. W., Blaschke, M., Coutard, B., Gebhardt, J., Gorbalenya, A., Canard, B., Tucker, P. A. and Rohayem, J. (2007). J. Virol. 81, 1858-1871.
19. Garriga, D., Ferrer-Orta, C., Querol-Audí, J., Oliva, B. and Verdaguer, N. (2013). J. Mol. Biol. 425, 2279-2287.
20. Gentile, I., Coppola, N., Buonomo, A. R., Zappulo, E. and Borgia, G. (2014). Expert Opin. Investig. Drugs, 23, 1211-1223.
21. Gong, P., Kortus, M. G., Nix, J. C., Davis, R. E. and Peersen, O. B. (2013). PLoS One, 8, e60272.
22. Gong, P. and Peersen, O. B. (2010). Proc. Natl Acad. Sci. USA, 107, 22505-22510.
23. Högbom, M., Jäger, K., Robel, I., Unge, T. and Rohayem, J. (2009). J. Gen. Virol. 90, 281-291.
24. Kabsch, W. (1976). Acta Cryst. A32, 922-923.
25. Kabsch, W. (2010). Acta Cryst. D66, 125-132.
26. Kleywegt, G. J. (1996). Acta Cryst. D52, 842-857.
27. Kuchta, R. D., Mizrahi, V., Benkovic, P. A., Johnson, K. A. and Benkovic, S. J. (1987). Biochemistry, 26, 8410-8417.
28. Lee, J.-H., Alam, I., Han, K. R., Cho, S., Shin, S., Kang, S., Yang, J. M. and Kim, K. H. (2011). J. Gen. Virol. 92, 1607-1616.
29. Moustafa, I. M., Shen, H., Morton, B., Colina, C. M. and Cameron, C. E. (2011). J. Mol. Biol. 410, 159-181.
30. Murshudov, G. N., Skubák, P., Lebedev, A. A., Pannu, N. S., Steiner, R. A., Nicholls, R. A., Winn, M. D., Long, F. and Vagin, A. A. (2011). Acta Cryst. D67, 355-367.
31. Ng, K. K.-S., Arnold, J. J. and Cameron, C. E. (2008). Curr. Top. Microbiol. Immunol. 320, 137-156.
32. Ng, K. K.-S., Cherney, M. M., Vazquez, A. L., Machin, A., Alonso, J. M., Parra, F. and James, M. N. G. (2002). J. Biol. Chem. 277, 1381-1387.
33. Ng, K. K.-S., Pendás-Franco, N., Rojo, J., Boga, J. A., Machín, A., Alonso, J. M. and Parra, F. (2004). J. Biol. Chem. 279, 16638-16645.
34. Ortín, J. and Parra, F. (2006). Annu. Rev. Microbiol. 60, 305-326.
35. Powdrill, M. H., Bernatchez, J. A. and Götte, M. (2010). Viruses, 2, 2169-2195.
36. Read, R. J. (2001). Acta Cryst. D57, 1373-1382.
37. Richards, F. M. and Kundrot, C. E. (1988). Proteins, 3, 71-84.
38. Rothwell, P. J. and Waksman, G. (2005). Adv. Protein Chem. 71, 401-440.
39. Sarafianos, S. G., Marchand, B., Das, K., Himmel, D. M., Parniak, M. A., Hughes, S. H. and Arnold, E. (2009). J. Mol. Biol. 385, 693-713.
40. Shen, H., Moustafa, I. M., Cameron, C. E. and Colina, C. M. (2012). J. Phys. Chem. B, 116, 14515-14524.
41. Shen, H., Sun, H. and Li, G. (2012). PLoS Comput. Biol. 8, e1002851.
42. Sholders, A. J. and Peersen, O. B. (2014). J. Mol. Biol. 426, 1407-1419.
43. Showalter, A. K., Lamarche, B. J., Bakhtina, M., Su, M.-I., Tang, K.-H. and Tsai, M.-D. (2006). Chem. Rev. 106, 340-360.
44. Steitz, T. A. (2006). EMBO J. 25, 3458-3468.
45. Tan, C.W., Lai, J. K. F., Sam, I.-C. and Chan, Y. F. (2014). J. Biomed. Sci. 21, 14.
46. Verdaguer, N. and Ferrer-Orta, C. (2012). Structure, 20, 1448-1450.
47. Wang, D., Bushnell, D. A., Huang, X., Westover, K. D., Levitt, M. and Kornberg, R. D. (2009). Science, 324, 1203-1206.
48. Weixlbaumer, A., Leon, K., Landick, R. and Darst, S. A. (2013). Cell, 152, 431-441.
49. Yang, X., Smidansky, E. D., Maksimchuk, K. R., Lum, D., Welch, J. L., Arnold, J. J., Cameron, C. E. and Boehr, D. D. (2012). Structure, 20, 1519-1527.
50. Zamyatkin, D. F., Parra, F., Alonso, J. M., Harki, D. A., Peterson, B. R., Grochulski, P. and Ng, K. K.-S. (2008). J. Biol. Chem. 283, 7705-7712.
51. Zamyatkin, D. F., Parra, F., Machín, A., Grochulski, P. and Ng, K. K.-S. (2009). J. Mol. Biol. 390, 10-16.