Structure of the SPRY domain of the human RNA helicase DDX1, a putative interaction platform within a DEAD-box protein

Acta Crystallographica Section:F Structural Biology Communications

Volumn 71, Issue , 2015, Pages 1176-1188

  Kellner, Julian N ^a   Meinhart, Anton ^a  

^a MAX PLANCK INSTITUTE FOR MEDICAL RESEARCH   (Germany)

Author keywords

DEAD box proteins; protein protein interaction; RNA processing; SPRY domains

Indexed keywords

DDX1 PROTEIN, HUMAN; DEAD BOX PROTEIN; PROTEIN BINDING;

AMINO ACID SEQUENCE; CHEMISTRY; CONSERVED SEQUENCE; CRYSTALLIZATION; HUMAN; METABOLISM; MOLECULAR GENETICS; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; STRUCTURAL HOMOLOGY; X RAY CRYSTALLOGRAPHY;

AMINO ACID SEQUENCE; CONSERVED SEQUENCE; CRYSTALLIZATION; CRYSTALLOGRAPHY, X-RAY; DEAD-BOX RNA HELICASES; HUMANS; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 84940925187     PISSN: None     EISSN: 2053230X     Source Type: Journal    
DOI: 10.1107/S2053230X15013709     Document Type: Article

References (66)

1. Baker, N. A., Sept, D., Joseph, S., Holst, M. J. & McCammon, J. A. (2001). Proc. Natl Acad. Sci. USA, 98, 10037-10041.
2. Balko, J. M. & Arteaga, C. L. (2011). Breast Cancer Res. Treat. 127, 65-67.
3. Biris, N., Yang, Y., Taylor, A. B., Tomashevski, A., Guo, M., Hart, P. J., Diaz-Griffero, F. & Ivanov, D. N. (2012). Proc. Natl Acad. Sci. USA, 109, 13278-13283.
4. Brünger, A. T. (1992). Nature (London), 355, 472-475.
5. 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.
6. Buchan, D.W.,Ward, S. M., Lobley, A. E., Nugent, T. C., Bryson, K. & Jones, D. T. (2010). Nucleic Acids Res. 38, W563-W568.
7. Chen, V. B., Arendall, W. B., Headd, J. J., Keedy, D. A., Immormino, R. M., Kapral, G. J., Murray, L. W., Richardson, J. S. & Richardson, D. C. (2010). Acta Cryst. D66, 12-21.
8. Chen, Y., Cao, F., Wan, B., Dou, Y. & Lei, M. (2012). Cell Res. 22, 598-602.
9. Collaborative Computational Project, Number 4 (1994). Acta Cryst. D50, 760-763.
10. D'Cruz, A. A., Babon, J. J., Norton, R. S., Nicola, N. A. & Nicholson, S. E. (2013). Protein Sci. 22, 1-10.
11. D'Cruz, A. A., Kershaw, N. J., Chiang, J. J.,Wang, M. K., Nicola, N. A., Babon, J. J., Gack, M. U. & Nicholson, S. E. (2013). Biochem. J. 456, 231-240.
12. DeLano, W. L. (2002). PyMOL v.1.7.4. http://www.pymol.org.
13. Edgcomb, S. P., Carmel, A. B., Naji , S., Ambrus-Aikelin, G., Reyes, J. R., Saphire, A. C., Gerace, L. & Williamson, J. R. (2011). J. Mol. Biol. 415, 61-74.
14. Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. (2010). Acta Cryst. D66, 486-501.
15. Fang, J., Acheampong, E., Dave, R., Wang, F., Mukhtar, M. & Pomerantz, R. J. (2005). Virology, 336, 299-307.
16. Fang, J., Kubota, S., Ya ng, B., Zhou, N., Zhang, H., Godbout, R. & Pomerantz, R. J. (2004). Virology, 330, 471-480.
17. Filippakopoulos, P., Low, A., Sharpe, T. D., Uppenberg, J., Yao, S., Kuang, Z., Sav itsky, P., Lewis, R. S., Nicholson, S. E., Norton, R. S. & Bullock, A. N. (2010). J. Mol. Biol. 401, 389-402.
18. Godbout, R., Hale, M. & Bisgrove, D. (1994). Gene, 138, 243-245.
19. Godbout R. Li L. Liu R.-Z. Roy K. 2007 Future Oncol. 3 575-587.
20. Godb out, R., Packer, M. & Bie, W. (1998). J. Biol. Chem. 273, 21161-21168.
21. Godbout, R. & Squire, J. (1993). Proc. Natl Acad. Sci. USA, 90, 7578-7582.
22. Grütter, C., Briand, C., Capitani, G., Mittl, P. R., Papin, S., Tschopp, J. & Grütter, M. G. (2006). FEBS Lett. 580, 99-106.
23. Han, C., Liu, Y.,Wan, G., Choi, H. J., Zhao, L., Ivan, C., He, X., Sood, A. K., Zhang, X. & Lu, X. (2014). Cell. Rep. 8, 1447-1460.
24. Högbom, M., Collins, R., Van Den Berg, S., Jenvert, R. M., Karlberg, T., Kotenyova, T., Flores, A., Karlsson Hedestam, G. B. & Schiavone, L. H. (2007). J. Mol. Biol. 372, 150-159.
25. Holm, L. & Rosenström, P. (2010). Nucleic Acids Res. 38, W545-W549.
26. James, L. C., Keeble, A. H., Khan, Z., Rhodes, D. A. & Trowsdale, J. (2007). Proc. Natl Acad. Sci. USA, 104, 6200-6205.
27. Jankowsky, E. & Fairman, M. E. (2007). Curr. Opin. Struct. Biol. 17, 316-324.
28. Kabsch, W. (1993). J. Appl. Cryst. 26, 795-800.
29. Kanai, Y., Dohmae, N. & Hirokawa, N. (2004). Neuron, 43, 513-525.
30. Keeble, A. H., Khan, Z., Forster, A. & James, L. C. (2008). Proc. Natl Acad. Sci. USA, 105, 6045-6050.
31. Kellner, J. N., Reinstein, J. & Meinhart, A. (2015). Nucleic Acids Res. 43, 2813-2828.
32. Kowalinski, E., Lunardi, T., McCarthy, A. A., Louber, J., Brunel, J., Grigorov, B., Gerlier, D. & Cusack, S. (2011). Cell, 147, 423-435.
33. Kuang, Z., Yao, S., Xu, Y., Lewis , R. S., Low, A., Masters, S. L., Willson, T. A., Kolesnik, T. B., Nicholson, S. E., Garrett, T. J. & Norton, R. S. (2009). J. Mol. Biol. 386, 662-674.
34. Laskowski, R. A., MacArth ur, M. W., Moss, D. S. & Thornton, J. M. (1993). J. Appl. Cryst. 26, 283-291.
35. Lau, K. & Van Petegem, F. (2014). Nature Commun. 5, 5397.
36. Linder, P., Lasko, P. F., Ashburner, M., Leroy, P., Nielsen, P. J., Nishi, K., Schnier, J. & Slonimski, P. P. (1989). Nature (London), 337, 121-122.
37. Livingstone, C. D. & Barton, G. J. (1993). Comput. Appl. Biosci. 9, 745-756.
38. Matthews, B. W. (1968). J. Mol. Biol. 33, 491-497.
39. 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.
40. 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.
41. Park E. Y. Kwon O.-B. Jeong B.-C. Yi J.-S. Lee C. S. Ko Y.-G. Song H. K.(2010). Proteins 78 790-795.
42. Perálvarez-Marin, A., Tae, H., Board, P. G., Casarotto, M. G., Dulhunty, A. F. & Samsó , M. (2011). PLoS One, 6, e25813.
43. Pérez-González, A., Pazo, A., Navajas, R., Ciordia, S., Rodriguez-Frandsen, A. & Nieto, A. (2014). PLoS One, 9, e90957.
44. Ponting, C., Schultz, J. & Bork, P. (1997). Trends Biochem. Sci. 22, 193-194.
45. Popow, J., Englert, M., Weitzer, S., Schleiffer, A., Mierzwa, B., Mechtler, K., Trowitzsch, S., Will, C. L., Lührmann, R., Söll, D. & Martinez, J. (2011). Science, 331, 760-764.
46. Popow, J., Jurkin, J., Schleiffer, A. & Martinez, J. (2014). Nature (London), 511, 104-107.
47. Rhodes, D. A., De Bono, B. & Trowsdale, J. (2005). Immunology, 116, 411-417.
48. Robertson-Anderson, R. M., Wang, J., Edgcomb, S. P., Carmel, A. B., Williamson, J. R. & Millar, D. P. (2011). J. Mol. Biol. 410, 959-971.
49. Santoro, M. M. & Bolen, D. W. (1988). Biochemistry, 27, 8063-8068.
50. Schmid, S. R. & Linder, P. (1992). Mol. Microbiol. 6, 283-292.
51. Story, R. M., Li, H. & Abelson, J. N. (2001). Proc. Natl Acad. Sci. USA, 98, 1465-1470.
52. Styhler, S., Nakamura, A. & Lasko, P. (2002). Dev. Cell, 3, 865-876.
53. Sutton, K. A., Black, P. J., Mercer, K. R., Garman, E. F., Owen, R. L., Snell, E. H. & Bernhard, W. A. (2013). Acta Cryst. D69, 2381-2394.
54. Tanaka, K., Okamoto, S., Ishikawa, Y., Tamura, H. & Hara, T. (2009). Oncogene, 28, 2142-2151.
55. Ten Eyck, L. F. (1973). Acta Cryst. A29, 183-191.
56. Trowitzsch, S. (2008). Dissertation. Georg-August-Universitä t, Göttingen, Germany.
57. Vagin, A. & Teplyakov, A. (2010). Acta Cryst. D66, 22-25.
58. Van Duyne, G. D., Standaert, R. F., Karplus, P. A., Schreiber, S. L. & Clardy, J. (1993). J. Mol. Biol. 229, 105-124.
59. Weinert, C., Grütter, C., Roschitzki-Voser, H., Mittl, P. R. & Grütter, M. G. (2009). J. Mol. Biol. 394, 226-236.
60. Winn, M. D. et al. (2011). Acta Cryst. D67, 235-242.
61. Winn, M. D., Isupov, M. N. & Murshudov, G. N. (2001). Acta Cryst. D57, 122-133.
62. Woo J.-S. Imm J.-H. Min C.-K. Kim K.-J. Cha S.-S. Oh B.-H. 2006. EMBO J. 25 1353-1363.
63. Woo, J.-S., Suh, H.-Y., Park, S.-Y. & Oh, B.-H. (2006). Mol. Cell, 24, 967-976.
64. Yang, H., Ji, X., Zhao, G., Ning, J., Zhao, Q., Aiken, C., Gronenborn, A. M., Zhang, P. & Xiong, Y. (2012). Proc. Natl Acad. Sci. USA, 109, 18372-18377.
65. Yedavalli, V. S. R. K., Neuveut, C., Chi, Y.-H., Kleiman, L. & Jeang, K.-T. (2004). Cell, 119, 381-392.
66. Zhang, Z., Bao, M., Lu, N., Weng, L., Yuan, B. & Liu, Y.-J. (2013). Nature Immunol. 14, 172-178.