The C-terminal RpoN domain of σ54 forms an unpredicted helix-turn-helix motif similar to domains of σ70

Journal of Biological Chemistry

Volumn 280, Issue 50, 2005, Pages 41530-41536

  Doucleff, Michaeleen ^a,b   Malak, Lawrence T ^a,b   Pelton, Jeffrey G ^a,b   Wemmer, David E ^a,b  

^a LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; ENZYMES; GENES; MOLECULAR STRUCTURE; NUCLEAR MAGNETIC RESONANCE; RNA; X RAY CRYSTALLOGRAPHY;

DNA-BINDING PROTEINS; HIGH RESOLUTION; HOMOLOGY; RNA POLYMERASE;

CELLS;

GLYCINE; HELIX LOOP HELIX PROTEIN; RNA POLYMERASE; SIGMA FACTOR; SIGMA FACTOR RPON; THREONINE; UNCLASSIFIED DRUG;

AMINO TERMINAL SEQUENCE; AQUIFEX AEOLICUS; ARTICLE; CARBOXY TERMINAL SEQUENCE; CONTROLLED STUDY; DNA BINDING; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN MOTIF; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS; X RAY CRYSTALLOGRAPHY;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; CRYSTALLOGRAPHY, X-RAY; DNA; DNA-DIRECTED RNA POLYMERASES; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; HELIX-TURN-HELIX MOTIFS; KLEBSIELLA; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; PLASMIDS; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; RNA POLYMERASE SIGMA 54; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, AMINO ACID; SIGMA FACTOR; STEREOISOMERISM;

AQUIFEX AEOLICUS; PROKARYOTA;

EID: 29244469944     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M509010200     Document Type: Article

References (54)

1. Burgess, R. R., Travers, A. A., Dunn, J. J., and Bautz, E. K. (1969) Nature 221, 43-46
2. Hirschman, J., Wong, P. K., Sei, K., Keener, J., and Kustu, S. (1985) Proc. Natl. Acad. Sci. U. S. A. 82, 7525-7529
3. Wosten, M. M. (1998) FEMS Microbiol. Rev. 22, 127-150
4. Lonetto, M., Gribskov, M., and Gross, C. A. (1992) J. Bacteriol. 174, 3843-3849
5. Paget, M. S., and Helmann, J. D. (2003) Genome Biol. 4, 203
6. Chilcott, G. S., and Hughes, K. T. (2000) Microbiol. Mol. Biol. Rev. 64, 694-708
7. Buck, M., Gallegos, M. T., Studholme, D. J., Guo, Y., and Gralla, J. D. (2000) J. Bacteriol. 182, 4129-4136
8. Fisher, M. A., Grimm, D., Henion, A. K., Elias, A. F., Stewart, P. E., Rosa, P. A., and Gherardini, F. C. (2005) Proc. Natl. Acad. Sci. U. S. A. 102, 5162-5167
9. Xu, H., and Hoover, T. R. (2001) Curr. Opin. Microbiol. 4, 138-144
10. Wedel, A., Weiss, D. S., Popham, D., Droge, P., and Kustu, S. (1990) Science 248, 486-490
11. Malhotra, A., Severinova, E., and Darst, S. A. (1996) Cell 87, 127-136
12. Campbell, E. A., Tupy, J. L., Gruber, T. M., Wang, S., Sharp, M. M., Gross, C. A., and Darst S. A. (2003) Mol. Cell 11, 1067-1078
13. Jain, D., Nickels, B. E., Sun, L., Hochschild, A., and Darst, S. A. (2004) Mol. Cell 13, 45-53
14. Sorenson, M. K., Ray, S. S., and Darst, S. A. (2004) Mol. Cell 14, 127-138
15. Campbell, E. A., Muzzin, O., Chienov, M., Sun, J. L., Olson, C. A., Weinman, O., Trester-Zedlitz, M. L., and Darst, S. A. (2002) Mol. Cell 9, 527-539
16. Murakami, K. S., Masuda, S., and Darst, S. A. (2002) Science 296, 1280-1284
17. Murakami, K. S., and Darst, S. A. (2003) Curr. Opin. Struct. Biol. 13, 31-39
18. Wong, C., Tintut, Y., and Gralla, J. D. (1994) J. Mol. Biol. 236, 81-90
19. Cannon, W. V., Chaney, M. K., Wang, X., and Buck, M. (1997) Proc. Natl. Acad. Sci. U. S. A. 94, 5006-5011
20. Bordes, P., Wigneshweraraj, S. R., Schumacher, J., Zhang, X., Chaney, M., and Buck, M. (2003) Proc. Natl. Acad. Sci. U. S. A. 100, 2278-2283
21. Taylor, M., Butler, R., Chambers, S., Casimiro, M., Badii, F., and Merrick, M. (1996) Mol. Microbiol. 22, 1045-1054
22. Svergun, D. I., Malfois, M., Koch, M. H., Wigneshweraraj, S. R., and Buck, M. (2000) J. Biol. Chem. 275, 4210-4214
23. Rappas, M., Schumacher, J., Beuron, F., Niwa, H., Bordes, P., Wigneshweraraj, S., Keetch, C. A., Robinson, C. V., Buck, M., and Zhang, X. (2005) Science 307, 1972-1975
24. Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994) Nucleic Acids Res. 22, 4673-4680
25. Cuff, J. A., and Barton, G. J. (2000) Proteins 40, 502-511
26. Cuff, J. A., Clamp, M. E., Siddiqui, A. S., Finlay, M., and Barton, G. J. (1998) Bioinformatics 14, 892-893
27. Marley, J., Lu, M., and Bracken, C. (2001) J. Biomol. NMR 20, 71-75
28. Delaglio, F., Grzesiek, S., Vuister, G. W., Zhu, G., Pfeifer, J., and Bax, A. (1995) J. Biomol. NMR 6, 277-293
29. Johnson, B. A., and Blevins, B. A. (1994) J. Biomol. NMR 4
30. Cornilescu, G., Delaglio, F., and Bax, A. (1999) J. Biomol. NMR 13, 289-302
31. Kuboniwa, H., Grzesiek, S., Delaglio, F., and Bax, A. (1994) J. Biomol. NMR 4, 871-878
32. Neri, D., Szyperski, T., Otting, G., Senn, H., and Wuthrich, K. (1989) Biochemistry 28, 7510-7516
33. Guntert, P., Mumenthaler, C., and Wuthrich, K. (1997) J. Mol. Biol. 273, 283-298
34. Koradi, R., Billeter, M., and Wuthrich, K. (1996) J. Mol. Graph 14, 51-55, 29-32
35. Laskowski, R. A., MacArthur, M. W., Moss, D. S., and Thornton, J. M. (1993) J. Appl. Crystallogr. 26, 283-291
36. Beitz, E. (2000) Bioinformatics 16, 135-139
37. Cavanagh, J., Wayne, J. F., Palmer, A. G., and Nicholas, J. S. (1996) Protein NMR Spectroscopy: Principles and Practice, Academic Press, San Diego, CA
38. Spera, S., and Bax, A. (1991) J. Am. Chem. Soc. 113, 5490-5492
39. Wintjens, R., and Rooman, M. (1996) J. Mol. Biol. 262, 294-313
40. Xu, H. E., Rould, M. A., Xu, W., Epstein, J. A., Maas, R. L., and Pabo, C. O. (1999) Genes Dev. 13, 1263-1275
41. Leonard, P. M., Smits, S. H., Sedelnikova, S. E., Brinkman, A. B., de Vos, W. M., van der Oost, J., Rice, D. W., and Rafferty, J. B. (2001) EMBO J. 20, 990-997
42. Murakami, K. S., Masuda, S., Campbell, E. A., Muzzin, O., and Darst, S. A. (2002) Science 296, 1285-1290
43. Sasse-Dwight, S., and Gralla, J. D. (1990) Cell 62, 945-954
44. Missailidis, S., Cannon, W. V., Drake, A., Wang, X. Y., and Buck, M. (1997) Mol. Microbiol. 24, 653-664
45. Garcia-Castellanos, R., Martero, A., Mallorqui-Fernandez, G., Potempa, J., Coli, M., and Gomis-Ruth, F. X. (2003) J. Biol. Chem. 278, 39897-39905
46. Garcia-Castellanos, R., Mallorqui-Fernandez, G., Martero, A., Potempa, J., Coll, M., and Gomis-Ruth, F. X. (2004) J. Biol. Chem. 279, 17888-17896
47. Cannon, W., Missailidis, S., Smith, C., Cottier, A., Austin, S., Moore, M., and Buck, M. (1995) J. Mol. Biol. 248, 781-803
48. Wang, L., and Gralla, J. D. (2001) J. Biol. Chem. 276, 8979-8986
49. Voskuil, M. I., and Chambliss, G. H. (2002) J. Mol. Biol. 322, 521-532
50. Burrows, P. C., Severinov, K., Ishihama, A., Buck, M., and Wigneshweraraj, S. R. (2003) J. Biol. Chem. 278, 29728-29743
51. Cannon, W., Claverie-Martin, F., Austin, S., and Buck, M. (1994) Mol. Microbiol. 11, 227-236
52. Pohl, E., Haller, J. C., Mijovilovich, A., Meyer-Klaucke, W., Carman, E., and Vasil, M. L. (2003) Mol. Microbiol. 47, 903-915
53. Mer, G., Bochkarev, A., Gupta, R., Bochkareva, E., Frappier, L., Ingles, C. J., Edwards, A. M., and Chazin, W. J. (2000) Cell 103, 449-456
54. Nichols, M. D., DeAngelis, K., Keck, J. L., and Berger, J. M. (1999) EMBO J. 18, 6177-6188