Structure, function, and tethering of DNA-binding domains in σ54 transcriptional activators

Biopolymers

Volumn 99, Issue 12, 2013, Pages 1082-1096

  Vidangos, Natasha ^a   Maris, Ann E ^a   Young, Anisa ^a   Hong, Eunmi ^a   Pelton, Jeffrey G ^a   Batchelor, Joseph D ^a   Wemmer, David E ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

bacterial transcription; DNA binding domain; sigma factor

Indexed keywords

ADENOSINE TRIPHOSPHATE HYDROLYSIS; BACTERIAL TRANSCRIPTION; CONFORMATIONAL CHANGE; DNA-BINDING DOMAIN; INVERSION STIMULATION; SIGMA FACTOR; TRANSCRIPTION INITIATION; TRANSCRIPTIONAL ACTIVATORS;

ADENOSINETRIPHOSPHATE; TRANSCRIPTION;

DNA;

ADENOSINE TRIPHOSPHATASE; ADENOSINE TRIPHOSPHATE; DNA BINDING DOMAIN; DNA BINDING PROTEIN; FACTOR FOR INVERSION STIMULATION; NITROGEN REGULATORY PROTEIN; SIGMA FACTOR RPON; UNCLASSIFIED DRUG; BACTERIAL PROTEIN; DNA; TRANSACTIVATOR PROTEIN; TRANSCRIPTION FACTOR;

AMINO TERMINAL SEQUENCE; AQUIFEX AEOLICUS; ARTICLE; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; DIMERIZATION; DNA BINDING; HYDROLYSIS; NONHUMAN; THERMOPHILE; TRANSCRIPTION INITIATION; CHEMISTRY; METABOLISM; PROTEIN MOTIF; PROTEIN TERTIARY STRUCTURE;

AMINO ACID MOTIFS; BACTERIAL PROTEINS; DNA; DNA-BINDING PROTEINS; PROTEIN STRUCTURE, TERTIARY; RNA POLYMERASE SIGMA 54; TRANS-ACTIVATORS; TRANSCRIPTION FACTORS;

EID: 84884933237     PISSN: 00063525     EISSN: 10970282     Source Type: Journal    
DOI: 10.1002/bip.22333     Document Type: Article

References (68)

1. Burgess, R. R.,;, Travers, A. A.,;, Dunn, J. J.,;, Bautz, E. K., Nature 1969, 221, 43-46.
2. Burgess, R. R., J Biol Chem 1969, 244, 6168-6176.
3. Wosten, M. M., FEMS Microbiol Rev 1998, 22, 127-150.
4. Wignestweraraj, S.,;, Bose, D. M.,;, Burrows, P. C.,;, Joly, N.,;, Schumacher, J.,;, Rappas, M.,;, Pape, T.,;, Zhang, X.,;, Stockley, P.,;, Severinov, K.,;, Buck, M., Mol Microbiol 2008, 68, 538-546.
5. Kazmierczak, M. K.,;, Wiedmann, M.,;, Boor, K. J., Mol Biol Rev 2005, 69, 527-543.
6. Buck, M.,;, Gallegos, M. T.,;, Studholme, D. J.,;, Guo, Y.,;, Gralla, J. D., J Bact 2000, 182, 4129-4136.
7. Reitzer, L.,;, Schneider, B. L., Microbiol Mol Biol Rev 2001, 65, 422-433.
8. Model, P.,;, Jovanovic, G.,;, Dworkin, J., Mol Microbiol 1997, 24, 255-261.
9. Porter, S. C.,;, North, A. K.,;, Kustu, S., Genes Dev 1993, 7, 2258-2273.
10. Lee, S. Y.,;, De La Torre, A.,;, Yan, D.,;, Kustu, S.,;, Nixon, B. T.,;, Wemmer, D. E., Genes Dev 2003, 17, 2552-2263.
11. De Carlo, S.,;, Chen, B.,;, Hoover, T. R.,;, Kondrashkina, E.,;, Nogales, E.,;, Nixon, B. T., Genes Dev 2006, 20, 1485-1495.
12. Studholme, D. J.,;, Dixon R., J Bact 2003, 185, 1757-1767.
13. Reitzer, L. J.,;, Magasanik, B., J Bact 1989, 171, 5512-5522.
14. Su, W.,;, Porter, S.,;, Kustu, S.,;, Echols, H., Proc Natl Acad Sci 1990, 87, 5504-5508.
15. Wedel, A.,;, Weiss, D. S.,;, Popham, D.,;, Droge, P.,;, Kustu, S., Science 1990, 248, 486-490.
16. Zhang, X.,;, Chaney, M.,;, Wigneshweraraj, S. R.,;, Schumacher, J.,;, Bordes, P.,;, Cannon, W.,;, Buck, M., Mol Microbiol 2002, 45, 895-903.
17. Hastings, C. A.,;, Lee, S. Y.,;, Cho, H. S.,;, Yan, D.,;, Kustu, S.,;, Wemmer, D. E., Biochemistry 2003, 42, 9081-9090.
18. Meyer, M.,;, Park, S.,;, Zeringue, L.,;, Staley, M.,;, McKinstry, M.,;, Kaufman, R. I.,;, Zhang, H.,;, Yan, D.,;, Yennawar, N.,;, Yennawar, H.,;, Farber, G. K.,;, Nixon, B. T., FASEB J 2001, 15, 1326-1328.
19. Rappas, M.,;, Schumacher, J.,;, Beuron, F.,;, Niwa, H.,;, Bordes, P.,;, Wigneshweraraj, S.,;, Keetch, C. A.,;, Robinson, C. V.,;, Buck, M.,;, Zhang, X., Science 2005, 307, 1972-1975.
20. Sallai, L.,;, Tucker, P., J Struct Biol 2005, 151, 160-170.
21. Schumacher, J.,;, Joly, N.,;, Rappas, M.,;, Zhang, X.,;, Buck, M., J Struct Biol 2006, 156, 190-199.
22. Pelton J. G.,;, Kustu S.,;, Wemmer D. E., J Mol Biol 1999, 292, 1095-1110.
23. Hunt, T. P.,;, Magasanik, B., Proc Natl Acad Sci 1985, 82, 8453-8457.
24. Hirschman, J.,;, Wong, P. K.,;, Sei, K.,;, Keener, J.,;, Kustu, S., Proc Natl Acad Sci 1985, 82, 7525-7529.
25. Deckert, G,;, Warren, P. V.,;, Gaasterland, T.,;, Young, W. G.,;, Lenox, A. L.,;, Graham, D. E.,;, Overbeek, R.,;, Snead, M. A.,;, Keller, M.,;, Aujay, M.,;, Huber, R.,;, Feldman, R. A.,;, Short, J. M.,;, Olson, G. J.,;, Swanson, R. V., Nature 1998, 392, 353-358.
26. Martinez-Argudo, I.,;, Little, R.,;, Shearer, N.,;, Johnson, P.,;, Dixon, R., J Bacteriol 2004, 186, 601-610.
27. Batchelor, J. D.,;, Doucleff, M.,;, Lee, C. J.,;, Matsubara, K.,;, De Carlo, S.,;, Heideker, J.,;, Lamers, M. H.,;, Pelton, J. G.,;, Wemmer, D. E., J Mol Biol 2008, 384, 1058-1075.
28. Vidangos, N.,;, Heideker, J.,;, Lyuvimov, A.,;, Lamers, M.,;, Huo, Y.,;, Pelton, J. G.,;, Ton, J.,;, Gralla, J.,;, Berger, J.,;, Wemmer, D. E., unpublished results.
29. Doucleff, M.,;, Chen, B.,;, Maris, A. E.,;, Wemmer, D. E.,;, Kondrashkina, E.,;, Nixon, B. T., J Mol Biol 2005, 353, 242-255.
30. Dominguez, C.,;, Boelens, R.,;, Bonvin, A. J., J Am Chem Soc 2003, 125, 1731-1737.
31. de Vries, S. J.,;, van Dijk, A. D. J.,;, Krzeminski, M.,;, van Dijk, M.,;, Thureau, A.,;, Hsu, V.,;, Wassenaar, T.,;, Bonvin, A. M. J. J., Proteins Struct Funct Bioinf 2007, 69, 726-733.
32. North, A.,;, Kustu, S., J Mol Biol 1997, 267, 17-36.
33. Schulz, A.,;, Langowski, J.,;, Rippe, K., J Mol Biol 2000, 300, 709-725.
34. Morett E.,;, Bork, P., FEBS Lett 1998, 433, 108-112.
35. Aravind, L.,;, Anantharaman, V.,;, Balaji, S.,;, Babu, M. M.,;, Lakshminarayan, M. I., FEMS Microbiol Rev 2005, 29, 231-262.
36. Rohs, R.,;, Jin, X.,;, West, S. M.,;, Joshi, R.,;, Honig, B.,;, Mann, R. S., Ann Rev Biochem 2010, 79, 233-269.
37. Huffman, J. L.,;, Brennan, R. G., Curr Opin Struct Biol 2002, 12, 98-106.
38. Chen, P.,;, Reitzer, L., J Bact 1995, 177, 2490-2496.
39. Klose, K. E.,;, North, A. K.,;, Stedman, K. M.,;, Kustu, S., J Mol Biol 1994, 241, 233-245.
40. Batchelor J. D.,;, Lee, P. S.,;, Wang, A. C.,;, Doucleff, M.,;, Wemmer, D. E., J Mol Biol 2013, 425, 156-170.
41. Cole C.,;, Barber, J. D.,;, Barton, G. J., Nuc Acids Res 2008, 36, W197-W201.
42. 54 transcriptional activation in Aquifex aeolicus, University of California, Berkeley, 2010.
43. Weiss, V.,;, Claverie-Martin, F.,;, Magasanik, B., Proc Natl Acad Sci 1992, 89, 5088-5092.
44. Scholl, D.,;, Nixon, B. T., J Biol Chem 1996, 271, 26435-26442.
45. Ababou, A.,;, Rostkova, E.,;, Mistry, S.,;, Le Masurier, C.,;, Gautel, M.,;, Pfuhl, M., J Mol Biol 2008, 384, 615-630.
46. Hsu, J. L.,;, Martinis, S. A., J Mol Biol 2007, 376, 482-491.
47. Poon, D. K.,;, Wither, S. G.,;, McIntosh, L. P., J Biol Chem 2007, 282, 2091-2100.
48. Vasilaki, E.,;, Siderakis, M.,;, Papakosta, P.,;, Skourti-Stathaki, K.,;, Mavridou, S.,;, Kardassis, D., Biochemistry 2009, 48, 8366-8378.
49. Klinge, S.,;, Núñez-Ramírez, R.,;, Llorca, O.,;, Pellegrini, L., EMBO J 2009, 28, 1978-1987.
50. Sean, P.,;, Nguyen, J. H.,;, Semler, B. L., Virology 2008, 378, 243-253.
51. Kercher, M. A.,;, Lu, P.,;, Lewis, M., Curr Opin Struct Biol 1997, 7, 76-85.
52. Swint-Kruse, L.,;, Matthews, K. S., Curr Opin Microbiol 2009, 12, 129-137.
53. Burke, J. R.,;, Deshong, A. J.,;, Pelton, J. G.,;, Rubin S. M., J Biol Chem 2010, 285, 16286-16293.
54. Lewis, R. J.,;, Scott, D. J.,;, Brannigan, J. A.,;, Ladds, J. C.,;, Cervin, M. A.,;, Spiegelman, G. B.,;, Hoggett, J. G.,;, Barak, I, Wilkinson, A. J., J Mol Biol 2002, 316, 235-245.
55. Wisedchaisri, G.,;, Wu, M.,;, Sherman, D. R.,;, Hol W. G. J., J Mol Biol 2008, 378, 227-242.
56. Kalodimos, C. G.,;, Folkers, H. E.,;, Boelens, R.,;, Kaptein, R., Proc Natl Acad Sci 2001, 22, 6039-6044.
57. Cheng, Y.,;, Wie-Zen Y.,;, Johnson R.,;, Yuan H., J Mol Biol 2000, 302, 1139-1151.
58. Stella S, Cascio, D.,;, Johnson, R. C., Genes Dev 2010, 24, 814-826.
59. Kumaraswami, M.,;, Howe, M. M.,;, Park, H. W., J Biol Chem 2004, 279, 16581-16590.
60. Kuriyan, J.,;, Eisenberg, D., Nature 2007, 450, 983-990.
61. Marley, J.,;, Lu, M.,;, Bracken, C., J Biomol NMR 2001, 20, 71-75.
62. Powell, H., Acta Cryst D Biol Cryst 1999, 55, 1690-1695.
63. Bailey, S., Acta Cryst D Biol Cryst 1994, 50, 760-763.
64. Holton, J.,;, Alber, T., Proc Natl Acad Sci 2004, 101, 1537-1542.
65. McCoy, A. J.,;, Grosse-Kustleve, R. W.,;, Adams, P. D.,;, Winn, M. D.,;, Storone, L. C.,;, Read, R. J., J Appl Cryst 2007, 40, 658-674.
66. Emsley, P.,;, Cowtan, K., Acta Cryst D Biol Cryst 2004, 60, 2126-2132.
67. Adams, P. D.,;, Grosse-Kunstleve, R. W.,;, Hung, L. W.,;, Ioerger, T. R.,;, McCoy, A. J.,;, Moriarty, N. W.,;, Read, R. J.,;, Sacchettini, J. C.,;, Sauter, N. K.,;, Twerwilliger, T. C., Acta Cryst D Biol Cryst 2002, 58, 1948-1954.
68. Santero E.,;, Hoover, T. R.,;, North, A. K.,;, Berger, D. K.,;, Porter, S. C.,;, Kustu, S., J Mol Biol 1992, 227, 602-620.