Amino acids important for DNA recognition by the response regulator OmpR

Journal of Biological Chemistry

Volumn 283, Issue 13, 2008, Pages 8664-8677

  Jee, Eun Rhee ^a   Sheng, Wanyun ^a   Morgan, Leslie K ^a   Nolet, Ryan ^a   Liao, Xiubei ^a   Kenney, Linda J ^a  

^a UNIVERSITY OF ILLINOIS AT CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINES; AMINO ACIDS; BACTERIOLOGY; BINDING ENERGY; BINDING SITES; CHEMICAL REACTIONS; CHEMICAL SHIFT; DNA; FLOW INTERACTIONS; GENES; MONOMERS; NUCLEAR MAGNETIC RESONANCE; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEIC ACIDS; PHOSPHORYLATION; PLANTS (BOTANY); PORT TERMINALS; SIGNAL TRANSDUCTION;

ASPARTIC ACIDS; ASYMMETRIC DIMERS; BACTERIAL SIGNAL TRANSDUCTIONS; BASE COMPOSITIONS; CONFORMATIONAL CHANGES; DEPHOSPHORYLATION; DNA BINDINGS; DNA RECOGNITIONS; DO-MAINS; FLEXIBLE LINKERS; HIGH AFFINITIES; MULTIPLE FACTORS; MULTIPLE ORIENTATIONS; NMR SPECTROSCOPIES; PHOSPHATE BACKBONES; PROTEIN/PROTEIN INTERACTIONS; RESPONSE REGULATORS; SOLUTION STRUCTURES; TERMINAL DOMAINS;

ORGANIC ACIDS;

AMINO ACID; DNA; OUTER MEMBRANE PROTEIN REGULATOR; PHOB PROTEIN; PROTEIN; UNCLASSIFIED DRUG; BACTERIAL PROTEIN; DISULFIDE; OSMOLARITY RESPONSE REGULATOR PROTEINS; OUTER MEMBRANE PROTEIN C; PORIN; TRANSACTIVATOR PROTEIN;

ALPHA HELIX; ARTICLE; BINDING SITE; CONFORMATIONAL TRANSITION; DNA BINDING; DNA RECOGNITION; MOLECULAR RECOGNITION; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DNA BINDING; PROTEIN DOMAIN; PROTEIN PHOSPHORYLATION; PROTEIN PROTEIN INTERACTION; PROTON NUCLEAR MAGNETIC RESONANCE; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; ESCHERICHIA COLI; GENETICS; METABOLISM; MUTATION; NUCLEAR MAGNETIC RESONANCE; PHENOTYPE; PHOSPHORYLATION; PROTEIN QUATERNARY STRUCTURE; PROTEIN TERTIARY STRUCTURE;

BACTERIA (MICROORGANISMS);

AMINO ACIDS; BACTERIAL PROTEINS; BINDING SITES; DISULFIDES; DNA; ESCHERICHIA COLI; MODELS, MOLECULAR; MUTATION; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; NUCLEIC ACID CONFORMATION; PHENOTYPE; PHOSPHORYLATION; PORINS; PROTEIN BINDING; PROTEIN STRUCTURE, QUATERNARY; PROTEIN STRUCTURE, TERTIARY; TRANS-ACTIVATORS;

EID: 43749083945     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M705550200     Document Type: Article

References (62)

1. Hoch, J. A., and Silhavy, T. J. (eds) (1995) Two-component Signal Transduction, American Society for Microbiology, Washington, DC
2. van Alphen, W., and Lugtenberg, B. (1977) J. Bacteriol. 131, 623-630
3. Basle, A., Rummel, G., Storici, P., Rosenbusch, J. P., and Schirmer, T. (2006) J. Mol. Biol. 362, 933-942
4. Cowan, S. W., Schirmer, T., Rummel, G., Steiert, M., Ghosh, R., Pauptit, R. A., Jansonius, J. N., and Rosenbusch, J. P. (1992) Nature 358, 727-733
5. Nikaido, H., Rosenberg, E. Y., and Foulds, J. (1983) J. Bacteriol. 153, 232-240
6. Oshima, T., Aiba, H., Masuda, Y., Kanaya, S., Sugiura, M., Wanner, B. L., Mori, H., and Mizuno, T. (2002) Mol. Microbiol. 46, 281-291
7. Guillier, M., and Gottesman, S. (2006) Mol. Microbiol. 59, 231-247
8. Dorman, C. J., Chatfield, S., Higgins, C. F., Hayward, C., and Dougan, G. (1989) Infect. Immun. 57, 2136-2140
9. Dorrell, N., Li, S. R., Everest, P. H., Dougan, G., and Wren, B. W. (1998) FEMS Microbiol. Lett. 165, 145-151
10. Bernardini, M. L., Fontaine, A., and Sansonetti, P. J. (1990) J. Bacteriol. 172, 6274-6281
11. Bernardini, M. L., Sanna, M. G., Fontaine, A., and Sansonetti, P. J. (1993) Infect. Immun. 61, 3625-3635
12. Brzostek, K., Raczkowska, A., and Zasada, A. (2003) FEMS Microbiol. Lett. 228, 265-271
13. Lee, A. K., Detweiler, C. S., and Falkow, S. (2000) J. Bacteriol. 182, 771-781
14. Lindgren, S. W., Stojiljkovic, I., and Heffron, F. (1996) Proc. Natl. Acad. Sci. U. S. A. 93, 4197-4201
15. Pickard, D., Li, J., Roberts, M., Maskell, D., Hone, D., Levine, M., Dougan, G., and Chatfield, S. (1994) Infect. Immun. 62, 3984-3993
16. Raczkowska, A., and Brzostek, K. (2004) Acta Microbiol. Pol. 53, 11
17. Romling, U., Sierralta, W. D., Eriksson, K., and Normark, S. (1998) Mol. Microbiol. 28, 249-264
18. Feng, X., Oropeza, R., and Kenney, L. J. (2003) Mol. Microbiol. 48, 1131-1143
19. Kato, M., Aiba, H., Tate, S., Nishimura, Y., and Mizuno, T. (1989) FEBS Lett. 249, 168-172
20. Tate, S., Kato, M., Nishimura, Y., Arata, Y., and Mizuno, T. (1988) FEBS Lett. 242, 27-30
21. Kenney, L. J., Bauer, M. D., and Silhavy, T. J. (1995) Proc. Natl. Acad. Sci. U. S. A. 92, 8866-8870
22. Aiba, H., Nakasai, F., Mizushima, S., and Mizuno, T. (1989) J. Biochem. (Tokyo) 106, 5-7
23. Harlocker, S. L., Bergstrom, L., and Inouye, M. (1995) J. Biol. Chem. 270, 26849-26856
24. Head, C. G., Tardy, A., and Kenney, L. J. (1998) J. Mol. Biol. 281, 857-870
25. Huang, K. J., and Igo, M. M. (1996) J. Mol. Biol. 262, 615-628
26. Ames, S. K., Frankema, J., and Kenney, L. J. (1999) Proc. Natl. Acad. Sci. U. S. A. 96, 11792-11797
27. Mattison, K., Oropeza, R., and Kenney, L. J. (2002) J. Biol. Chem. 277, 32714-32721
28. Rampersaud, A., Harlocker, S. L., and Inouye, M. (1994) J. Biol. Chem. 269, 12559-12566
29. Yoshida, T., Qin, L., Egger, L. A., and Inouye, M. (2006) J. Biol. Chem. 281, 17114-17123
30. Cai, S. J., and Inouye, M. (2002) J. Biol. Chem. 277, 24155-24161
31. Toro-Roman, A., Mack, T. R., and Stock, A. M. (2005) J. Mol. Biol. 349, 11-26
32. King-Scott, J., Nowak, E., Mylonas, E., Panjikar, S., Roessle, M., Svergun, D. I., and Tucker, P. A. (2007) J. Biol. Chem. 282, 37717-37729
33. Tran, V. K., Oropeza, R., and Kenney, L. J. (2000) J. Mol. Biol. 299, 1257-1270
34. Walthers, D., Tran, V. K., and Kenney, L. J. (2003) J. Bacteriol. 185, 317-324
35. Slauch, J., and Silhavy, T. J. (1989) J. Mol. Biol. 210, 291-292
36. Clore, G. M., and Gronenborn, A. M. (1998) Trends Biotechnol. 16, 22-34
37. Wishart, D. S., Bigam, C. G., Yao, J., Abildgaard, F., Dyson, H. J., Oldfield, E., Markley, J. L., and Sykes, B. D. (1995) J. Biomol. NMR 6, 135-140
38. Kanelis, V., Forman-Kay, J. D., and Kay, L. E. (2001) IUBMB Life 52, 291-302
39. Clore, G. M., Gronenborn, A. M., Nilges, M., and Ryan, C. A. (1987) Biochemistry 26, 8012-8023
40. Wuthrich, K., Billeter, M., and Braun, W. (1983) J. Mol. Biol. 169, 949-961
41. Wishart, D. S., and Case, D. A. (2001) Methods Enzymol. 338, 3-34
42. Guntert, P., Mumenthaler, C., and Wuthrich, K. (1997) J. Mol. Biol. 273, 283-298
43. Koradi, R., Billeter, M., and Wuthrich, K. (1996) J. Mol. Graphics 14, 51-55
44. Doreleijers, J. F., Rullmann, J. A., and Kaptein, R. (1998) J. Mol. Biol. 281, 149-164
45. Haldimann, A., and Wanner, B. L. (2001) J. Bacteriol. 183, 6384-6393
46. Russo, F. D., and Silhavy, T. J. (1991) J. Mol. Biol. 222, 567-580
47. Hall, M., and Silhavy, T. J. (1981) J. Mol. Biol. 151, 1-15
48. Hall, M. N., and Silhavy, T. J. (1981) J. Mol. Biol. 146, 23-43
49. Miller, J. (1972) Experiments in Molecular Genetics, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
50. Kondo, H., Nakagawa, A., Nishihira, J., Nishimura, Y., Mizuno, T., and Tanaka, I. (1997) Nat. Struct. Biol. 4, 28-31
51. Martinez-Hackert, E., and Stock, A. M. (1997) Structure (Lond.) 5, 109-124
52. Blanco, A. G., Sola, M., Gomis-Ruth, F. X., and Coll, M. (2003) Structure (Lond.) 10, 701-713
53. Makino, K., Amemura, M., Kawamoto, T., Kimura, S., Shinagawa, H., Nakata, A., and Suzuki, M. (1996) J. Mol. Biol. 259, 15-26
54. Feng, X., Walthers, D., Oropeza, R., and Kenney, L. J. (2004) Mol. Microbiol. 54, 823-835
55. Pratt, L. A., and Silhavy, T. J. (1995) Mol. Microbiol. 17, 565-573
56. Maris, A., Walthers, D., Mattison, K., Byers, N., and Kenney, L. J. (2005) J. Mol. Biol. 350, 843-856
57. Igo, M. M., and Silhavy, T. J. (1988) J. Bacteriol. 170, 5971-5973
58. Delgado, J., Forst, S., Harlocker, S., and Inouye, M. (1993) Mol. Microbiol. 10, 1037-1047
59. Mattison, K., Oropeza, R., Byers, N., and Kenney, L. J. (2002) J. Mol. Biol. 315, 497-511
60. Tsuzuki, M., Aiba, H., and Mizuno, T. (1994) J. Mol. Biol. 242, 607-613
61. Hong, E., Lee, H. M., Ko, H., Kim, D. U., Jeon, B. Y., Jung, J., Shin, J., Lee, S. A., Kim, Y., Jeon, Y. H., Cheong, C., Cho, H. S., and Lee, W. (2007) J. Biol. Chem. 282, 20667-20675
62. Nara, F., Matsuyama, S., Mizuno, T., and Mizushima, S. (1986) Mol. Gen. Genet. 202, 194-199