Structural and functional analysis of SmeT, the repressor of the Stenotrophomonas maltophilia multidrug efflux pump SmeDEF

Journal of Biological Chemistry

Volumn 284, Issue 21, 2009, Pages 14428-14438

  Hernández, Alvaro ^a   Maté, María J ^b,d   Sánchez Díaz, Patricia C ^a,e   Romero, Antonio ^c   Rojo, Fwenando ^a   Martínez, José L ^a,b  

^a CENTRO NACIONAL DE BIOTECNOLOGÍA   (Spain)

^b CIBER EPIDEMIOLOGÍA Y SALUD PÚBLICA CIBERESP   (Spain)

^c CENTRO DE INVESTIGACIONES BIOLÓGICAS   (Spain)

^d AIX MARSEILLE UNIVERSITY   (France)

^e UNIVERSITY OF TEXAS HEALTH SCIENCE CENTER AT SAN ANTONIO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBIOTIC RESISTANCE; BACTERIAL SPECIES; BINDING POCKETS; DNA STRANDS; EFFLUX PUMPS; IN-VITRO; MULTIDRUG EFFLUX; RNA POLYMERASE; STENOTROPHOMONAS MALTOPHILIA; STERIC HINDRANCES; STRUCTURAL FEATURE; TRANSCRIPTIONAL REPRESSORS;

ANTIBIOTICS; CHEMICAL REACTIONS; DNA; GENES; NUCLEIC ACIDS; PROTEINS; RNA;

CRYSTAL STRUCTURE;

CARRIER PROTEIN; COMPLEMENTARY DNA; PROTEIN SMEDEF; PROTEIN SMET; PROTEIN TETR; PSEUDOPEPTIDE; REPRESSOR PROTEIN; RNA POLYMERASE; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG; BACTERIAL DNA; BACTERIAL PROTEIN; LIGAND;

AMINO TERMINAL SEQUENCE; ANTIBIOTIC RESISTANCE; ARTICLE; BINDING SITE; CARBOXY TERMINAL SEQUENCE; COMPARATIVE STUDY; CONTROLLED STUDY; CRYSTAL STRUCTURE; DNA BINDING; DRUG TRANSPORT; GENETIC TRANSCRIPTION; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN ANALYSIS; PROTEIN ASSEMBLY; PROTEIN BINDING; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN STRUCTURE; STENOTROPHOMONAS MALTOPHILIA; STEREOSPECIFICITY; TRANSCRIPTION REGULATION; CHEMICAL STRUCTURE; CHEMISTRY; GENETICS; METABOLISM; MOLECULAR GENETICS; MULTIDRUG RESISTANCE; NUCLEOTIDE SEQUENCE; OPERATOR GENE; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; STRUCTURAL HOMOLOGY; X RAY CRYSTALLOGRAPHY;

BACTERIA (MICROORGANISMS); STENOTROPHOMONAS MALTOPHILIA;

BACTERIAL PROTEINS; BASE SEQUENCE; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; DNA, BACTERIAL; DRUG RESISTANCE, MULTIPLE, BACTERIAL; LIGANDS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; OPERATOR REGIONS, GENETIC; PROMOTER REGIONS, GENETIC; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; REPRESSOR PROTEINS; STENOTROPHOMONAS MALTOPHILIA; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 67649827837     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M809221200     Document Type: Article

References (66)

1. WHO (2000) in World Health Organization Report in Infectious Diseases, Geneva
2. Fajardo, A., Martinez-Martin, N., Mercadillo, M., Galan, J. C., Ghysels, B., Matthijs, S., Cornelis, P., Wiehlmann, L., Tummler, B., Baquero, F., and Martinez, J. L. (2008) PLoS ONE 3, e1619
3. Martinez, J. L., Fajardo, A., Garmendia, L., Hernandez, A., Linares, J. F., Martinez-Solano, L., and Sanchez, M. B. (2009) FEMS Microbiol. Rev. 33, 44-65
4. Vila, J., and Martinez, J. L. (2008) Curr. Drug Targets 9, 797-807
5. Piddock, L. J. (2006) Clin. Microbiol. Rev. 19, 382-402
6. Poole, K. (2005) J. Antimicrob. Chemother. 56, 20-51
7. Li, X. Z., and Nikaido, H. (2004) Drugs 64, 159-204
8. Martinez, J. L., Sanchez, M., Martinez-Solano, L., Hernandez, A., Garmendia, L., Fajardo, A., and Alvarez-Ortega, C. (2009) FEMS Microbiol. Rev. 33, 430-449
9. Grkovic, S., Brown, M. H., and Skurray, R. A. (2002) Microbiol. Mol. Biol. Rev. 66, 671-701
10. Alonso, A., Morales, G., Escalante, R., Campanario, E., Sastre, L., and Martinez, J. L. (2004) J. Antimicrob. Chemother. 53, 432-434
11. Linares, J. F., Lopez, J. A., Camafeita, E., Albar, J. P., Rojo, F., and Martinez, J. L. (2005) J. Bacteriol. 187, 1384-1391
12. Sanchez, P., Linares, J. F., Ruiz-Diez, B., Campanario, E., Navas, A., Baquero, F., and Martinez, J. L. (2002) J. Antimicrob. Chemother. 50, 657-664
13. Crossman, L. C., Gould, V. C., Dow, J. M., Vernikos, G. S., Okazaki, A., Sebaihia, M., Saunders, D., Arrowsmith, C., Carver, T., Peters, N., Adlem, E., Kerhornou, A., Lord, A., Murphy, L., Seeger, K., Squares, R., Rutter, S., Quail, M. A., Rajandream, M. A., Harris, D., Churcher, C., Bentley, S. D., Parkhill, J., Thomson, N. R., and Avison, M. B. (2008) Genome Biology 9, http://genomebiology.com/2008/9/4/R74
14. Alonso, A., and Martinez, J. L. (1997) Antimicrob. Agents Chemother. 41, 1140-1142
15. Alonso, A., and Martinez, J. L. (2000) Antimicrob. Agents Chemother. 44, 3079-3086
16. Alonso, A., and Martinez, J. L. (2001) Antimicrob. Agents Chemother. 45, 1879-1881
17. Zhang, L., Li, X. Z., and Poole, K. (2001) Antimicrob. Agents Chemother. 45, 3497-3503
18. Sanchez, P., Moreno, E., and Martinez, J. L. (2005) Antimicrob. Agents Chemother. 49, 781-782
19. Sanchez, P., Alonso, A., and Martinez, J. L. (2002) Antimicrob. Agents Chemother. 46, 3386-3393
20. Sanchez, P., Alonso, A., and Martinez, J. L. (2004) Antimicrob. Agents Chemother. 48, 2274-2276
21. Ramos, J. L., Martinez-Bueno, M., Molina-Henares, A. J., Teran, W., Watanabe, K., Zhang, X., Gallegos, M. T., Brennan, R., and Tobes, R. (2005) Microbiol. Mol. Biol. Rev. 69, 326-356
22. Orth, P., Schnappinger, D., Hillen, W., Saenger, W., and Hinrichs, W. (2000) Nat. Struct. Biol. 7, 215-219
23. Hinrichs, W., Kisker, C., Duvel, M., Muller, A., Tovar, K., Hillen, W., and Saenger, W. (1994) Science 264, 418-420
24. Orth, P., Cordes, F., Schnappinger, D., Hillen, W., Saenger, W., and Hinrichs, W. (1998) J. Mol. Biol. 279, 439-447
25. Schumacher, M. A., Miller, M. C., Grkovic, S., Brown, M. H., Skurray, R. A., and Brennan, R. G. (2002) EMBO J. 21, 1210-1218
26. Alguel, Y., Meng, C., Teran, W., Krell, T., Ramos, J. L., Gallegos, M. T., and Zhang, X. (2007) J. Mol. Biol. 369, 829-840
27. Hillen, W., and Berens, C. (1994) Annu. Rev. Microbiol. 48, 345-369
28. Engohang-Ndong, J., Baillat, D., Aumercier, M., Bellefontaine, F., Besra, G. S., Locht, C., and Baulard, A. R. (2004) Mol. Microbiol. 51, 175-188
29. Resch, M., Striegl, H., Henssler, E. M., Sevvana, M., Egerer-Sieber, C., Schiltz, E., Hillen, W., and Muller, Y. A. (2008) Nucleic Acids Res. 36, 4390-4401
30. Reichheld, S. E., and Davidson, A. R. (2006) J. Mol. Biol. 361, 382-389
31. Kamionka, A., Bogdanska-Urbaniak, J., Scholz, O., and Hillen, W. (2004) Nucleic Acids Res. 32, 842-847
32. Jeng, W. Y., Ko, T. P., Liu, C. I., Guo, R. T., Liu, C. L., Shr, H. L., and Wang, A. H. (2008) Nucleic Acids Res. 36, 1567-1577
33. Atlas, R. M. (1993) Handbook of Microbiological Media, p. 492, CRC Press, Boca Raton, FL
34. Chong, S., Mersha, F. B., Comb, D. G., Scott, M. E., Landry, D., Vence, L. M., Perler, F. B., Benner, J., Kucera, R. B., Hirvonen, C. A., Pelletier, J. J., Paulus, H., and Xu, M. Q. (1997) Gene (Amst.) 192, 271-281
35. Chong, S., Montello, G. E., Zhang, A., Cantor, E. J., Liao, W., Xu, M. Q., and Benner, J. (1998) Nucleic Acids Res. 26, 5109-5115
36. Leslie, A. G. (2006) Acta Crystallogr. D Biol. Crystallogr. 62, 48-57
37. CCP4 (1994) Acta Crystallogr. D Biol. Crystallogr. 50, 760-763
38. Pape, T., and Schneider, T. R. (2004) J. Appl. Crystallogr. 37, 843-844
39. Schneider, T. R., and Sheldrick, G. M. (2002) Acta Crystallogr. D Biol. Crystallogr. 58, 1772-1779
40. Sheldrick, G. M. (2002) Z. Kristallogr. 217, 644-650
41. Terwilliger, T. C. (2003) Acta Crystallogr. D Biol. Crystallogr. 59, 1688-1701
42. 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., and Terwilliger, T. C. (2002) Acta Crystallogr. D Biol. Crystallogr. 58, 1948-1954
43. Perrakis, A., Morris, R., and Lamzin, V. S. (1999) Nat. Struct. Biol. 6, 458-463
44. Murshudov, G. N., Vagin, A. A., and Dodson, E. J. (1997) Acta Crystallogr. D Biol. Crystallogr. 53, 240-255
45. Emsley, P., and Cowtan, K. (2004) Acta Crystallogr. D Biol. Crystallogr. 60, 2126-2132
46. Pinter, J., and Merritt, E. A. (2006) J. Appl. Crystallogr. 39, 109-111
47. Davis, I. W., Leaver-Fay, A., Chen, V. B., Block, J. N., Kapral, G. J., Wang, X., Murray, L. W., Arendall, W. B., III, Snoeyink, J., Richardson, J. S., and Richardson, D. C. (2007) Nucleic Acids Res. 35, 375-383
48. Merritt, E. A. (1999) Acta Crystallogr. D Biol. Crystallogr. 55, 1109-1117
49. Moretti, S., Armougom, F., Wallace, I. M., Higgins, D. G., Jongeneel, C. V., and Notredame, C. (2007) Nucleic Acids Res. 35, 645-648
50. Rockwell, N. C., and Lagarias, J. C. (2007) BMC Bioinformatics 8, 123
51. Baker, N. A., Sept, D., Joseph, S., Holst, M. J., and McCammon, J. A. (2001) Proc. Natl. Acad. Sci. U. S. A. 98, 10037-10041
52. Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., and Ferrin, T. E. (2004) J. Comput. Chem. 25, 1605-1612
53. DeLano, W. L. (2002) The PyMOL Molecular Graphics System, DeLano Scientifics, Palo Alto, CA
54. Li, W., and Godzik, A. (2006) Bioinformatics 22, 1658-1659
55. Rojo, F., and Alonso, J. C. (1995) Nucleic Acids Res. 23, 3181-3188
56. Dyson, H. J., and Wright, P. E. (2005) Nat. Rev. Mol. Cell Biol. 6, 197-208
57. Murray, D. S., Schumacher, M. A., and Brennan, R. G. (2004) J. Biol. Chem. 279, 14365-14371
58. Brady, G. P., Jr., and Stouten, P. F. (2000) J. Comput. Aided Mol. Des. 14, 383-401
59. Huang, B., and Schroeder, M. (2006) BMC Struct. Biol. 6, 19
60. Dundas, J., Ouyang, Z., Tseng, J., Binkowski, A., Turpaz, Y., and Liang, J. (2006) Nucleic Acids Res. 34, 116-118
61. Willems, A. R., Tahlan, K., Taguchi, T., Zhang, K., Lee, Z. Z., Ichinose, K., Junop, M. S., and Nodwell, J. R. (2008) J. Mol. Biol. 376, 1377-1387
62. Brooks, B. E., Piro, K. M., and Brennan, R. G. (2007) J. Am. Chem. Soc. 129, 8389-8395
63. Peters, K. M., Schuman, J. T., Skurray, R. A., Brown, M. H., Brennan, R. G., and Schumacher, M. A. (2008) Biochemistry 47, 8122-8129
64. Schumacher, M. A., Miller, M. C., Grkovic, S., Brown, M. H., Skurray, R. A., and Brennan, R. G. (2001) Science 294, 2158-2163
65. Dover, L. G., Corsino, P. E., Daniels, I. R., Cocklin, S. L., Tatituri, V., Besra, G. S., and Futterer, K. (2004) J. Mol. Biol. 340, 1095-1105
66. Petrek, M., Otyepka, M., Banas, P., Kosinova, P., Koca, J., and Damborsky, J. (2006) BMC Bioinformatics 7, 316