Intradomain LexA rotation is a prerequisite for DNA binding specificity

FEBS Letters

Volumn 581, Issue 25, 2007, Pages 4816-4820

  Butala, Matej ^a   Hodošček, Milan ^b   Anderluh, Gregor ^a   Podlesek, Zdravko ^a   Žgur Bertok, Darja ^a  

^a UNIVERSITY OF LJUBLJANA   (Slovenia)

^b NATIONAL INSTITUTE OF CHEMISTRY   (Slovenia)

Author keywords

DNA binding; Domain rotation; LexA repressor

Indexed keywords

CYSTEINE; LEXA PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; DNA BINDING; DRUG DESIGN; GEL MOBILITY SHIFT ASSAY; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN STRUCTURE; ROTATION; SURFACE PLASMON RESONANCE;

BACTERIAL PROTEINS; COLICINS; DIMERIZATION; DNA-BINDING PROTEINS; MODELS, MOLECULAR; MUTATION; OPERATOR REGIONS (GENETICS); PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; ROTATION; SERINE ENDOPEPTIDASES;

BACTERIA (MICROORGANISMS);

EID: 34948876428     PISSN: 00145793     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.febslet.2007.09.006     Document Type: Article

References (32)

1. Wade J.T., Reppas N.B., Church G.M., and Struhl K. Genomic analysis of LexA binding reveals the permissive nature of the Escherichia coli genome and identifies unconventional target sites. Genes Dev. 19 (2005) 2619-2630
2. Cascales E., et al. Colicin biology. Microbiol. Mol. Biol. Rev. 71 (2007) 158-229
3. Quinones M., Kimsey H.H., and Waldor M.K. LexA cleavage is required for CTX prophage induction. Mol. Cell 17 (2005) 291-300
4. Bisognano C., et al. A recA-LexA-dependent pathway mediates ciprofloxacin-induced fibronectin binding in Staphylococcus aureus. J. Biol. Chem. 279 (2004) 9064-9071
5. Little J.W., Edmiston S.H., Pacelli L.Z., and Mount D.W. Cleavage of the Escherichia coli lexA protein by the recA protease. Proc. Natl. Acad. Sci. USA 77 (1980) 3225-3229
6. Hurstel S., Granger-Schnarr M., and Schnarr M. Contacts between the LexA repressor - or its DNA-binding domain - and the backbone of the recA operator DNA. EMBO J. 7 (1988) 269-275
7. Luo Y., et al. Crystal structure of LexA: a conformational switch for regulation of self-cleavage. Cell 106 (2001) 585-594
8. Fogh R.H., Ottleben G., Ruterjans H., Schnarr M., Boelens R., and Kaptein R. Solution structure of the LexA repressor DNA binding domain determined by 1H NMR spectroscopy. Embo J. 13 (1994) 3936-3944
9. Schnarr M., Granger-Schnarr M., Hurstel S., and Pouyet J. The carboxy-terminal domain of the LexA repressor oligomerises essentially as the entire protein. FEBS Lett. 234 (1988) 56-60
10. Chattopadhyaya R., and Pal A. Improved model of a LexA repressor dimer bound to recA operator. J. Biomol. Struct. Dyn. 21 (2004) 681-689
11. Thliveris A.T., and Mount D.W. Genetic identification of the DNA binding domain of Escherichia coli LexA protein. Proc. Natl. Acad. Sci. USA 89 (1992) 4500-4504
12. Knegtel R.M., Fogh R.H., Ottleben G., Ruterjans H., Dumoulin P., Schnarr M., Boelens R., and Kaptein R. A model for the LexA repressor DNA complex. Proteins 21 (1995) 226-236
13. Brooks R.D., Bruccoleri R.E., Olafson B.D., states D.J., Swaminathan S., and Karplus M. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 4 (1983) 187-217
14. Borstnik U., Hodoscek M., and Janezic D. Improving the performance of molecular dynamics simulations on parallel clusters. J. Chem. Inf. Comput. Sci. 44 (2004) 359-364
15. Humphrey W., Dalke A., and Schulten K. VMD: visual molecular dynamics. J. Mol. Graph. 14 33-8 (1996) 27-28
16. Mrak P., Podlesek Z., van Putten J.P., and Zgur-Bertok D. Heterogeneity in expression of the Escherichia coli colicin K activity gene cka is controlled by the SOS system and stochastic factors. Mol. Genet. Genom. 277 (2007) 391-401
17. Munteanu M.G., Vlahovicek K., Parthasarathy S., Simon I., and Pongor S. Rod models of DNA: sequence-dependent anisotropic elastic modelling of local bending phenomena. Trends Biochem. Sci. 23 (1998) 341-347
18. Im W., Lee M.S., and Brooks III C.L. Generalized born model with a simple smoothing function. J. Comput. Chem. 24 (2003) 1691-1702
19. Mackerell Jr. A.D., Feig M., and Brooks III C.L. Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J. Comput. Chem. 25 (2004) 1400-1415
20. Foloppe N., and Mackerell Jr. A.D. All-atom empirical force field for nucleic acids: parameter optimization based on small molecule and condensed phase macromolecular target data. J. Comput. Chem. 21 (2000) 86-104
21. Anderluh G., Pungercar J., Strukelj B., Macek P., and Gubensek F. Cloning, sequencing, and expression of equinatoxin II. Biochem. Biophys. Res. Commun. 220 (1996) 437-442
22. Anderluh G., Gokce I., and Lakey J.H. Expression of proteins using the third domain of the Escherichia coli periplasmic-protein TolA as a fusion partner. Protein Expr. Purif. 28 (2003) 173-181
23. Lewis L.K., Harlow G.R., Gregg-Jolly L.A., and Mount D.W. Identification of high affinity binding sites for LexA which define new DNA damage-inducible genes in Escherichia coli. J. Mol. Biol. 241 (1994) 507-523
24. Mulec J., Podlesek Z., Mrak P., Kopitar A., Ihan A., and Zgur-Bertok D. A cka-gfp transcriptional fusion reveals that the colicin K activity gene is induced in only 3 percent of the population. J. Bacteriol. 185 (2003) 654-659
25. Mount D.W., Walker A.C., and Kosel C. Effect of tsl mutations in decreasing radiation sensitivity of a recA- strain of Escherichia coli K-12. J. Bacteriol. 121 (1975) 1203-1207
26. Lloubes R., Granger-Schnarr M., Lazdunski C., and Schnarr M. LexA repressor induces operator-dependent DNA bending. J. Mol. Biol. 204 (1988) 1049-1054
27. Little J.W., and Hill S.A. Deletions within a hinge region of a specific DNA-binding protein. Proc. Natl. Acad. Sci. USA 82 (1985) 2301-2305
28. Sousa F.J., et al. Tetramerization of the LexA repressor in solution: implications for gene regulation of the E. coli SOS system at acidic pH. J. Mol. Biol. 359 (2006) 1059-1074
29. Mohana-Borges R., Pacheco A.B., Sousa F.J., Foguel D., Almeida D.F., and Silva J.L. LexA repressor forms stable dimers in solution. The role of specific dna in tightening protein-protein interactions. J. Biol. Chem. 275 (2000) 4708-4712
30. Beaber J.W., Hochhut B., and Waldor M.K. SOS response promotes horizontal dissemination of antibiotic resistance genes. Nature 427 (2004) 72-74
31. Ubeda C., Maiques E., Knecht E., Lasa I., Novick R.P., and Penades J.R. Antibiotic-induced SOS response promotes horizontal dissemination of pathogenicity island-encoded virulence factors in Staphylococci. Mol. Microbiol. 56 (2005) 836-844
32. Mellies J.L., Haack K.R., and Galligan D.C. SOS regulation of the type III secretion system of enteropathogenic Escherichia coli. J. Bacteriol. 189 (2007) 2863-2872