Dimerization allows dna target site recognition by the narl response regulator

Nature Structural Biology

Volumn 9, Issue 10, 2002, Pages 771-778

  Maris, Ann E ^a   Sawaya, Michael R ^a   Kaczor Grzeskowiak, Maria ^a   Jarvis, Michael R ^a,b   Bearson, Shawn M D ^a,c   Kopka, Mary L ^a   Schröder, Imke ^a   Gunsalus, Robert P ^a   Dickerson, Richard E ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c NATIONAL ANIMAL DISEASE CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR NARL; UNCLASSIFIED DRUG;

ARTICLE; BINDING SITE; CONTROLLED STUDY; DIMERIZATION; DNA BINDING; DNA HELIX; ESCHERICHIA COLI; HYDROGEN BOND; MOLECULAR INTERACTION; NONHUMAN; PRIORITY JOURNAL; REACTION ANALYSIS; REGULATORY MECHANISM; SIGNAL TRANSDUCTION;

BACTERIAL PROTEINS; CLONING, MOLECULAR; CRYSTALLOGRAPHY, X-RAY; DIMERIZATION; DNA; DNA-BINDING PROTEINS; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; NUCLEIC ACID CONFORMATION; PROMOTER REGIONS (GENETICS); PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; RECOMBINANT PROTEINS; STRUCTURE-ACTIVITY RELATIONSHIP;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; PROKARYOTA;

EID: 0036786677     PISSN: 10728368     EISSN: None     Source Type: Journal    
DOI: 10.1038/nsb845     Document Type: Article

References (42)

1. Parkinson, J.S. & Kofoid, E.C. Communication modules in bacterial signalling proteins. Annu. Rev. Genet. 26, 71-112 (1992).
2. Stock, A.M., Robinson, V.L. & Goudreau, RN. Two-component signal transduction. Annu. Rev. Biochem. 69, 183-215 (2000).
3. Robinson, V.L., Buckler, D.R. & Stock, A.M. A tale of two components: a novel kinase and a regulatory switch. Nature Struct. Biol. 7, 626-633 (2000).
4. Stewart, V. & Rabin, R.S. in Two-Component Signal Transduction (eds Hoch, J.A. & Silhavy, T.J.) 233-252 (American Society for Microbiology, Washington, D.C.; 1995).
5. Volz, K. & Matsumura, P. Crystal Structure of Escherichia coli Che Y refined at 1.7 Å resolution. J. Biol. Chem 266, 15511-15519 (1991).
6. Baikalov, I. et al. Structure of the Escherichia coll response regulator NarL. Biochemistry 35, 11053-11061 (1996).
7. Baikalov, I. et al. NarL dimerization? Suggestive evidence from a new crystal form. Biochemistry 37, 3665-3676 (1998).
8. Pabo, C.O. & Nekludova, L. Geometric analysis and comparison of protein-DNA interfaces: why is there no simple code? J. Mol. Biol. 301, 597-624 (2000).
9. Darwin, A.J., Tyson, K.L., Busby, S.J.W. & Stewart, V. Differential regulation by the homologous response regulators NarL and NarP of Escherichia coli K-12 depends on DNA binding site arrangement. Mol. Micro. 25, 583-595 (1997).
10. Lonetto, M.A. et al. Identification of a contact site for different transcription activators in region 4 of the Escherichia coli RNA polymerase σ70 subunit. J. Mol. Biol. 284, 1353-1365 (1998).
11. Dickerson, R.E. & Chiu, T.K. Helix bending as a factor in protein/DNA recognition. Biopolymers 44, 361-403 (1998).
12. Dickerson, R.E. DNA bending: the prevalence of kinkiness and the virtues of normality. Nucleic Acids Res. 26, 1906-1926 (1998).
13. Lu, X.-J., Shakked, Z. & Olson, W.K. A-form conformational motifs in ligand-bound DNA structures. J. Mol. Biol. 300, 819-840 (2000).
14. Ng, H.-L., Kopka, M.L. & Dickerson, R.E. The structure of a stable intermediate in the A to B DNA helix transition. Proc. Natl. Acad. Sci. USA 97, 2035-2039 (2000).
15. Berman, H.M. et al. The Nucleic Acid Database: A comprehensive relational database of three-dimensional structures of nucleic acids. Biophys. J. 63, 751-759 (1992).
16. Woda, J., Schneider, B., Patel, K., Mistry, K. & Berman, H.M. An analysis of the relationship between hydration and protein-DNA interactions. Biophys. J. 75, 2170-2177 (1998).
17. Blanco, A.G., Sola, M., Gomis-Rueth, F.X. & Coll, M. Tandem DNA recognition by PhoB, a two-component signal transduction transcriptional activator. Structure 10, 701-713 (2002).
18. Tran, V.K., Oropeza, R. & Kenney, L.J. A single amino acid substitution in the C terminus of OmpR alters DNA recognition and phosphorylation. J. Mol. Biol. 299, 1257-1270 (2000).
19. Laughon, A. DNA binding specificity of homeodomains. Biochemistry 30, 11357-11367 (1991).
20. Fraenkel, E., Rould, M.A., Chambers, K.A. & Pabo, C.O. Engrailed homeodomain-DNA complex at 2.2 Å resolution: a detailed view of the interface and comparison with other engrailed structures. J. Mol. Biol. 284, 351-361 (1998).
21. Han, G.W., Kopka, M.L., Cascio, D., Grzeskowiak, K. & Dickerson, R.E. Structure of a DNA analog of the primer for HIV-1 RT second strand synthesis. J. Mol. Biol. 269, 811-826 (1997).
22. Hines, C.S. et al. DNA structure and flexibility in the sequence-specific binding of Papillomavirus E2 proteins. J. Mol. Biol. 276, 809-818 (1998).
23. Kim, S.-S., Tam, J.K., Wang, A.-F. & Hegde, R.S. The structural basis of DNA target discrimination by Papillomavirus E2 proteins. J. Biol. Chem 275, 31245-31254 (2000).
24. Hizver, J., Rozenberg, H., Frolow, F., Rabinovich, D. & Shakked, Z. DNA bending by an adenine-thymine tract and its role in gene regulation. Proc. Natl. Acad. Sci. USA 98, 8490-8495 (2001).
25. Gajiwala, K.S. et al. Structure of the winged-helix protein hRFX1 reveals a new mode of DNA binding. Nature 403, 916-919 (2000).
26. Djordjevic, S., Goudreau, P.N., Xu, Q., Stock, A.M. & West, A.H. Structural basis for methylesterase CheB regulation by a phosphorylation-activated domain. Proc. Natl. Acad. Sci. USA 95, 1381-1386 (1998).
27. Buckler, D.R., Zhou, Y. & Stock, A.M. Evidence of intradomain and interdomain flexibility in an OmpR/PhoB homolog from Thermotoga maritima. Structure 10, 153-164 (2002).
28. Zhang, R.-G. et al. Structure of a bacterial quorum-sensing transcription factor complexed with pheromone and DNA. Nature 417, 971-974 (2002).
29. Schroeder, I., Wolin, C.D., Cavicchioli, R. & Gunsalus, R.P. Phosphorylation and dephosphorylation of the NarX, NarL, and NarQ proteins of the nitrate dependent two-component regulatory system of Escherichia coli. J. Bacteriol. 176, 4985-4992 (1994).
30. Van Duyne, G.D., Standaert, R.F., Karplus, P.A., Schreiber, S.L. & Clardy, J. Atomic structures of the human immunophilin FKBP-12 complexes with FK506 and rapamycin. J. Mol. Biol. 229, 105-124 (1993).
31. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-326 (1997).
32. c/DNA complex. PhD. thesis, Univ. California (2002).
33. Terwilliger, T.C. & Berendzen, J. Automated MAD and MIR structure solution. Acta Crystallogr. D 55, 849-861 (1999).
34. Jones, T.A., Zhou, J.-Y., Cowan, S.W. & Kjeldgaard, M. Improved methods for the building of protein models in electron density maps and the location of errors in these maps. Acta Crystallogr. A 47, 110-119 (1991).
35. Collaborative Computational Project, Number 4. The CCP4 suite: programs for protein crystallography. Acta. Crystallogr. D 50, 760-763 (1994).
36. McRee, D.E. XtalView/Xfit-A versatile program for manipulating atomic coordinates and electron density. J. Struct. Biol. 125, 156-165 (1999).
37. Tong, L. & Rossman, M.G. The locked rotation function. Acta Crystallogr. A 46, 783-792 (1990).
38. Brünger, A.T. et al. Crystallography and NMR System (CNS): a new software package for macromolecular structure determination. Acta Crystallogr. D 54, 905-921 (1998).
39. Bearson, S.M.D., Albrecht, J.A. & Gunsalus, R.R Oxygen and nitrate-dependent regulation of dmsABC operon expression in Escherichia coli: sites for Fnr and NarL protein interactions. BMC Micro. 2, 13 (2002).
40. El Hassan, M.A. & Calladine, C.R. Conformational characteristics of DNA: empirical classifications and a hypothesis for the conformational behaviour of dinucleotide steps. Phil. Trans. R. Soc. Lond. A 355, 43-100 (1997).
41. Lavery, R. & Skelnar, H. The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids. J. Biomol. Struct. Dynam. 6, 63-91 (1988).
42. Laskowski, R.A., MacArthur, M.W., Moss, D.S. & Thornton, J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26, 283-291 (1993).