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Dimerization allows DNA target site recognition by the NarL response regulator

Nature Structural Biology volume 9, pages 771–778 (2002)Cite this article

Abstract

Two-component signal transduction systems are modular phosphorelay regulatory pathways common in prokaryotes. In the co-crystal structure of the Escherichia coli NarL signal output domain bound to DNA, we observe how the NarL family of two-component response regulators can bind DNA. DNA recognition is accompanied by the formation of a new dimerization interface, which could occur only in the full-length protein via a large intramolecular domain rearrangement. The DNA is recognized by the concerted effects of solvation, van der Waals forces and inherent DNA deformability, rather than determined primarily by major groove hydrogen bonding. These subtle forces permit a small DNA-binding domain to perturb the DNA helix, leading to major DNA curvature and a transition from B- to A-form DNA at the binding site, where valine on the recognition helix interacts unexpectedly with the polar major groove floor.

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Figure 1: DNA recognition by NarL.
Figure 2: NarLC–DNA structure and DNA contacts.
Figure 3: Stereo views of major groove recognition.
Figure 4: DNA parameters of zp, the groove width, roll and sugar pseudorotation angle (P).
Figure 5: Impossibility of DNA binding to the full-length NarL without considerable domain movement.

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References

  1. Parkinson, J.S. & Kofoid, E.C. Communication modules in bacterial signalling proteins. Annu. Rev. Genet. 26, 71–112 (1992).

    Article  CAS  Google Scholar 

  2. Stock, A.M., Robinson, V.L. & Goudreau, P.N. Two-component signal transduction. Annu. Rev. Biochem. 69, 183–215 (2000).

    Article  CAS  Google Scholar 

  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).

    Article  CAS  Google Scholar 

  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).

    Google Scholar 

  5. Volz, K. & Matsumura, P. Crystal Structure of Escherichia coli CheY refined at 1.7 Å resolution. J. Biol. Chem 266, 15511–15519 (1991).

    CAS  PubMed  Google Scholar 

  6. Baikalov, I. et al. Structure of the Escherichia coli response regulator NarL. Biochemistry 35, 11053–11061 (1996).

    Article  CAS  Google Scholar 

  7. Baikalov, I. et al. NarL dimerization? Suggestive evidence from a new crystal form. Biochemistry 37, 3665–3676 (1998).

    Article  CAS  Google Scholar 

  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).

    Article  CAS  Google Scholar 

  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).

    Article  CAS  Google Scholar 

  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).

    Article  CAS  Google Scholar 

  11. Dickerson, R.E. & Chiu, T.K. Helix bending as a factor in protein/DNA recognition. Biopolymers 44, 361–403 (1998).

    Article  Google Scholar 

  12. Dickerson, R.E. DNA bending: the prevalence of kinkiness and the virtues of normality. Nucleic Acids Res. 26, 1906–1926 (1998).

    Article  CAS  Google Scholar 

  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).

    Article  CAS  Google Scholar 

  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).

    Article  CAS  Google Scholar 

  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).

    Article  CAS  Google Scholar 

  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).

    Article  CAS  Google Scholar 

  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).

    Article  CAS  Google Scholar 

  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).

    Article  CAS  Google Scholar 

  19. Laughon, A. DNA binding specificity of homeodomains. Biochemistry 30, 11357–11367 (1991).

    Article  CAS  Google Scholar 

  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).

    Article  CAS  Google Scholar 

  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).

    Article  CAS  Google Scholar 

  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).

    Article  CAS  Google Scholar 

  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).

    Article  CAS  Google Scholar 

  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).

    Article  CAS  Google Scholar 

  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).

    Article  CAS  Google Scholar 

  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).

    Article  CAS  Google Scholar 

  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).

    Article  CAS  Google Scholar 

  28. Zhang, R.-G. et al. Structure of a bacterial quorum-sensing transcription factor complexed with pheromone and DNA. Nature 417, 971–974 (2002).

    Article  CAS  Google Scholar 

  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).

    Article  Google Scholar 

  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).

    Article  CAS  Google Scholar 

  31. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997).

    Article  CAS  Google Scholar 

  32. Maris, A.E. Molecular studies in protein/DNA recognition: crystallographic trials of the retrovirus integrase protein and the crystal structure of the Escherichia coli response regulator NarLC/DNA complex. PhD. thesis, Univ. California (2002).

    Google Scholar 

  33. Terwilliger, T.C. & Berendzen, J. Automated MAD and MIR structure solution. Acta Crystallogr. D 55, 849–861 (1999).

    Article  CAS  Google Scholar 

  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).

    Article  Google Scholar 

  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).

    Article  CAS  Google Scholar 

  37. Tong, L. & Rossman, M.G. The locked rotation function. Acta Crystallogr. A 46, 783–792 (1990).

    Article  Google Scholar 

  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).

    Article  Google Scholar 

  39. Bearson, S.M.D., Albrecht, J.A. & Gunsalus, R.P. 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).

    Article  CAS  Google Scholar 

  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).

    Article  CAS  Google Scholar 

  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).

    Article  CAS  Google Scholar 

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Acknowledgements

We thank A. Colasanti for his insightful discussions regarding B-to-A DNA transitions; D. Cascio for X-ray technical assistance and discussions; and G. Katsir, T. Chiu and H.-L. Ng for technical assistance and discussion. This work was supported by NIH grants.

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Author notes

  1. Michael R. Jarvis

    Present address: Department of Pathology and Laboratory Medicine, University of California, Los Angeles, California, 90095, USA

  2. Shawn M.D. Bearson

    Present address: United States Department of Agriculture, National Animal Disease Center, 2300 Dayton Road, Ames, Iowa, 50010, USA

Authors and Affiliations

  1. Department of Chemistry and Biochemistry, University of California, Los Angeles, P.O. Box 951569, Los Angeles, 90095-1569, California, USA

    Ann E. Maris & Richard E. Dickerson

  2. Molecular Biology Institute, University of California, Los Angeles, P.O. Box 951570, Los Angeles, 90095-1570, California, USA

    Ann E. Maris, Michael R. Sawaya, Maria Kaczor-Grzeskowiak, Mary L. Kopka, Robert P. Gunsalus & Richard E. Dickerson

  3. Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, 1602 Molecular Sciences Building, Los Angeles, 90095, California, USA

    Michael R. Jarvis, Shawn M.D. Bearson, Imke Schröder & Robert P. Gunsalus

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Maris, A., Sawaya, M., Kaczor-Grzeskowiak, M. et al. Dimerization allows DNA target site recognition by the NarL response regulator. Nat Struct Mol Biol 9, 771–778 (2002). https://doi.org/10.1038/nsb845

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