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Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs

Nature Structural & Molecular Biology volume 17, pages 423–429 (2010)Cite this article

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Abstract

p53 binds as a tetramer to DNA targets consisting of two decameric half-sites separated by a variable spacer. Here we present high-resolution crystal structures of complexes between p53 core-domain tetramers and DNA targets consisting of contiguous half-sites. In contrast to previously reported p53–DNA complexes that show standard Watson-Crick base pairs, the newly reported structures show noncanonical Hoogsteen base-pairing geometry at the central A-T doublet of each half-site. Structural and computational analyses show that the Hoogsteen geometry distinctly modulates the B-DNA helix in terms of local shape and electrostatic potential, which, together with the contiguous DNA configuration, results in enhanced protein-DNA and protein-protein interactions compared to noncontiguous half-sites. Our results suggest a mechanism relating spacer length to protein-DNA binding affinity. Our findings also expand the current understanding of protein-DNA recognition and establish the structural and chemical properties of Hoogsteen base pairs as the basis for a novel mode of sequence readout.

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Figure 1: DNA binding sites of type I and type II complexes.
Figure 2: Overall structure of the p53 core-domain tetramer bound to DNA with contiguous half-sites.
Figure 3: Comparison of p53 core dimers bound to DNA half-sites in type I and type II complexes.
Figure 4: Interdimer interfaces.
Figure 5: Comparison of Hoogsteen and Watson-Crick base pairs.
Figure 6: DNA helix parameters in type I and type II complexes.
Figure 7: Recognition of DNA shape and electrostatic potential by Arg248 residues in type II complexes.

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References

  1. Vogelstein, B., Lane, D. & Levine, A.J. Surfing the p53 network. Nature 408, 307–310 (2000).

    Article  CAS  Google Scholar 

  2. Vousden, K.H. & Lu, X. Live or let die: the cell's response to p53. Nat. Rev. Cancer 2, 594–604 (2002).

    Article  CAS  Google Scholar 

  3. Oren, M. Decision making by p53: life, death and cancer. Cell Death Differ. 10, 431–442 (2003).

    Article  CAS  Google Scholar 

  4. Laptenko, O. & Prives, C. Transcriptional regulation by p53: one protein, many possibilities. Cell Death Differ. 13, 951–961 (2006).

    Article  CAS  Google Scholar 

  5. el-Deiry, W.S., Kern, S.E., Pietenpol, J.A., Kinzler, K.W. & Vogelstein, B. Definition of a consensus binding site for p53. Nat. Genet. 1, 45–49 (1992).

    Article  CAS  Google Scholar 

  6. Funk, W.D., Pak, D.T., Karas, R.H., Wright, W.E. & Shay, J.W. A transcriptionally active DNA binding site for human p53 protein complexes. Mol. Cell. Biol. 12, 2866–2871 (1992).

    Article  CAS  Google Scholar 

  7. Wei, C.L. et al. A global map of p53 transcription-factor binding sites in the human genome. Cell 124, 207–219 (2006).

    Article  CAS  Google Scholar 

  8. Friedman, P.N., Chen, X., Bargonetti, J. & Prives, C. The p53 protein is an unusually shaped tetramer that binds directly to DNA. Proc. Natl. Acad. Sci. USA 90, 3319–3323 (1993).

    Article  CAS  Google Scholar 

  9. Weinberg, R.L., Veprintsev, D.B. & Fersht, A.R. Cooperative binding of tetrameric p53 to DNA. J. Mol. Biol. 341, 1145–1159 (2004).

    Article  CAS  Google Scholar 

  10. Ko, L.J. & Prives, C. p53: puzzle and paradigm. Genes Dev. 10, 1054–1072 (1996).

    Article  CAS  Google Scholar 

  11. Levine, A.J. p53, the cellular gatekeeper for growth and division. Cell 88, 323–331 (1997).

    Article  CAS  Google Scholar 

  12. May, P. & May, E. Twenty years of p53 research: structural and functional aspects of the p53 protein. Oncogene 18, 7621–7636 (1999).

    Article  CAS  Google Scholar 

  13. Olivier, M. et al. The IARC TP53 database: new online mutation analysis and recommendations to users. Hum. Mutat. 19, 607–614 (2002).

    Article  CAS  Google Scholar 

  14. Qian, H., Wang, T., Naumovski, L., Lopez, C.D. & Brachmann, R.K. Groups of p53 target genes involved in specific p53 downstream effects cluster into different classes of DNA binding sites. Oncogene 21, 7901–7911 (2002).

    Article  CAS  Google Scholar 

  15. Weinberg, R.L., Veprintsev, D.B., Bycroft, M. & Fersht, A.R. Comparative binding of p53 to its promoter and DNA recognition elements. J. Mol. Biol. 348, 589–596 (2005).

    Article  CAS  Google Scholar 

  16. Tokino, T. et al. p53 tagged sites from human genomic DNA. Hum. Mol. Genet. 3, 1537–1542 (1994).

    Article  CAS  Google Scholar 

  17. Joerger, A.C. & Fersht, A.R. Structural biology of the tumor suppressor p53. Annu. Rev. Biochem. 77, 557–582 (2008).

    Article  CAS  Google Scholar 

  18. Cho, Y., Gorina, S., Jeffrey, P.D. & Pavletich, N.P. Crystal structure of a p53 tumor suppressor-DNA complex: understanding tumorigenic mutations. Science 265, 346–355 (1994).

    Article  CAS  Google Scholar 

  19. Kitayner, M. et al. Structural basis of DNA recognition by p53 tetramers. Mol. Cell 22, 741–753 (2006).

    Article  CAS  Google Scholar 

  20. Ho, W.C., Fitzgerald, M.X. & Marmorstein, R. Structure of the p53 core domain dimer bound to DNA. J. Biol. Chem. 281, 20494–20502 (2006).

    Article  CAS  Google Scholar 

  21. Malecka, K.A., Ho, W.C. & Marmorstein, R. Crystal structure of a p53 core tetramer bound to DNA. Oncogene 28, 325–333 (2009).

    Article  CAS  Google Scholar 

  22. Chen, Y., Dey, R. & Chen, L. Crystal structure of the p53 core domain bound to a full consensus site as a self-assembled tetramer. Structure 18, 246–256 (2010).

    Article  CAS  Google Scholar 

  23. Hoogsteen, K. The crystal and molecular structure of a hydrogen-bonded complex between 1-methylthymine and 9-methyladenine. Acta Crystallogr. 16, 907–916 (1963).

    Article  CAS  Google Scholar 

  24. Suad, O. et al. Structural basis of restoring sequence-specific DNA binding and transactivation to mutant p53 by suppressor mutations. J. Mol. Biol. 385, 249–265 (2009).

    Article  CAS  Google Scholar 

  25. Dehner, A. et al. Cooperative binding of p53 to DNA: regulation by protein-protein interactions through a double salt bridge. Angew. Chem. Int. Edn Engl. 44, 5247–5251 (2005).

    Article  CAS  Google Scholar 

  26. Rohs, R. et al. The role of DNA shape in protein-DNA recognition. Nature 461, 1248–1253 (2009).

    Article  CAS  Google Scholar 

  27. Rice, P.A., Yang, S., Mizuuchi, K. & Nash, H.A. Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn. Cell 87, 1295–1306 (1996).

    Article  CAS  Google Scholar 

  28. Patikoglou, G.A. et al. TATA element recognition by the TATA box-binding protein has been conserved throughout evolution. Genes Dev. 13, 3217–3230 (1999).

    Article  CAS  Google Scholar 

  29. Aishima, J. et al. A Hoogsteen base pair embedded in undistorted B-DNA. Nucleic Acids Res. 30, 5244–5252 (2002).

    Article  CAS  Google Scholar 

  30. Nair, D.T., Johnson, R.E., Prakash, S., Prakash, L. & Aggarwal, A.K. Replication by human DNA polymerase-iota occurs by Hoogsteen base-pairing. Nature 430, 377–380 (2004).

    Article  CAS  Google Scholar 

  31. Nair, D.T., Johnson, R.E., Prakash, L., Prakash, S. & Aggarwal, A.K. Human DNA polymerase iota incorporates dCTP opposite template Gvia a G.C + Hoogsteen base pair. Structure 13, 1569–1577 (2005).

    Article  CAS  Google Scholar 

  32. Abrescia, N.G., Gonzalez, C., Gouyette, C. & Subirana, J.A. X-ray and NMR studies of the DNA oligomer d(ATATAT): Hoogsteen base pairing in duplex DNA. Biochemistry 43, 4092–4100 (2004).

    Article  CAS  Google Scholar 

  33. De Luchi, D., Tereshko, V., Gouyette, C. & Subirana, J.A. Structure of the DNA coiled coil formed by d(CGATATATATAT). ChemBioChem 7, 585–587 (2006).

    Article  CAS  Google Scholar 

  34. Joshi, R. et al. Functional specificity of a Hox protein mediated by the recognition of minor groove structure. Cell 131, 530–543 (2007).

    Article  CAS  Google Scholar 

  35. Rohs, R. et al. Origins of specificity in protein-DNA recognition. Annu. Rev. Biochem. (in the press) (2010).

  36. Vousden, K.H. & Prives, C. Blinded by the light: the growing complexity of p53. Cell 137, 413–431 (2009).

    Article  CAS  Google Scholar 

  37. Lavery, R. & Sklenar, H. Defining the structure of irregular nucleic acids: conventions and principles. J. Biomol. Struct. Dyn. 6, 655–667 (1989).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  39. Brunger, A.T. et al. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr. 54, 905–921 (1998).

    Article  CAS  Google Scholar 

  40. Brunger, A.T. Version 1.2 of the Crystallography and NMR system. Nat. Protoc. 2, 2728–2733 (2007).

    Article  CAS  Google Scholar 

  41. Vagin, A. & Teplyakov, A. MOLREP: an automated program for molecular replacement. J. Appl. Crystallogr. 30, 1022–1025 (1997).

    Article  CAS  Google Scholar 

  42. Collaborative Computational Project. Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 50, 760–763 (1994).

  43. Murshudov, G.N., Vagin, A.A. & Dodson, E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D Biol. Crystallogr. 53, 240–255 (1997).

    Article  CAS  Google Scholar 

  44. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126–2132 (2004).

    Article  Google Scholar 

  45. 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 

  46. DeLano, W.L. The PyMOL Molecular Graphics System (San Carlos, California, USA, 2002).

  47. Rocchia, W. et al. Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: applications to the molecular systems and geometric objects. J. Comput. Chem. 23, 128–137 (2002).

    Article  CAS  Google Scholar 

  48. Cornell, W.D. et al. A 2nd generation force-field for the simulation of proteins, nucleic-acids, and organic-molecules. J. Am. Chem. Soc. 117, 5179–5197 (1995).

    Article  CAS  Google Scholar 

  49. Petrey, D. & Honig, B. GRASP2: visualization, surface properties, and electrostatics of marcomolecular structures and sequences. Methods Enzymol. 374, 492–509 (2003).

    Article  CAS  Google Scholar 

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Acknowledgements

We thank our colleagues Y. Halfon, A. Kapitkovsky, A. Eldar and Y. Diskin-Posner for help and the staff at the European Synchrotron Radiation Facility (Grenoble) for facilitating X-ray data collection. The work was supported by grants from the Israel Science Foundation (grant no. 954/08), the Kimmelman Center for Biomolecular Structure and Assembly, the EC (FP6) program, the German-Israeli Foundation for Scientific Research & Development and the Minerva Foundation with funding from the Federal German Ministry of Education and Research (Z.S.) and the US National Institutes of Health grant U54 CA121852 (B.H.). Z.S. holds the Helena Rubinstein Professorial chair in Structural Biology.

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Author notes

  1. Malka Kitayner, Haim Rozenberg and Remo Rohs: These authors contributed equally to this work.

  2. Dov Rabinovich: Deceased 6 September 2008.

Authors and Affiliations

  1. Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel

    Malka Kitayner, Haim Rozenberg, Oded Suad, Dov Rabinovich & Zippora Shakked

  2. Howard Hughes Medical Institute, Columbia University, New York, New York, USA

    Remo Rohs & Barry Honig

  3. Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, USA

    Remo Rohs & Barry Honig

  4. Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, USA

    Remo Rohs & Barry Honig

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  1. Malka Kitayner
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Contributions

M.K., H.R., O.S., D.R. and Z.S. performed the X-ray structure analyses; R.R. performed the computational work; M.K., H.R., R.R., B.H. and Z.S. contributed to the writing of the paper.

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Correspondence to Barry Honig or Zippora Shakked.

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Supplementary Figures 1–7, Supplementary Table 1, Supplementary Discussion and Supplementary Methods (PDF 784 kb)

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Kitayner, M., Rozenberg, H., Rohs, R. et al. Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs. Nat Struct Mol Biol 17, 423–429 (2010). https://doi.org/10.1038/nsmb.1800

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