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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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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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