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Structural basis of Hoogsteen base pair recognition by the DNA-binding domain of the transcription factor p53


p53 is a tumor suppressor protein activated during DNA damage and cell stress that plays a central role in apoptosis, cell cycle arrest, DNA repair, and senescence. In human, 50% of cancer cases have a mutation in p53. Approximately, 85% of these mutation cases occur within the DNA-binding domain (DBD) of p53, which is known to interfere with its ability to bind to the p53 response elements (p53REs). Many structures of the p53DBD in complex with DNA have been previously solved. However, how p53DBD recognizes DNA is not fully understood. In this work, I address how p53DBD recognizes the center of its half-site response elements. First, I investigated the specificity of p53DBD to the central base pair of the half -site REs by fluorescence anisotropy. The results show that p53DBD favors adenine and thymine over cytosine and guanine. Furthermore, I obtained high-resolution crystal structures of p53DBD bound as a dimer to its half-sites. Theses structures show a Hoogsteen conformation at the central A-T, A-A and T-T doublets of DNA sequences. Moreover, in all of the obtained structures, the Arg248 residue from each p53DBD monomer contacts the central base pairs by water-mediated hydrogen bonds through the DNA minor groove. These findings indicate the significance of Hoogsteen base pairs conformation to the function of p53 as a transcription factor. Furthermore, it reveals the importance of Arg248 residues in p53 recognition to its activating REs

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