2IOI

Crystal structure of the mouse p53 core domain at 1.55 A

Summary for 2IOI

• Entry DOI: 10.2210/pdb2ioi/pdb
• Related: 2IOM 2IOO
• Descriptor: Cellular tumor antigen p53, ZINC ION, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, ... (4 entities in total)
• Functional Keywords: ig fold, transcription, antitumor protein
• Biological source: Mus musculus (house mouse)
• Cellular location: Cytoplasm (By similarity): P02340
• Total number of polymer chains: 1
• Total formula weight: 23001.61

Authors

Ho, W.C.,Luo, C.,Zhao, K.,Chai, X.,Fitzgerald, M.X.,Marmorstein, R. (deposition date: 2006-10-10, release date: 2006-12-05, Last modification date: 2024-02-21)

Primary citation

Ho, W.C.,Luo, C.,Zhao, K.,Chai, X.,Fitzgerald, M.X.,Marmorstein, R.
High-resolution structure of the p53 core domain: implications for binding small-molecule stabilizing compounds.
Acta Crystallogr.,Sect.D, 62:1484-1493, 2006

PubMed Abstract: The p53 transcriptional regulator is the most frequently mutated protein in human cancers and the majority of tumor-derived p53 mutations map to the central DNA-binding core domain, with a subset of these mutations resulting in reduced p53 stability. Here, the 1.55 A crystal structure of the mouse p53 core domain with a molecule of tris(hydroxymethyl)aminomethane (Tris) bound through multiple hydrogen bonds to a region of p53 shown to be important for repair of a subset of tumor-derived p53-stability mutations is reported. Consistent with the hypothesis that Tris binding stabilizes the p53 core domain, equilibrium denaturation experiments are presented that demonstrate that Tris binding increases the thermodynamic stability of the mouse p53 core domain by 3.1 kJ mol(-1) and molecular-dynamic simulations are presented revealing an overall reduction in root-mean-square deviations of the core domain of 0.7 A when Tris is bound. It is also shown that these crystals of the p53 core domain are suitable for the multiple-solvent crystal structure approach to identify other potential binding sites for possible core-domain stabilization compounds. Analysis of the residue-specific temperature factors of the high-resolution core-domain structure, coupled with a comparison with other core-domain structures, also reveals that the L1, H1-S5 and S7-S8 core-domain loops, also shown to mediate various p53 activities, harbor inherent flexibility, suggesting that these regions might be targets for other p53-stabilizing compounds. Together, these studies provide a molecular scaffold for the structure-based design of p53-stabilization compounds for development as possible therapeutic agents.

PubMed: 17139084
DOI: 10.1107/S090744490603890X

Experimental method

X-RAY DIFFRACTION (1.55 Å)