Journal Article

An induced fit mechanism regulates p53 DNA binding kinetics to confer sequence specificity

Emamzadah, Soheila, Vauthey, Eric, Petty, Tom J, Costantino, Lorenzo, Petkova, Irina, Halazonetis, Thanos D, Stavridi, Elena S, Saven, Jeffery G

2011

Overview

The p53 tumour suppressor gene, the most frequently mutated gene in human cancer, encodes a transcription factor that contains sequence‐specific DNA binding and homo‐tetramerization domains. Interestingly, the affinities of p53 for specific and non‐specific DNA sites differ by only one order of magnitude, making it hard to understand how this protein recognizes its specific DNA targets in vivo . We describe here the structure of a p53 polypeptide containing both the DNA binding and oligomerization domains in complex with DNA. The structure reveals that sequence‐specific DNA binding proceeds via an induced fit mechanism that involves a conformational switch in loop L1 of the p53 DNA binding domain. Analysis of loop L1 mutants demonstrated that the conformational switch allows DNA binding off‐rates to be regulated independently of affinities. These results may explain the universal prevalence of conformational switching in sequence‐specific DNA binding proteins and suggest that proteins like p53 rely more on differences in binding off‐rates, than on differences in affinities, to recognize their specific DNA sites. This crystal structure of the p53 DNA binding and homo‐tetramerization domains identifies a conformational change involved in an induced fit mechanism of binding to DNA and demonstrates that binding specificity is determined not by affinity but by the dissociation rate of the transcription factor.

• Publisher: John Wiley & Sons, Ltd,Nature Publishing Group UK,Springer Nature B.V,Nature Publishing Group
• Subject: affinity / Binding Sites / Chromatin / Crystallography / Crystallography, X-Ray / Deoxyribonucleic acid / DNA / DNA - metabolism / DNA Mutational Analysis / DNA-Binding Proteins - chemistry / DNA-Binding Proteins - metabolism / EMBO09 / EMBO13 / Fluorescence Polarization / Humans / induced fit / Kinetics / Models, Molecular / Molecular biology / Mutagenesis, Site-Directed / Mutant Proteins - chemistry / Mutant Proteins - metabolism / Mutation / off-rate / p53 / Protein Binding / Protein Conformation / Proteins / Tumor Suppressor Protein p53 - chemistry / Tumor Suppressor Protein p53 - metabolism