61 High-resolution crystal structures of p53 mutants and their interaction with DNA

Abstract

In response to cellular stress, the tumor suppressor protein p53 acts as a transcription factor by binding to its DNA targets, leading to the expression of several genes that participate in a variety of biological processes including DNA repair, cell cycle arrest or apoptosis. Thus, p53 “protects” the integrity of the genome. p53 binds as a tetramer to DNA response elements made of two decameric half-sites of the consensus sequence RRRCWWGYYY (R = A/G, Y = T/C, W = A/T) separated by a variable number of base pairs (Kitayner et al., 2006; 2010). About 50% of all invasive cancer cases show mutations in p53 and 97% of these mutations occur within the DNA-binding domain (DBD), among them, mutations in six “hot spot” codons account for more than 30% of cancer cases. These mutations lead to p53 loss of function. It was shown that several oncogenic mutants can be rescued by second-site suppressor mutations, resulting in wild-type-like activity in terms of DNA binding and transcriptional activation. To understand the structural effects caused by hot-spot mutations and the mechanisms of their rescue by suppressor mutations, we determined several crystal structures of human p53DBD incorporating these mutations as well as the rescued proteins and their complexes with DNA. These included DNA contact mutants, R273H and R273C, a structural mutant G245S, and the rescued proteins incorporating both the oncogenic mutation and the corresponding suppressor mutation. The crystal structures elucidate the structural basis of loss of function caused by the hot-spot mutations. The crystal structures of the rescued proteins bound to DNA reveal different rescue mechanisms: formation of alternative p53-DNA interactions for the DNA-contact mutants, and intramolecular or intermolecular stabilizing interactions for the structural mutant which compensate for the loss of p53 stability caused by the oncogenic mutation. In contrast to cancer-related mutations, specific mutations in other regions of p53DBD such as its DNA-binding loop (L1), which is part of the loop–sheet–helix motif at the p53-DNA interface, were shown to modulate the protein’s DNA-binding affinity and transactivation (Zupnick & Prives, 2006; Resnick & Inga, 2003). In particular, the replacement of T123 in the L1 loop by T123A or T123P largely increases p53 transactivation capacity relative to wild-type p53 (Resnick & Inga, 2003). The crystal structures of these mutants and their complexes with DNA provide a structural basis for understanding their biological activity.