Long-range regulation of p53 DNA binding by its intrinsically disordered N-terminal transactivation domain

Significance

The tumor suppressor p53 plays a central role in mediating the cellular response to stress and DNA damage. p53 is a tetramer containing both structured and intrinsically disordered domains that function synergistically to regulate p53 activity. Using intein technology and NMR spectroscopy, we show that the disordered N-terminal transactivation domain of p53 makes intramolecular interactions with the structured DNA-binding domain. These interactions impair binding of p53 to nonspecific DNA sequences but not to p53-specific DNA sequences, providing a means whereby p53 can discriminate more effectively between cognate sites and the vastly more abundant noncognate sites in the genome.

Abstract

Atomic resolution characterization of the full-length p53 tetramer has been hampered by its size and the presence of extensive intrinsically disordered regions at both the N and C termini. As a consequence, the structural characteristics and dynamics of the disordered regions are poorly understood within the context of the intact p53 tetramer. Here we apply trans-intein splicing to generate segmentally ¹⁵N-labeled full-length p53 constructs in which only the resonances of the N-terminal transactivation domain (NTAD) are visible in NMR spectra, allowing us to observe this region of p53 with unprecedented detail within the tetramer. The N-terminal region is dynamically disordered in the full-length p53 tetramer, fluctuating between states in which it is free and fully exposed to solvent and states in which it makes transient contacts with the DNA-binding domain (DBD). Chemical-shift changes and paramagnetic spin-labeling experiments reveal that the amphipathic AD1 and AD2 motifs of the NTAD interact with the DNA-binding surface of the DBD through primarily electrostatic interactions. Importantly, this interaction inhibits binding of nonspecific DNA to the DBD while having no effect on binding to a specific p53 recognition element. We conclude that the NTAD:DBD interaction functions to enhance selectivity toward target genes by inhibiting binding to nonspecific sites in genomic DNA. This work provides some of the highest-resolution data on the disordered N terminus of the nearly 180-kDa full-length p53 tetramer and demonstrates a regulatory mechanism by which the N terminus of p53 transiently interacts with the DBD to enhance target site discrimination.