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Updated: Jun 28, 2026

Iterative Optimization of DNA Duplexes for Crystallization of SeqA-DNA Complexes
Published on: November 1, 2012
Crystal structure of a p53 core tetramer bound to DNA
K A Malecka1, W C Ho, R Marmorstein
1The Wistar Institute, Philadelphia, PA 19104, USA.
Abstract:
The tumor suppressor p53 regulates downstream genes in response to many cellular stresses and is frequently mutated in human cancers. Here, we report the use of a crosslinking strategy to trap a tetrameric p53 DNA-binding domain (p53DBD) bound to DNA and the X-ray crystal structure of the protein/DNA complex. The structure reveals that two p53DBD dimers bind to B form DNA with no relative twist and that a p53 tetramer can bind to DNA without introducing significant DNA bending. The numerous dimer-dimer interactions involve several strictly conserved residues, thus suggesting a molecular basis for p53DBD-DNA binding cooperativity. Surface residue conservation of the p53DBD tetramer bound to DNA highlights possible regions of other p53 domain or p53 cofactor interactions.
Insights
The tumor suppressor p53 protein
Area of Science:
- Molecular biology
- Structural biology
- Cancer research
Background:
- The tumor suppressor p53 protein is crucial for regulating cellular responses to stress.
- Mutations in p53 are common in human cancers, highlighting its importance in cancer development.
- Understanding p53's DNA-binding mechanism is key to developing cancer therapies.
Purpose of the Study:
- To elucidate the structural basis of the p53 DNA-binding domain (p53DBD) tetramer formation.
- To investigate how p53DBD interacts with DNA at a molecular level.
- To identify potential sites for therapeutic intervention targeting p53 function.
Main Methods:
- Employed a crosslinking strategy to stabilize the p53DBD tetramer bound to DNA.
- Determined the X-ray crystal structure of the p53DBD-DNA complex.
Main Results:
- Revealed that two p53DBD dimers bind to B-form DNA without relative twist.
- Demonstrated that p53 tetramers bind DNA without significant DNA bending.
- Identified conserved residues involved in dimer-dimer interactions, suggesting cooperativity in DNA binding.
Conclusions:
- The study provides a high-resolution structure of the p53DBD tetramer bound to DNA.
- The findings offer insights into the molecular mechanisms of p53 DNA binding and cooperativity.
- Conserved surface residues suggest potential interaction sites for other p53 domains or cofactors.
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