The p53 protein is a tumor suppressor whose primary function is preventing tumor formation. This ability is linked to its interaction with DNA, which allows p53 to control genes that regulate cell growth and division.
The Architecture of p53
Large proteins are often modular, built from distinct regions called domains, each with a specific function. The p53 protein is composed of several such domains, including a transactivation domain that activates gene expression and a tetramerization domain that allows four p53 proteins to assemble into a functional unit.
Situated centrally within the protein’s structure is the DNA binding domain (DBD). This core domain is responsible for making direct physical contact with DNA. The architecture of the DBD consists of a beta-sandwich, which acts as a scaffold for the structural elements that recognize and bind to the genetic code.
Core Function of the DNA Binding Domain
The primary job of the DNA binding domain is to recognize and attach to specific, short sequences of DNA. These target sites are known as “p53 response elements” and are located near the genes that p53 controls. The DBD is precisely structured to identify the unique pattern of these response elements, ensuring that p53 only activates the appropriate set of genes.
The unique three-dimensional fold of the DBD is stabilized by a single zinc ion. This zinc ion is coordinated by specific amino acids, holding parts of the domain in the correct orientation to interact with DNA. The domain’s ability to fold correctly is dependent on the presence of zinc. The interaction can be compared to a key fitting into a specific lock, where the zinc ion maintains the key’s shape.
Once bound, the protein acts as a platform to assemble the cellular machinery needed to read the genetic information encoded in the target genes. The stability and precision of this binding initiate the cascade of events that protect the cell.
Consequences of DNA Binding
Once the p53 protein binds to a response element, it functions as a switch that activates a program of gene expression. The consequences of this activation lead to one of three main outcomes, depending on the cellular context and the extent of the damage.
The first outcome is cell cycle arrest, which pauses cell division to provide time for DNA repair. This occurs through the activation of the p21 gene, an inhibitor of enzymes that drive the cell cycle forward. By halting the cell cycle, p53 prevents the replication of damaged DNA, which could otherwise lead to permanent mutations.
If the DNA damage is repairable, p53 can activate genes involved in the DNA repair process itself. However, if the damage is too severe to be repaired, p53 initiates a process called apoptosis, or programmed cell death. This is achieved by activating genes like BAX and PUMA, which trigger the cell’s self-destruction sequence, eliminating the potentially cancerous cell.
When the Domain Fails
The gene that codes for p53, known as TP53, is the most frequently mutated gene in human cancers. A significant majority of these cancer-causing mutations, over 75%, are missense mutations that occur directly within the DNA binding domain. These mutations disrupt the domain’s ability to bind to its target DNA sequences, disabling its tumor-suppressing functions.
These mutations can be grouped into two categories. The first are “contact mutations,” which alter the specific amino acids that make direct contact with the DNA. For example, mutations at residues like Arg248 and Arg273 prevent the DBD from properly recognizing its DNA target.
The second category consists of “structural mutations.” These mutations occur in amino acids important for maintaining the domain’s three-dimensional shape. A common example is the R175H mutation, which disrupts the coordination of the zinc ion, causing the domain to become unstable and misfolded. In either case, the p53 protein is unable to perform its function, allowing cells with damaged DNA to proliferate and develop into a tumor.
Therapeutic Approaches Targeting the Domain
The high frequency of p53 mutations in cancer has made its DNA binding domain a focus for therapeutic intervention. Research has focused on developing small-molecule drugs known as “p53 reactivators.” These molecules are designed to specifically bind to the mutated and often misfolded DBD to restore its function.
The goal of these reactivator compounds is to stabilize the mutant protein and restore its correct, functional fold. For example, some molecules target specific structural defects, such as those caused by the Y220C mutation, by binding to a crevice created by the mutation. Other compounds, classified as zinc metallochaperones, aim to fix mutations that impair zinc binding by restoring its proper coordination.
By restoring the DBD’s native structure, these drugs can enable the mutant p53 to once again bind to its DNA response elements. This restored binding would reactivate the pathways leading to cell cycle arrest or apoptosis in cancer cells. Several such compounds are in various stages of development, representing an active field of cancer research.