From Proteopedia

Revision as of 00:57, 4 July 2012

This is a joint project of La Canada High School and University of Southern California students, mentored by Professor Remo Rohs.

A Base Pairing Variant Enhances p53 Binding to a Response Element

Introduction and Biological Role of the Tumor Suppressor p53

Figure 1: Crystal structure of a p53 DBD tetramer-DNA complex; PDB ID# 3KZ8^[1].

Figure 3: Frequency of p53 mutants associated with cancer derived from IARC TP53 database. Domain architecture; N-ter=N-terminal, DBD=DNA binding domain^[1], Tet=Tetramerization^[2], and C-ter=C-terminal domain. Intermediate regions are fairly disordered.

Also known as the Guardian of the Genome, the tumor suppressor p53 is central in the natural defense against human cancer. The protein is activated by stress factors that can compromise the genomic integrity of the cell, and this activation unleashes the function of p53 as transcription factor. It binds as a tetramer (Figure 1) to a large range of DNA response elements. The p53 consensus site (Figure 2) is formed by two decameric half-sites, each containing a core element (red), that are separated by a variable number of base pairs (blue).

Binding of p53 to different response elements leads to distinct biological responses, such as cell-cycle arrest, senescence, or apoptosis. These different pathways correspond, at least in part, to differences in p53-DNA binding affinity and stability, which are determined by specific protein-DNA interactions.

Mutations of p53 residues are associated with 50% of human cancers. Such mutations are predominantly located in the p53-DNA binding domain (DBD) based on an analysis of human tumors (Figure 3). Particularly, arginine residues in the p53-DNA interface were found in tumors with high frequencies.

Structural Description of p53-DNA Complex

Domain Architecture and Tetramerization

spinqualitylabelsall models Figure 4: Crystal structure of p53 tetramerization domain, PDB ID 1C26. Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

spinqualitylabelsall models Figure 5: Crystal structure of p53 DBD tetramer-DNA complex, PDB ID 3KZ8. Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

The p53 protein consists of the N-terminal transactivation, the DNA binding or core, the tetramerization, and the C-terminal regulatory domain (Figure 3). This Proteopedia page discusses protein-DNA recognition by p53, thus focuses on the DBD of p53. The only other domain for which structural information is available is the , which forms as a dimer of dimers with one alpha helix and one beta strand contributed by each p53 monomer.

The , which consists of two half sites. These decameric half sites can be separated by a spacer of flexible length but in this case the spacer is of length zero base pairs. The with each dimer binding to one half site of the response element.

The p53 DBD assumes the conformation of an , which binds the response element in the major groove. A functionally important and, thus, stabilizes the fold of the DBD.

Protein-Protein Interactions

The p53 tetramer forms a relatively small and, in comparison, a large . The actual molecular interactions and strength in binding can vary as a function of the sequence and spacer length of the response element.

Major Groove Base Readout

Figure 6: p53 binding site motif with G/C base pairs most conserved.

Protein side chains and base pairs form direct contacts in the major groove among which the contributes most to binding specificity. This highly specific readout is due to the . As a result the identity of the G/C base pairs in the CWWG core elements is the most conserved position in p53 response elements (Figure 5).

Minor Groove Shape Readout

domains

domains

Further Reading

A more general discussion of structural origins of binding specificity in protein-DNA recognition has been published along with a suggestion for a new classification of protein-DNA readout modes that goes beyond the historical description of direct and indirect readout^[3].

Acknowledgements

This Proteopedia page originates from the partnership of the Rohs Laboratory at the University of Southern California with La Canada High School. This partnership was initiated by Remo Rohs and Patty Compeau in September 2011 as Bioinformatics Institute, which is part of the Institutes of the 21st Century. Contributors to this page are USC graduate students Ana Carolina Dantas Machado, Proteopedia editor Eran Hodis, and La Canada High School students (xxx). Research presented in this article has been conducted in the Shakked Lab at the Weizmann Institute of Science, the Rohs and L. Chen Labs at USC, and the Honig Lab at Columbia University. Furthermore, technical help by Proteopedia editors Eran Hodis, Eric Martz, Jaime Prilusky, and Joel Sussman is acknowledged.

References

1. ↑ ^{1.0 1.1} Kitayner M, Rozenberg H, Rohs R, Suad O, Rabinovich D, Honig B, Shakked Z. Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs. Nat Struct Mol Biol. 2010;17(4):423-9.
2. ↑ Jeffrey PD, Gorina S, Pavletich NP. Crystal structure of the p53 tetramerization domain. Science 1995;267:1498-502.
3. ↑ Rohs R, Jin X, West SM, Joshi R, Honig B, Mann RS. Origins of specificity in protein-DNA recognition. Annu Rev Biochem. 2010;79:233-69.