P53-DNA Recognition: Difference between revisions

[[Image:p53-intro.jpg|thumb|left|300px|Figure 1: Crystal structure of a p53 DBD tetramer-DNA complex; [http://www.proteopedia.org/wiki/index.php/3kz8 PDB ID# 3KZ8]<ref name='kitayner'>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. [http://www.ncbi.nlm.nih.gov/pubmed/20364130 PMID:20364130].</ref>.]]

 

[[Image:consensus.jpg|thumb|right|250px|Figure 2: p53 consensus site; R= A or G, Y= C or T, and W=A or T.]]

 

[[Image:p53-domains.jpg|thumb|right|400px|Figure 3:  Frequency of p53 mutants associated with cancer derived from [http://www-p53.iarc.fr/ IARC TP53 database]. Domain architecture; N-ter=N-terminal, DBD=DNA binding domain<ref name='kitayner'/>, Tet=Tetramerization<ref name='tetra'>Jeffrey PD, Gorina S, Pavletich NP. Crystal structure of the p53 tetramerization domain. Science 1995;267:1498-502. [http://www.ncbi.nlm.nih.gov/pubmed/7878469 PMID:7878469].</ref>, and C-ter=C-terminal domain. Intermediate regions are fairly disordered.]]

 

Also known as the '''Guardian of the Genome''', the tumor suppressor p53 is crucial in the natural defense against human cancer. The protein is activated by stress factors that can compromise the genomic integrity of the cell. This activation unleashes the function of p53 as a 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).  

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.

 

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 focusing on the DBD of p53. The only other domain for which structural information is available is the <scene name='Sandbox_Reserved_170/Tetra/2'>tetramerization domain</scene>, which forms as a dimer of dimers with one alpha helix and one beta strand contributed by each p53 monomer.

<Structure load='3kz8bio-4mon.pdb.zip' size='400' frame='true' align='right' caption='Figure 5: Crystal structure of p53 DBD tetramer-DNA complex, [http://proteopedia.com/wiki/index.php/3kz8 PDB ID 3KZ8].' scene='Sandbox_Reserved_170/Complex/6' />

 

The p53 DBD assumes the conformation of an <scene name='Sandbox_Reserved_170/Beta/1'>immunoglobulin-like fold consisting of a beta sandwich</scene>, which binds the response element in the major groove. A functionally important <scene name='Sandbox_Reserved_170/Zn/1'>Zn2+ ion coordinates the Cys176, His179, Cys238, Cys242 residues</scene> and, thus, stabilizes the fold of the DBD. The iodide ions shown in the structure (magenta) are included due to crystallization.

The human p53 tetramer forms a relatively small <scene name='Sandbox_Reserved_170/Intra-dimer/4'>intra-dimer interface with two salt bridges between Glu180 and Arg181 residues</scene> and, in comparison, a large <scene name='Sandbox_Reserved_170/Inter-dimer/4'>inter-dimer interface with an extensive network of interactions</scene>. The actual molecular interactions and strength in binding can vary as functions of the sequence and spacer length of the response element.

[[Image:p53-motif.jpg|thumb|right|300px|Figure 6: p53 binding site motif with G/C base pairs most conserved. PLoS has provided permission for usage of this figure<ref>Horvath MM, Wang X, Resnick MA, Bell DA. Divergent evolution of human p53 binding sites: cell cycle versus apoptosis. PLoS Genet. 2007 Jul;3(7):e127. [http://www.ncbi.nlm.nih.gov/pubmed/17677004 PMID:17677004].</ref>.]]

 

Protein side chains and base pairs form direct contacts in the major groove. Among which, the <scene name='Sandbox_Reserved_170/Arg280_contact/5'>contact between Arg280 and the guanine of the core element</scene> contributes most to binding specificity. This highly specific readout is due to the <scene name='Sandbox_Reserved_170/Arg280_contact/4'>bidentate hydrogen bond formed between Arg280 and guanine</scene>. As a result of this '''base readout''' the G/C base pairs in the CWWG core elements are the most conserved positions in p53 response elements (Figure 6).

Another arginine residue, <scene name='Sandbox_Reserved_170/Arg273/2'>Arg273, contacts the phosphodiester backbone</scene> and seems to be important for human p53-DNA binding. Moreover, Arg273 is the second most common missense mutation in human cancer (Figure 3).

 

[[Image:Kitayner-etal-Figure7.jpg|thumb|right|400px|Figure 7: DNA shape readout of narrow minor groove regions with enhanced electrostatic potential by Arg248. Nature Publishing Group has provided permission for usage of this figure<ref name='kitayner'/>.]]

Most commonly, however, the residue Arg248 is found mutated in human tumors, <scene name='Sandbox_Reserved_170/Arg248/2'>Arg248 contacts the minor groove</scene> although it does not usually form hydrogen bonds with the bases. Arg248 was shown to recognize regions of narrow minor groove associated with enhanced negative electrostatic potential (Figure 7)<ref name='kitayner'/>.  This observation provides a novel molecular explanation of the importance of Arg248 for p53-DNA binding and its role in cancer. The described mechanism known as '''shape readout''' was found to be broadly employed by arginine residues<ref name="nature">Rohs R, West SM, Sosinsky A, Liu P, Mann RS, Honig B. The role of DNA shape in protein-DNA recognition. Nature. 2009;461(7268):1248-53. [http://www.ncbi.nlm.nih.gov/pubmed/19865164 PMID:19865164].</ref>.

The distinct <scene name='Sandbox_Reserved_170/Arg248/2'>shape of the minor groove recognized by Arg248</scene> is due to a transition of the four A/T base pairs of the CATG core elements to a Hoogsteen base pairing geometry. Regions with Hoogsteen base pairs (green) <scene name='Sandbox_Reserved_170/Hg_helix/2'>decrease the diameter of the double helix</scene> compared to regions with Watson-Crick base pairs (blue).