Crystal Structure of a Multidomain Human p53 Tetramer Bound to the Natural CDKN1A (p21) p53-Response Element

Abstract

The p53 tumor suppressor protein is a sequence-specific DNA-binding transcription factor. Structures of p53 bound to DNA have been described, but, so far, no structure has been determined of p53 bound to a natural p53-response element. We describe here the structure of a human p53 homotetramer encompassing both the DNA-binding and homo-oligomerization domains in complex with the natural p53-response element present upstream of the promoter of the CDKN1A (p21) gene. Similar to our previously described structures of human p53 tetramers bound to an artificial consensus DNA site, p53 DNA binding proceeds via an induced fit mechanism with loops L1 of two subunits adopting recessed conformations. Interestingly, the conformational change involving loop L1 is even more extreme than the one previously observed with the artificial consensus DNA site. In fact, the previously determined loop L1 conformation seems to be a transition intermediate between the non-DNA-bound and CDKN1A-bound states. Thus, the new structure further supports our model that recognition of specific DNA by p53 is associated with conformational changes within the DNA-binding domain of p53. Mol Cancer Res; 9(11); 1493-9. Ó2011 AACR.

Structure of p73 DNA-binding domain tetramer modulates p73 transactivation

“…3A). REs with 2-bp spacers or shorter allow the formation of tetramers, as in crystal forms 1 and 2 or in reported structures of p53 and p63 (17)(18)(19)(20)(21)(22)(23). When p73 DBD binds to DNA with spacers larger than 2 bp, it does not form tetramers and the inability to tetramerize might explain the lack of p73β transactivation observed in the yeast-based assay.…”

“…When p73 DBD binds to DNA with spacers larger than 2 bp, it does not form tetramers and the inability to tetramerize might explain the lack of p73β transactivation observed in the yeast-based assay. Regarding the DNA conformation, some studies on p53 have shown DNA bending (17,18,20), whereas others have not (19,21,23). In the case of p73 DBDs, dimers bind to an undisturbed B-DNA half-site RE and bending in the half-sites is not observed; on the other hand, when two oligonucleotides stack to form the 20-bp RE with 1-or 2-bp spacers, the p73 DBD tetramer is still able to recognize both half-site REs and compensates the insertions by unwinding the DNA 30°and 60°, respectively (Fig.…”

“…The first structure of p53 DBD bound to DNA showed a loop-sheet-helix motif contacting the bases and the phosphate backbone of one quarter-site RE (15). More recent structures of p53 and p63 DBDs in complex with DNA have shown a dimer of DBD dimers where each monomer binds to one of the four basic 5-bp inverted repeat recognition sequences, creating dimerization and tetramerization interfaces (16)(17)(18)(19)(20)(21)(22)(23), but no structure of p73 in complex with DNA is known.…”

Crystal Structures of the DNA-binding Domain Tetramer of the p53 Tumor Suppressor Family Member p73 Bound to Different Full-site Response Elements

“…The DBD is a 200-amino acid immunoglobulin-like domain with two ␤-sheets packed as a ␤-sandwich (16). Several structures of the members of the p53 transcription factor family in complex with DNA have been solved (17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27). The DBD binds as a tetramer to response elements (REs), with each monomer recognizing a 5-bp quartersite of the 20-bp full-site RE.…”

Structural Visualization of the p53/RNA Polymerase II Assembly

“…How full-length wild-type human p53 associates with its binding targets remains inconclusive, in large part due to the inherent structural plasticity of the protein at its N-terminal and C-terminal domains (Okorokov et al 2006;Emamzadah et al 2011;Melero et al 2011;Pham et al 2012). For instance, p53, along with other potent transcriptional activators (e.g., VP16), contains intrinsically disordered regions that fold upon interaction with different partners (Triezenberg 1995;Dyson and Wright 2005;Jonker et al 2005;Lee et al 2009;Park et al 2011).…”