3US0

Structure of p63 DNA Binding Domain in Complex with a 22 Base Pair A/T Rich Response Element Containing a Two Base Pair "AT" Spacer Between Half Sites

Summary for 3US0

• Entry DOI: 10.2210/pdb3us0/pdb
• Related: 3QYM 3QYN 3US1 3US2
• Descriptor: Tumor protein 63, 5'-D(*AP*AP*AP*CP*AP*TP*GP*TP*TP*TP*AP*TP*AP*AP*AP*CP*AP*TP*GP*TP*TP*T)-3', ZINC ION, ... (4 entities in total)
• Functional Keywords: b-dna double helix, zinc binding, beta sandwich, greek key, transcription factor, nucleus, transcription activator-dna complex, transcription activator/dna
• Biological source: Homo sapiens (human)
• Cellular location: Nucleus : Q9H3D4
• Total number of polymer chains: 6
• Total formula weight: 104493.91

Authors

Chen, C.,Herzberg, O. (deposition date: 2011-11-22, release date: 2012-02-01, Last modification date: 2023-09-13)

Primary citation

Chen, C.,Gorlatova, N.,Herzberg, O.
Pliable DNA Conformation of Response Elements Bound to Transcription Factor p63.
J.Biol.Chem., 287:7477-7486, 2012

PubMed Abstract: We show that changes in the nucleotide sequence alter the DNA conformation in the crystal structures of p63 DNA-binding domain (p63DBD) bound to its response element. The conformation of a 22-bp canonical response element containing an AT spacer between the two half-sites is unaltered compared with that containing a TA spacer, exhibiting superhelical trajectory. In contrast, a GC spacers abolishes the DNA superhelical trajectory and exhibits less bent DNA, suggesting that increased GC content accompanies increased double helix rigidity. A 19-bp DNA, representing an AT-rich response element with overlapping half-sites, maintains superhelical trajectory and reveals two interacting p63DBD dimers crossing one another at 120°. p63DBD binding assays to response elements of increasing length complement the structural studies. We propose that DNA deformation may affect promoter activity, that the ability of p63DBD to bind to superhelical DNA suggests that it is capable of binding to nucleosomes, and that overlapping response elements may provide a mechanism to distinguish between p63 and p53 promoters.

PubMed: 22247550
DOI: 10.1074/jbc.M111.315820

Experimental method

X-RAY DIFFRACTION (2.5 Å)