CRYSTAL STRUCTURES OF PAPILLOMAVIRUS E2-DNA TARGETS
H. Rozenberg1, J. Hizver1, D. Rabinovich1, F. Frolow1, R.S. Hegde2 and Z. Shakked1
1Department of Structural
Biology, Weizmann Institute of Science, Rehovot, Israel
2Skirball Inst. of Biomolecular
Medicine, NYU Medical center, New York, USA
Transcriptional regulation in papillomaviruses is dependent on sequence-specific binding of the E2 protein to several sites in the viral genome. In bovine papillomavirus-1, the E2 binding sites are 12 base-pair long palindromes with the consensus sequence d(ACCGNNNNCGGT) where the central N4 sequence is highly variable. To understand the role of DNA structure in this system, several dodecamers incorporating the consensus sequence were investigated and their structures compared to the structure of the DNA target in its complex with the DNA binding domain of the bovine E2 protein [1]. The DNA structures were solved by ULTIMA and MFT [2] and refined by X-PLOR and SHELXL at resolutions of 1.6 to 2.8A.
The free targets adopt a new conformational
variant of B-DNA characterized by a roll-induced writhe and an
average helical repeat of 10.5 bp/turn. These features are
largely retained in the bound target particularly at the
ACCG/CGGT identity elements which interact directly with the
protein. However, the central region of the bound DNA which is
not contacted by the protein is largely deformed with respect to
the free molecules in a manner that enables the
symmetrically-disposed recognition elements to form
sequence-specific contacts to the protein. This observation
demonstrates that deformability of the core DNA which is not
contacted by the protein is critical for its recognition by the
E2 protein.