Book of Abstracts: Albany 2003
June 17-21 2003
The Crystal Structure of the Human Papillomavirus E2 Binding Site: A High-resolution View of DNA Bending by an Adenine-thymine Tract
Although it has been known for almost two decades that DNA sequences containing short adenine tracts (A-tracts) are intrinsically curved, the stereochemical origins of this bend remain disputed. To gain insight into the structural basis of the DNA curvature by such sequence motifs and their role in protein-DNA recognition, we have determined at 1.6 Å resolution the crystal structure of a DNA target of the cancer-related human papillomavirus type-18 E2 protein (HPV18-E2): ACCGAAAACGGT. In all papillomavirus strains, the E2 proteins make direct and water mediated contacts with the consensus half-sites only (underlined above). However, it was shown that the binding affinity is highly dependent upon the sequence of the non-contacted central region of the DNA target that is A/T rich in the human papillomavirus E2 systems. The minor groove is extremely compressed in the A-tract region and the duplex is bent toward the central minor groove in accord with solution studies. A detailed analysis of the structural parameters provides new insights into the mechanism of DNA bending by A-tract motifs. The DNA duplex is highly hydrated with 113 water molecules and two magnesium ions in the asymmetric unit. The structure exhibits the characteristic spine of hydration at the minor groove of the A-tract. The magnesium ions are located in the major groove, one at each G/C rich edge of the double helix and do not appear to affect the A-tract geometry.
Key words: A-tract, DNA curvature, HPV-E2 binding site, X-ray crystallography.