ZIF268 PROTEIN-DNA COMPLEX REFINED AT 1.6-ANGSTROM - A MODEL SYSTEM FOR UNDERSTANDING ZINC FINGER-DNA INTERACTIONS

Background: Zinc fingers of the Cys,His, class recognize a wide variet y of different DNA sequences and are one of the most abundant DNA-bind ing motifs found in eukaryotes. The previously determined 2.1 Angstrom structure of a complex containing the three zinc fingers from Zif268 has served as a basis for many modeling and design studies, and Zif268 has proved to be a very useful model system for studying how TFIIIA-l ike zinc fingers recognize DNA. Results: We have refined the structure of the Zif268 protein-DNA complex at 1.6 Angstrom resolution. Our str ucture confirms all the basic features of the previous model and allow s us to focus on some critical details at the protein-DNA interlace. I n particular, our refined structure helps explain the roles of several acidic residues located in the recognition helices and shows that the zinc fingers make a number of water-mediated contacts with bases and phosphates. Modeling studies suggest that the distinctive DNA conforma tion observed in the Zif268-DNA complex is correlated with finger-fing er interactions and the length of the linkers between adjacent fingers , Circular dichroism studies indicate that at least some of the featur es of this distinctive DNA conformation are induced upon complex forma tion. Conclusions: Our 1.6 Angstrom structure should provide an excell ent framework for analyzing the effects of Zif268 mutations, for model ing related zinc finger-DNA complexes, and for designing and selecting Zif268 variants that will recognize other DNA sites.