High-resolution structures of variant Zif268-DNA complexes: implications for understanding zinc finger-DNA recognition.
Elrod-Erickson, M., Benson, T.E., Pabo, C.O.(1998) Structure 6: 451-464
- PubMed: 9562555 
- DOI: https://doi.org/10.1016/s0969-2126(98)00047-1
- Primary Citation of Related Structures:  
1A1F, 1A1G, 1A1H, 1A1I, 1A1J, 1A1K, 1A1L - PubMed Abstract: 
Zinc fingers of the Cys2-His2 class comprise one of the largest families of eukaryotic DNA-binding motifs and recognize a diverse set of DNA sequences. These proteins have a relatively simple modular structure and key base contacts are typically made by a few residues from each finger. These features make the zinc finger motif an attractive system for designing novel DNA-binding proteins and for exploring fundamental principles of protein-DNA recognition. Here we report the X-ray crystal structures of zinc finger-DNA complexes involving three variants of Zif268, with multiple changes in the recognition helix of finger one. We describe the structure of each of these three-finger peptides bound to its corresponding target site. To help elucidate the differential basis for site-specific recognition, the structures of four other complexes containing various combinations of these peptides with alternative binding sites have also been determined. The protein-DNA contacts observed in these complexes reveal the basis for the specificity demonstrated by these Zif268 variants. Many, but not all, of the contacts can be rationalized in terms of a recognition code, but the predictive value of such a code is limited. The structures illustrate how modest changes in the docking arrangement accommodate the new sidechain-base and sidechain-phosphate interactions. Such adaptations help explain the versatility of naturally occurring zinc finger proteins and their utility in design.
Organizational Affiliation: 
Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.