The DNA Binding Arm of λ Repressor: Critical Contacts from a Flexible Region

Segments of protein that do not adopt a well-ordered conformation in the absence of DNA can still contribute to site-specific recognition of DNA. The first six residues (NH$_2$-Ser$^1$-Thr$^2$-Lys$^3$-Lys$^4$-Lys$^5$-Pro$^6$-) of phage λ repressor are flexible but are important for site-specific binding. Low-temperature x-ray crystallography and codondirected saturation mutagenesis were used to study the role of this segment. All of the functional sequences have the form [X]$^1$-[X]$^2$-[Lys or Arg]$^3$-[Lys]$^4$-[Lys or Arg]$^5$-[X]$^6$. A high-resolution (1.8 angstrom) crystal structure shows that Lys$^3$ and Lys$^4$ each make multiple hydrogen bonds with guanines and that L~ss interacts with the phosphate backbone. The symmetry of the complex breaks down near the center of the site, and these results suggest a revision in the traditional alignment of the six λ operator sites.