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 α 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 α operator sites.