Crystal structure of LacI member, PurR, bound to DNA: Minor groove binding by α helices

The three-dimensional structure of a ternary complex of the purine repressor, PurR, bound to both its compressor, hypoxanthine, and the 16-base pair purF operator site has been solved at 2.7 Å resolution by x-ray crystallography. The bipartite structure of PurR consists of an amino-terminal DNA-binding domain and a larger carboxyl-terminal corepressor binding and dimerization domain that is similar to that of the bacterial periplasmic binding proteins. The DNA-binding domain contains a helix-turn-helix motif that makes base-specific contacts in the major groove of the DNA. Base contacts are also made by residues of symmetry-related α helices, the "hinge" helices, which bind deeply in the minor groove. Critical to hinge helix-minor groove binding is the intercalation of the side chains of Leu⁵⁴ and its symmetry-related mate, Leu^54′, into the central CpG-base pair step. These residues thereby act as "leucine levers" to pry open the minor groove and kink the purF operator by 45 degrees.