The crystal structure of the DNase domain of colicin E7 in complex with its inhibitor Im7 protein

Background: Colicin E7 (ColE7) is one of the bacterial toxins classified as a DNase-type E-group colicin, The cytotoxic activity of a colicin in a col icin-producing cell can be counteracted by binding of the colicin to a high ly specific immunity protein. This biological event is a good model system for the investigation of protein recognition. Results: The crystal structure of a one-to-one complex between the DNase do main of colicin E7 and its cognate immunity protein Im7 has been determined at 2.3 Angstrom resolution. Im7 in the complex is a varied four-helix bund le that is identical to the structure previously determined for uncomplexed Im7. The structure of the DNase domain of ColE7 displays a novel alpha/bet a fold and contains a Zn2+ ion bound to three histidine residues and one wa ter molecule in a distorted tetrahedron geometry, Im7 has a V-shaped struct ure, extending two arms to clamp the DNase domain of ColE7, One arm (alpha 1*-loop 12-alpha 2*; where * represents helices in Im7) is located in the r egion that displays the greatest sequence variation among members of the im munity proteins in the same subfamily, This arm mainly uses acidic sidechai ns to interact with the basic sidechains in the DNase domain of ColE7, The other arm (loop 23-alpha 3*-loop 34) is more conserved and it interacts not only with the sidechain but also with the mainchain atoms of the DNase dom ain of ColE7. Conclusions: The protein interfaces between the DNase domain of ColE7 and I m7 are charge-complementary and charge interactions contribute significantl y to the tight and specific binding between the two proteins. The more vari able an in Im7 dominates the binding specificity of the immunity protein to its cognate colicin. Biological and structural data suggest that the DNase active site for ColE7 is probably near the metal-binding site.