Identification of the domains for DNA binding and transactivation function of C protein from bacteriophage Mu

The C protein, a middle gene product of bacteriophage Mu, is the determinant of the transition from middle to late gene expression. C activates transcription from four late gene promoters, P_lys, P_I, P_P, and P_mom by binding to a site overlapping their -35 elements. Site-specific, high-affinity binding of C to its recognition sequence results in both axial and torsional distortion of DNA at P_mom, which appears to play a role in recruitment of RNA polymerase to the promoter for mom gene transactivation. To identify the regions of C protein important for its function, deletion and site-directed mutagenesis were carried out. We demonstrate here that a helix-turn-helix (HTH) motif located toward the carboxy terminal end of the protein is the DNA-binding domain and amino acid residues involved in transactivation overlap the HTH motic. Mutagenesis studies also aided in the identification of the region important for dimerization. Structure-based sequence alignment and molecular modeling in conjunction with mutational analysis suggest that the HTH motif is part of a three-helix bundle, with remarkable similarity to paired (prd), a developmental regulatory protein from Drosophila. Additional key residues identified in the model to be crucial for C protein structure and DNA binding were shown to be important by mutagenesis. These results provide a structural framework for C function and insight into the mechanism of transactivation at the mom promoter.