Solution structure and DNA-binding properties of the C-terminal domain of UvrC from E.coli

The C-terminal domain of the UvrC protein (UvrC CTD) is essential for 5' incision in the prokaryotic nucleotide excision repair process. We have determined the three-dimensional structure of the UvrC CTD using heteronuclear NMR techniques. The structure shows two helix±hairpin±helix (HhH) motifs connected by a small connector helix. The UvrC CTD is shown to mediate structure-specificity DNA binding. The domain binds to a single-stranded±double-stranded junction DNA, with a strong specificity towards looped duplex DNA that contains at least six unpaired bases per loop (`bubble DNA'). Using chemical shift perturbation experiments, the DNA-binding surface is mapped to the first hairpin region encompassing the conserved glycine±valine±glycine residues followed by lysine±arginine±arginine, a positively charged surface patch and the second hairpin region consisting of glycine±isoleucine±serine. A model for the protein± DNA complex is proposed that accounts for this specificity