Fig. 1.

Structure of HetR–DNA complex. (A) Overall structure of the complex of HetR with a 29-bp DNA duplex. The HTH motifs of the DNA-binding unit penetrate the major groove of the DNA. The flap domains interact with the phosphate backbone. The hood domain is presented to the solvent and is available for interactions. Potential peptide RGSGR binding sites identified previously (14) within the DNA-binding unit and on the interface between the HTH and flap domains would interfere with the formation of the protein–DNA complex. DNA curvature is shown as a line through the center of the DNA helix. (B) Charge distribution on the HetR surface interacting with DNA using 21-bp DNA. (C) Conformational changes of the HetR protein on DNA binding. The largest changes are observed within the flap domains. Apo form HetR (in pale) (PDB entry 3QOD) and HetR with the 21-bp DNA bound (in blue and green) are compared. The protein dimers were superimposed: a total of 588 protein residues from HetR-DNA and 574 from Apo-HetR, with an overall rmsd of 2.43 Å with Cα positions. The DNA-binding unit and hood domain of the dimer are well superimposed, but the flap domains of the HetR-DNA complex deviate from that of the apo form, making the dimer more symmetric in the presence of DNA. Overall, the flaps fit better to the extended DNA in both directions away from the twofold axis.