Allosteric Control of DNA in a Repressor to Activator Switch: The Crystal Structure of the Repressor CueR/DNA Complex.

摘要

Prokaryotic organisms have developed elegant systems that maintain the proper metal quota needed for the cell to survive in various environments. Due to the potential toxic effects of copper, the levels of this metal are tightly controlled in bacteria. Genes encoded in the cue regulon of E. coli are induced by extremely low levels of cytoplasmic copper. This control is achieved by the Cu I-sensing regulator CueR, which regulates the transcription of two copper detoxification genes, cueO and copA, which encode for a multi-copper oxidase and a CuI-transporting ATPase. CueR, a member of the MerR family of transcription-control proteins, functions as a dual regulator, repressing and activating transcription while bound to one site of the core promoter. The crystal structure of CueR bound to DNA in the activator conformation, that is, bound to the metal cofactor, demonstrates that the promoter DNA is highly kinked at the center and underwound. This distortion remodels the promoter into a favorable substrate for RNA polymerase.;Here, we describe the crystal structure of metal-free CueR bound to promoter DNA in the repressor state. The structure, the first of its kind for the MerR family, offers atomic-level details of the DNA distortions involved in the repressor function of the protein: repressor CueR bends the DNA at the distal edges, preventing the RNA polymerase from contacting the -35 and -10 promoter elements simultaneously, and thus, inhibiting formation of the closed transcription complex. This structure demonstrates that the repression and activation of CueR-regulated genes at the genetic level is achieved by modulating the stereochemistry, i.e. the shape, of the promoter DNA. Moreover, we report extensive mutational studies of the residues and domains involved in metal-binding and allosteric signaling. These, along with the crystal structures of repressor and activator CueR bound to DNA, demonstrate a clear path for the allosteric transition that occurs upon the conversion of CueR from the repressor to the activator state. The results shown here advance our knowledge of transcription regulation by MerR family proteins. We describe the allosteric transition that occurs when CueR binds its metal cofactor and the effects of this switch on the shape of the promoter DNA. This mechanism of DNA distortion serves as a model for transcription regulation in numerous systems.