Studies of IscR reveal a unique mechanism for metal-dependent regulation of DNA binding specificity

IscR from Escherichia coli is an unusual metalloregulator in that it globally regulates transcription by recognizing two different DNA motifs in a Fe-S dependent manner. Here, we report structural and biochemical studies of IscR, which suggest remodeling of the protein-DNA interface upon Fe-S ligation broadens the DNA binding specificity from binding a type 2 motif to both type 1 and 2 motifs. Analysis of an apo-IscR variant with relaxed target-site discrimination identified a key residue in wild-type apo-IscR that we propose makes unfavorable interactions with a type 1 motif. Upon Fe-S binding, these interactions are apparently removed, thereby allowing holo-IscR to bind both type 1 and 2 motifs. These data suggest a novel mechanism of ligand-mediated DNA site recognition, whereby metallocluster ligation relocates a protein specificity determinant to expand DNA target site selection, allowing a broader transcriptomic response by holo-IscR.