Structures of ? repressors bound to direct and inverted DNA repeats explain modulation of transcription
Journal - Nucleic Acids Research
Repressor ? regulates transcription of genes required for copy number control, accurate segregation and stable maintenance of inc18 plasmids hosted by Gram-positive bacteria. ? belongs to homodimeric ribbon-helix-helix (RHH2) repressors typified by a central, antiparallel ß-sheet for DNA major groove binding. Homodimeric ?2 binds cooperatively to promotors with 7 to 10 consecutive non-palindromic DNA heptad repeats (5'-A/TATCACA/T-3', symbolized by ?) in palindromic inverted, converging (??) or diverging (??) orientation and also, unique to ?2 and contrasting other RHH2 repressors, to non-palindromic direct (??) repeats. Here we investigate with crystal structures how ?2 binds specifically to heptads in minimal operators with (??) and (??) repeats. Since the pseudo-2-fold axis relating the monomers in ?2 passes the central C–G base pair of each heptad with ~0.3 Å downstream offset, the separation between the pseudo-2-fold axes is exactly 7 bp in (??), ~0.6 Å shorter in (??) but would be ~0.6 Å longer in (??). These variations grade interactions between adjacent ?2 and explain modulations in cooperative binding affinity of ?2 to operators with different heptad orientations.