Crystal structure of ω transcriptional repressor encoded by Streptococcus pyogenes plasmid pSM19035 at 1.5 Å resolution

The 71 amino acid residue ω protein encoded by the Streptococcus pyogenes non-conjugative plasmid pSM19035 is a transcriptional repressor that regulates expression of genes for copy number control and stable maintenance of plasmids. The crystal structure of ω protein has been determined by multiple isomorphous replacement, including anomalous scattering and refined to an R-factor of 21.1 % (Rfree=23.2 %) at 1.5 Å resolution. Two monomers related by a non-crystallographic 2-fold axis form a homodimer that occupies the asymmetric unit. Each polypeptide chain is folded into two α-helices and one β-strand forming an antiparallel β-ribbon in the homodimer. The N-terminal regions (1–23 and 1–22 in subunits I and II, respectively) are not defined in the electron density due to proteolysis of the N-terminal 20 amino acid residues during crystallisation and partial disorder. The ω protein belongs to the structural superfamily of MetJ/Arc repressors featuring a ribbon-helix-helix DNA-binding motif with the β-ribbon located in and recognizing the major groove of operator DNA; according to a modelled ω protein-DNA complex, residues Arg31 and Arg31′ on the β-ribbon are in positions to interact with a nucleobase, especially guanine.