Fig. 5
Specific protein–DNA contacts determine stoichiometry of the interaction. a Map of observed and hypothesized interactions for the fadRSa and Saci_1123 operators. Colored base and amino acid residues without an asterisk represent contacts identified in the FadRSa–DNA cocrystal structure (using the same color code for the subunits as in panel (a)). Colored residues with an asterisk are hypothesized to be established in the natural operators. Black residues in bold are those that theoretically could support binding in case a GC (AT) or CG (TA) would have been present on the crucial Gly48-interacting positions, which are indicated with red ovals. b Zoom of the Gly48–G14 interaction in the interface between subunit E and the X–Y DNA duplex in the FadRSa–DNA cocrystal structure. c EMSAs with 45-bp DNA fragments representing a wildtype or mutated variant of the Saci_1123 operator region, performed with wildtype or N37A mutant FadRSa. Molar protein concentrations are shown above the autoradiograph, whereas populations of free DNA (F) and FadRSa–bound DNA (B, B1, and B2) are indicated with an arrowhead, as well as with schematical representations of the binding stoichiometry
