Figure 6.

Gentamicin interrupts IcaR and DNA interaction. (A) The effects of antibiotics to the IcaR binding to ica operator in EMSA experiment. Only two aminoglycosides are capable of interfering the DNA binding, whereas gentamicin inhibited the binding to a significantly greater extent than streptomycin. The other four antibiotics kanamycin, tetracycline, ampicillin and chloramphenicol did not show significant effect on the IcaR–DNA binding. (B) Possible effect of gentamicin on the IcaR binding to ica operator. A negatively charged cavity was observed in each IcaR monomer, near the dimer interface. Binding of gentamicin to this cavity may result in conformation changes that lead to a larger separation of the N-terminal domains. (C) A schematic diagram of the putative antibiotics-binding cavity. The cavity is located at the dimer interface and surrounded by helices α5, α6, α7 and α8 of one monomer as well as α8′ and α9′ of the counter monomer. The α8–α9 loop has different conformations in the two crystal forms (Figure 1D), suggesting some functional flexibility.