Figure 11.

Structure and function of anti-activation by TraM. A) Model of symmetric (TraR_NGR-TraM_NGR)₂ in solution. The model was generated by applying the C2 rotational symmetry of the NTDs to the closed form of dimeric TraR_NGR-TraM_NGR. The repositioned TraR_NGR-TraM_NGR pair is colored in red and blue, and the original pair is in magenta and cyan. The main TraM-binding site, α10 and the linker, is in green, and the DNA binding helix, α12, is in orange. The bound 3-oxo-C8-HSL is shown in ball-and-stick representation. B) The interaction between TraR_NGR α10 with TraM_NGR (PDB ID: 2Q0O). TraM_NGR residues (cyan) that are in contact with Pro178, Leu182 and Trp186 (magenta) of TraR_NGR α10 are shown. Leu199 from α11 is also shown. The dotted lines denote hydrogen bonds between TraR_NGR Trp186 and TraM_NGR His39 and Gln85. C) The interaction of TraR_NGR L199 with the hydrophobic C-terminal tail of TraM_NGR. Surface is colored according to the underlying atoms: red for oxygen, blue for nitrogen, and gray for carbon. Side chains of the hydrophobic TraM_NGR residues (gray), along with that of L199 (magenta), are shown. D) Structural comparison of TraR_At-DNA with TraR_NGR-TraM_NGR. The NTDs of the both structures are superimposed, but for clarity only one monomer of TraR_NGR (in red) and TraR_At (in purple, the extended form) from each structure is shown. The large domain movement is highlighted with an arrow. DNA is displayed as a double coil and is light orange, and the DNA-binding helix α12 is yellow in TraR_At-DNA complex and orange in TraR_NGR-TraM_NGR complex. TraM_NGR is light blue, and the TraM-binding site (α10 and the linker) is cyan in TraR_At-DNA and green in TraR_NGR-TraM_NGR.