Fig. 3.

Structural analysis of the TraR_NGR–TraM_NGR complex. (A) The TraR_NGR–TraM_NGR interactions at TraR_NGR W186. Side chains from TraR_NGR are colored in magenta, and those from TraM_NGR are in cyan. The oxygen atom is in red, and nitrogen atoms are in blue. (B) Interactions of TraR_NGR L199 (in magenta) with the hydrophobic cluster at the C termini of TraM_NGR. Hydrophobic side chains of the cluster are colored in gray, whereas those that interact directly with L199 are colored in cyan. (C) The extensive intermolecular hydrogen-bonding network. Residues from TraM_NGR and TraR_NGR are colored in blue and red, respectively. The values (in angstroms) denote the distance between hydrogen donors and acceptors. Only interacting moieties, i.e., side chains of TraM_NGR and backbones of TraR_NGR, are shown. (D) Multiple sequence alignment of the antiactivator TraM proteins by using CLUSTALW (30). Amino acid sequences are from the following bacteria: RhNGR (or TraM_NGR in the text), Rhizobium sp. NGR234; AtR10 (TraM_At), A. tumefaciens R10; AtK588, A. tumefaciens K588; ATC58, A. tumefaciens C58; AtA4, A. tumefaciens A4; AtA_1, A. tumefaciens A6; AtA_2, A. tumefaciens A6 traM2; RhETLI, Rhizobium etli CFN42; RhLEGU, R. leguminosarum; SmMELI, Sinorhizobium meliloti AK631; and NiHAMB, Nitrobacter hamburgensis X14; OlCARB, Oligotropha carboxidovorans. Invariant residues are highlighted in black, and highly conserved resides are shaded in grey. Secondary structure elements of TraM_NGR are indicated above. A and B were generated by using MOLSCRIPT and RASTER 3D (28, 29).