Volume 16, Issue 2, Pages 301-307 (October 2004) Structure of EthR in a Ligand Bound Conformation Reveals Therapeutic Perspectives against Tuberculosis  Frédéric Frénois, Jean Engohang-Ndong, Camille Locht, Alain R. Baulard, Vincent Villeret  Molecular Cell  Volume 16, Issue 2, Pages 301-307 (October 2004) DOI: 10.1016/j.molcel.2004.09.020

Figure 1 Structure of the Ligand Bound EthR Homodimer, Viewed Perpendicular to the 2-Fold Dimer Axis EthR consists of nine helices: α1 (23–38), α2 (47–54), α3 (56–64), α4 (68–92), α5 (99–115), α6 (118–129), α7 (132–158), α8 (168–188), and α9 (196–212). Overall, the two DNA recognition helices α3-α3′ are separated by 52 Å. Molecular Cell 2004 16, 301-307DOI: (10.1016/j.molcel.2004.09.020)

Figure 2 Composite Electron Density Omit Map, Contoured at the 1.5 σ Level, Calculated by Excluding HexOc from the Model Carbon, nitrogen, and oxygen atoms are colored yellow, light blue, and red, respectively. Molecular Cell 2004 16, 301-307DOI: (10.1016/j.molcel.2004.09.020)

Figure 3 Stereoviews of Ligand Binding Regions (A) Ligand recognition by EthR. Only residues for which atoms lie in a 5 Å sphere around the ligand are depicted. The ligand is shown in dark green, while carbons, nitrogens, oxygens, and sulfur that belong to the amino acids are in gold, light blue, red, and green, respectively. There is a buried water molecule hydrogen bonded to N179. Recognition of the ligand involves residues from the six helices forming the ligand binding domain. (B) Comparison of ligand binding regions of EthR and QacR with their respective ligands. Superimposition of the core ligand binding region (α4–α9) of EthR (in blue) in complex with HexOc (in dark green) and that of QacR (in brown) in complex with ethidium (in gold) or rhodamine (dark red). F114 may play an important role in EthR induction, in a way analogous to that played by the Y92 region switch in QacR. The QacR structure highlights the multisite binding pocket found in this repressor. Although both repressors share the ligand entrance and have adjacent partially overlapping binding sites, they have nevertheless drastically divergent overall binding cavities. The ligand in EthR is mainly deeply buried in the hydrophobic core of the ligand binding domain, in a cavity that develops parallel to the axes of helices α4 and α7. In contrast, the multisite binding pocket in QacR runs nearly parallel to α6. The displacement of α5 in EthR relative to that of QacR abolishes this cavity in EthR. Molecular Cell 2004 16, 301-307DOI: (10.1016/j.molcel.2004.09.020)

Figure 4 Synergistic Effect of Benzylacetone and ETH on the Growth of M. smegmatis The synergistic effect (see Experimental Procedures) was assayed by spotting 4 μl of serial dilutions (A: 10−2; B: 10−3; C: 10−4; D: 10−5) of a mid-log phase culture of M. smegmatis mc2155 onto LB plates containing no drug, 5 μg/ml ETH alone (ETH), 1 mM benzylacetone alone (BA), or a combination of both compounds (ETH + BA). Plates were incubated 4 days at 37°C. Reduction of growth was observed only on ETH + BA (compare spots A on each plate). Molecular Cell 2004 16, 301-307DOI: (10.1016/j.molcel.2004.09.020)