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Figure 7
Complexes of AtlE with NAG-NAM and MDP. The AtlE structure is presented with a transparent surface, which makes the regions and residues in contact with the ligands visible. The averaged kick Fobs − Fcalc electron-density map (Pražnikar et al., 2009BB44) contoured at 0.8σ and 1.2σ around the ligands is shown for (a) MDP and (b) the disaccharide NAG-NAM, respectively. The ligand residues and AtlE residues in contact with the ligands are marked, and their side chains are drawn in stick representation. The colours cyan, yellow and green indicates that the binding sites are built from three chain regions. The N-acetyl group of NAM is positioned equivalently in both complexes. Hydrogen bonds (grey dashed lines) pin NAM to the main-chain atoms of the Gly164 NH group and the Tyr224 carbonyl, while the O atoms of the lactyl moieties form a hydrogen bond to the OH group of the Tyr201 side chain. (a) The alanine hydrophobic side chain of MDP is positioned within the hydrophobic environment formed by the side chains of Ile163, Gly164 and Phe196, whereas the D-­Glu residue is disordered and points into the solvent, while (b) the N-acetyl group of the NAG residue forms a hydrogen bond to the main-chain NH group of Gln223. (c) Comparison of similar ligands superimposed on the AtlE structure. AtlE is shown as a transparent white surface with the catalytic Glu138 side chain labelled. The crystal structures of the muramyl dipeptide and the NAG-NAM disaccharide determined in complex with AtlE are shown as stick models in red and orange, respectively. They are labelled MDP and disaccharide. The muramyl dipeptide ligand bound to T4 lysozyme (T4_L; PDB entry 148l) is shown in green and labelled T4-muropeptide. The disaccharide and trisaccharide structures determined in complex with ACOD (PDB entry 3gxr) are shown in blue and labelled ACOD NAG. This figure was prepared with MAIN (Turk, 2013BB48) and rendered with Raster3D (Merritt & Bacon, 1997BB36).

IUCrJ
Volume 4| Part 2| March 2017| Pages 185-198
ISSN: 2052-2525
https://doi.org/10.1107/S2052252517000367