Figure 2 - full size

 

Figure 2.
Figure 2. Comparison of the open and closed conformations of Ddl. A: A stereoview of the superposition of the structures of Tca Ddl (slate blue), Eco DdlB (yellow, PDB ID: 2DLN), Lme D-Ala:D-Lac ligase (green, PDB ID: 1EHI) and Efa VanA (violet, PDB ID: 1E4E). B: Stereoview of the superposition of Tca Ddl (open form: slate blue) and Eco DdlB (closed form: yellow) complexed with ATP (violet) and phosphorylated phosphinate (green: labeled as PHY). The swing motion (about 16 Å) of lid loop and the rotation (about 17°) of central domain (red dotted circle) may induce the closed conformation. Lys215 and Tyr216 on a mobile lid loop make hydrogen bonds with Ser150 and Ser151, respectively, on a central domain, which fixes the lid loop so that it covers the substrate binding site in the closed conformation.

The above figure is reprinted by permission from John Wiley & Sons, Inc.: Proteins (2006, 64, 1078-1082) copyright 2006.