A. An unambiguous positive electron density (2.5 σ) colored in green is present in the Fo-Fc electron density map calculated for the final model with omitted ligand di(GM5P) after several cycles of the simulated annealing performed in Phenix (Adams et al., 2010). The final model of di(GM5P), colored in yellow, fits perfectly within the Y-shaped substrate-binding groove. The different moieties comprising the di(GM5P) substrate are annotated in blue. The surface of the LytA amidase domain is colored white.
B. Orthogonal view of the LytAAmi/di(GM5P) complex reveals that the scissile bond formed between the lactyl moiety of NAM2 and residue L-Ala5 is buried within the active site of LytA underneath the carbohydrate chain. The LytA protein is displayed as a semitransparent white surface. The carbon atoms of the glycan chain and the peptide stems are in yellow and cyan, respectively.