Introduction - This script shows some aspects of the mechanism of lysozyme. Lysozyme hydrolyzes the glycosidic linkage bewteen N-acetylmuramic acid (NAM) and N-acetylglucosamine (NAG) in bacterial cell walls. Scroll down until the text corresponding to the view is visible. (Based on 1lzc.pdb, K.Maenaka et al. J. Mol. Biol. 247 281 91995) and 9lyz.pdb, J.A.Kelly et al. Nature 282 875 (1970)).
Lysozyme has a long cleft that will hold up to six residues of the sugar polymer (YELLOW) - only four are shown here. The active site residues Glu 35 and Asp 52 are shown in GREEN.
Note how they are poised to hydrolyze the glycosidic bond between the fourth and fifth sugar residue in the polymer.
In the transition state the NAM at residue 4 adopts a half-chair conformation. Here we see residues 2, 3, and 4 as they appear when bound to lysozyme.
Here is the NAM at position 2. Note that it is in the chair conformation.
Here is the NAM at position 4. Note it is in the half-chair conformation.
The half-chair conformation is favored because of steric interactions between the C 6 group of NAM 4 (MAGENTA) and the acetamido group of NAG 3 (GREEN).