Fig. 6. Active-site cleft and substrate-binding mode.

a Surface representation of H. sapiens c-type lysozyme (1LZS) and B. bacteriovorus DslA, with alternating views of active-site cleft. The protein surfaces (1LZS calculated without ligand) have been colored to demonstrate charge using coulombic methods, −10 to +10 kcal/(mol·e), red to blue. The two enzymes demonstrate a similar patterning at the active-site cleft, despite DslA binding deacetylated peptidoglycan. b Comparison of DslA to non-catalytic members of the lysozyme superfamily. The fold of DslA and residues E143, E154, and Y228-W229 are shown overlaid with equivalent residues from mouse α-lactalbumin (1NF5, gray)²⁴, mouse sperm lysozyme-like protein (4YF2, maroon)²⁵, and the active enzyme H. sapiens lysozyme (1LZS, yellow)¹⁸. The YW motif on an active-site loop of DslA is shared with α-lactalbumin and sperm lysozyme-like protein and is equivalent to an AW motif in H. sapiens lysozyme. The D helix catalytic residue of DslA, E143, is replaced by Thr in the two inactive enzymes, but the β-sheet catalytic residue, E154, is retained as either a Glu or an Asp. c DslA superimposed with substrate from a liganded form of lysozyme (1LZS). The classic “4 + 2” lysozyme saccharide binding pose is shown, with the ligand coordinates from 1LZS superimposed into DslA using the ES motif of both enzymes as a guide. The cell-wall sugar rings are labeled a–f, with GlcNAc and MurNAc residues colored blue and green, respectively. The 2′ N-acetyl group of rings c and e face inwardly into the rear face of the active-site cleft and provide a model for deacetylation specificity: the sidechains of residues Y228 and M150 (vdw surface shown in transparent) sterically occupy the same space as the acetyl group atoms.