FIGURE 6.

In silico docking of LPE and LPC into the active site of St_βIB1i. A, surface rendering of St_βIB1i (tan), with lysophosphatidylcholine (blue) and lysophosphatidylethanolamine (lavender) docked into the active site. The magnesium cofactor is shown as a small green sphere interacting with the phosphate group of each substrate. For both substrates, the headgroup is situated in a binding pocket that has been previously identified as potentially important for substrate specificity (24). B, side chains in the putative headgroup binding pocket of St_βIB1i (tan; PDB code 4Q6X) compared with those of LiRecDT1, an α clade protein from L. intermedia (green; PDB code 3RLH). The two pockets are quite similar but contain amino acid sequence differences at positions 95, 134, and 195 (see also amino acid residues in blue boxes in Fig. 2). Residue numbering is referenced to Ll_αIII1/SMase I.