Fig. 3
Overall structure of the LIP dimer. (a) Overall structure of LIP. The lectin module and the middle and C-terminal moieties of the aerolysin module of the LIP subunit are shown in blue, orange, and green, respectively. The prestem hairpin (the putative transmembrane region) is shown in pink. The N and C termini as well as the bound glycerol are labeled. (b) Superimposition of LIP with Dln1. The second subunit of LIP in the asymmetric unit is shown in sandy brown, and Dln1 is shown in purple. (c) Topology diagram of the LIP monomer. (d) Comparison of the ligand-binding sites of LIP (sandy brown) and Dln1 (blue). The interactions of the bound glycerol molecule and residues Gly15, Ser132, Asp133 and Asp135 of the lectin module in LIP are presented (upper panel). The lectin modules of LIP and Dln1 are superimposed. The interactions of the bound sucrose and the residues in the pocket in Dln1 are labeled, as are the corresponding residues in LIP (upper panel). The hydrophobicity of the surfaces of LIP and Dln1 is depicted according to the Kyte-Doolittle scale with colors ranging from Dodger blue for the most hydrophilic to white at 0.0 and orange-red for the most hydrophobic [33] (middle panel). The red circles are the ligand-binding sites. These sites are almost identical, except for the part on the left, which is an asparagine (Asn) in LIP but a serine (Ser) in Dln1. The green triangle is the channel extending from the binding site. Surface representations of LIP and Banlec (lower panel). Banlec and LIP are superimposed, and the ligands from Banlec are presented with the surface of LIP. The belt-shaped channel is marked with a red rectangle. (e) Multiple-sequence alignment of the putative transmembrane region from different aerolysin members. The members include LIP (Lampetra japonica), aerolysin (Aeromonas sobria), E-toxin (Clostridium perfringens), Mtx2 (Lysinibacillus sphaericus) and LSL (Laetiporus sulphureus). Alignments were generated based on the alternating patterns of polar and hydrophobic residues. The hydrophilic residues (facing the pore lumen) and hydrophobic residues (facing the lipid bilayer) are marked in black and red, respectively. (f) Schematic representation of the antiparallel strands forming the β-barrel of LIP and the corresponding residues of aerolysin. The alignment is based on previous reports [21] and sequence similarity. The residues are depicted either facing the lipid bilayer or lining the lumen of the pore