Figure 1

Sequence comparison of Dn-ACP with known bacterial PliC/MliC and ACP proteins. (A) Sequence alignment, secondary structure prediction and analysis. The sequences were aligned with ClustalX2 and annotated with secondary structure as predicted by Jpred4 for the two Dn-ACP domains. For comparison, the secondary structure of St-PliC and Ng-ACP is also given (PDBs 3OE3 and 6GQ4 respectively, determined by DSSP). Position of Loop 4 is highlighted by the bracket. Figure prepared using ESPrint. (B) Phylogenetic tree. FigTree was used to convert the sequence alignment to a phylogenetic tree. The PliC and MliC proteins are shown as red branches, while the ACP proteins are shown in blue. The Dn-ACP N- and C-terminal domains were aligned and are shown as green branches. Interestingly, the N-terminal ACP domain groups with other ACP proteins, while the C-terminal Dn-ACP domain more closely related to the PliC/MliC family. Ba-PliC (PDB:4ML7), St-PliC (PDB:3OE3), Nm-ACP (PDB:5MY7) and Ng-ACP (PDB:6GQ4) are shown as cartoon next to the respective branch. The reported homology models for Dn-ACP N- and C-terminal domains are also shown. (C) Homology modelling of the Dn-ACP N- and C-terminal domains. Structure models for the N- and C-terminal domains of Dn-ACP were predicted using MODELLER and are shown in dark and light green respectively. The boxed overlay highlights subtle structural differences as predicted. For comparison, known structures of Nm-ACP (PDB:5MY7, light blue, with labelled beta strands), Ng-ACP (PDB:6GQ4, blue), St-PliC (PDB:3OE3, pink) and Ba-PliC (PDB:4ML7, dark red) are shown in identical orientation. In all structures, the functional Loop 4 region has been annotated. Additionally, the site of the lysozyme binding interface determined for Ba-PliC has been indicated.