Extended Data Fig. 7: Structural modelling of DdmABC and DdmDE.
From: Two defence systems eliminate plasmids from seventh pandemic Vibrio cholerae
Cartoon representations showing the predicted structures of V. cholerae strain A1552 DdmABC and DdmDE, highlighting identified functional domains. Side chains of residues predicted to be involved in either nuclease activity or nucleotide binding and hydrolysis are shown as red sticks: DdmA, active site residues of the PD-(D/E)xK superfamily nuclease motif (42D…55QDK57); DdmC, the predicted ATP-binding site formed by the N-terminal Walker A motif (34GSSKSGKS41) and the abnormal C-terminal Walker B motif (560YIIYDQ565) and DdmD, superfamily II helicase motifs I (52GIGKT56), II (272DEID275), III (543SATA546) and VI (851QAVGRAGR858) that comprise the predicted ATP-binding site, and active site residues of the PD-(D/E)xK superfamily nuclease motif (1085D…1100DSK1102). Active site residues of the PD-(D/E)xK motif are shown in bold. Residues targeted by site-directed mutagenesis are underlined. The position of the DdmD residue E891, which in 6th pandemic classical V. cholerae strains is typically K891, is shown as a green sphere, located adjacent to the arginine finger (Motif VI). Structural modelling was done using RoseTTAFold (DdmABC) and AlphaFold2 (DdmDE). Images were prepared using PYMOL.
