Polymorphic toxins are weapons of bacterial warfare which are being used to restrict competitors, aid kin selection and shape bacterial communities. Polymorphic toxin systems (PTSs) are well studied in Gram-negative bacteria; however, there are limited studies in Gram-positive bacteria. In Bacillus subtilis, several members of toxin–immunity protein pairs including YeeF-YezG, YobL-Y, and obK YxiD-YxxD, have been reported. There are few studies describing structural/mechanistic details of these toxin–immunity pairs. This toxin requires a Type VII secretion system. We have shown that the C-terminal domain of YeeF (YeeF-CT) harbours the toxin with DNase activity. The expression of YeeF-CT causes growth defect and leads to morphological changes in Escherichia coli, while the co-expression of the toxin–immunity pair restores normal bacterial growth. Here, we report the crystal structure of YeeF^-CT bound to its cognate antitoxin YezG at 2.1 Å resolution. The crystal structure reveals that the toxin (YeeF-CT) undergoes major conformational changes upon binding its cognate immunity protein (YezG). Comparative structural analysis reveals that six β-sheets of the toxin, required for nuclease activity, are ripped apart into two sub-domains upon binding the immunity protein. This mechanism is unlike other Type II toxin–antitoxin systems, where an intrinsically disordered region of the antitoxin binds at the active site of the toxin, hence sterically occluding the binding of its substrate. We are currently working on the structure-guided detailed characterization of this toxin–immunity protein pair.