The restriction fold turns to the dark side: a bacterial homing endonuclease with a PD-(D/E)-XK motif

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Abstract
The homing endonuclease I‐Ssp6803I causes the insertion of a group I intron into a bacterial tRNA gene—the only example of an invasive mobile intron within a bacterial genome. Using a computational fold prediction, mutagenic screen and crystal structure determination, we demonstrate that this protein is a tetrameric PD‐(D/E)‐XK endonuclease—a fold normally used to protect a bacterial genome from invading DNA through the action of restriction endonucleases. I‐Ssp6803I uses its tetrameric assembly to promote recognition of a single long target site, whereas restriction endonuclease tetramers facilitate cooperative binding and cleavage of two short sites. The limited use of the PD‐(D/E)‐XK nucleases by mobile introns stands in contrast to their frequent use of LAGLIDADG and HNH endonucleases—which in turn, are rarely incorporated into restriction/modification systems.