A low activity DNA endonuclease yielding 3'-hydroxyl ends (Probable). Expression of a repaired protein increases the frequency of recA-independent recombination, but also decreases viability probably via DNA damage as measured by induction of the SOS repair response; in a RecA strain expression has no effect on viability but does induce the SOS repair response (PubMed:26162088, PubMed:26618540). RecA-independent DNA recombination leads to replacement of recipient genes with large segments of donor DNA rather than DNA addition to the donor strain; increased expression of RpnD leads to smaller replacement segments, suggesting this protein may play a role in generating crossover events (PubMed:26162088, PubMed:26618540). Upon expression enhances RecA-independent DNA recombination 4.7-fold, concomitantly reducing viability by 94% and inducing DNA damage (PubMed:28096446). May play a role in horizontal gene transfer (PubMed:26162088, PubMed:26618540, PubMed:28096446). A quadruple rpnA-rpnB-rpnC-rpnD deletion shows no change in basal RecA-independent recombination (PubMed:28096446). Belongs to the Rpn/YhgA-like nuclease family.