A low activity DNA endonuclease yielding 3'-hydroxyl ends, equally active on ss or dsDNA, not active on dsRNA (PubMed:28096446). Shows no sequence specificity (PubMed:28096446). Upon expression enhances RecA-independent DNA recombination 49-fold, concomitantly reducing viability by 88% and probably inducing DNA damage as measured by induction of the SOS repair response in RecA cells (PubMed:28096446). 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 RpnA leads to smaller replacement segments, suggesting this protein may play a role in generating crossover events (PubMed:28096446). Endonuclease activity partially supported by Mn(2+). Inhibited by EDTA, Zn(2+) and by Mg(2+) plus Mn(2+); stimulated by Ca(2+) in the presence of Mg(2+). Optimum pH is 9.0, active between pH 7.5 and 10.5. Cells grow to slightly higher density than wild-type in sublethal levels of streptomycin (PubMed:25316676). 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.