The histone-like protein HU isolated from Escherichia coli exhibited, after several purification steps, a Mg2+-dependent nuclease activity. We show here that this activity can be dissociated from HU by a denaturation-renaturation step, and is due to a small fraction of ribosomal protein S16 co-purifying with HU. S16 is an essential component of the 30S ribosomal particles. We have cloned, overproduced, and purified a histidine-tagged S16 and shown that this protein is a DNA-binding protein carrying a Mg2+-Mn2+-dependent endonuclease activity. This is an unexpected property for a ribosomal protein.