CRISPR (clustered regularly interspaced short palindromic repeat), is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids). CRISPR clusters contain sequences complementary to antecedent mobile elements and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). Cas3 plus Cascade participate in CRISPR interference, the third stage of CRISPR immunity. The N-terminal domain (residues 6-260) acts as a ssDNA endonuclease, has no activity on dsDNA. The ssDNA endonuclease activity (residues 6-260) is stimulated by Mn(2+), Co(2+), Ni(2+), Cu(2+) and Zn(2+), but not by Mg(2+) or Ca(2+). A Ni(2+) ion is seen in crystals upon soaking. Inhibited by EDTA, Mg(2+) and Ca(2+). Proteins of this family have an N-terminal nuclease domain and a C-terminal helicase/ATPase domain. In some CRISPR/Cas systems the domains are swapped, in others they are encoded separately. In the N-terminal section; belongs to the CRISPR-associated nuclease Cas3-HD family. In the central section; belongs to the CRISPR-associated helicase Cas3 family.