HNH Cas9-type (IPR033114). Type II CRISPR-Cas systems generate double-strand breaks in invasive DNA using the RNA-guided DNA endonuclease Cas9. During the adaptive bacterial immune response, The HNH domain is found in all known Cas9 enzymes. It cuts the target strand, which is the DNA strand that matches the guide RNA sequence. Another thing that is needed is a RuvC nuclease domain to cut the non-target strand, which makes a double-strand DNA break (DSB).