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 spacers, sequences complementary to antecedent mobile elements, and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). In type II CRISPR systems correct processing of pre-crRNA requires a trans-encoded small RNA (tracrRNA), endogenous ribonuclease 3 (rnc) and this protein. The tracrRNA serves as a guide for ribonuclease 3-aided processing of pre-crRNA. Subsequently Cas9/crRNA/tracrRNA endonucleolytically cleaves linear or circular dsDNA target complementary to the spacer; Cas9 is inactive in the absence of the 2 guide RNAs (gRNA). Cas9 recognizes the protospacer adjacent motif (PAM) in the CRISPR repeat sequences to help distinguish self versus nonself, as targets within the bacterial CRISPR locus do not have PAMs. PAM recognition is also required for catalytic activity. Monomer. Binds crRNA and tracrRNA. Has a bilobed architecture with a recognition lobe (REC, residues 41-425) and a discontinuous nuclease lobe (NUC, residues 1-40 and 453-1053); the crRNA-target DNA lies in a channel between the 2 lobes (PubMed:26317473). The NUC lobe has 2 endonuclease domains. The discontinuous RuvC-like domain in NUC cleaves the target DNA noncomplementary to crRNA while the HNH nuclease domain cleaves the target DNA complementary to crRNA (PubMed:26317473). Coexpression of Cas9 with an artificial sgRNA which fuses crRNA with the tracrRNA in human cells has shown it is possible to target and modify DNA sequences of interest (PubMed:25830891, PubMed:26098369). The smaller size of Cas9 from this organism (1053 residues versus 1368 for Streptococcus pyogenes) makes it easier to package the gene in an adeno-associated virus for delivery to 5-6 week old C57/BL6 mice; 2 different target genes were modifed as desired (PubMed:25830891). Belongs to the CRISPR-associated Cas9 family. Subtype II-A subfamily.