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 Cas9. The tracrRNA serves as a guide for ribonuclease 3-aided processing of pre-crRNA (Probable). Cas9/crRNA/tracrRNA endonucleolytically cleaves linear or circular dsDNA target complementary to the spacer yielding blunt ends; Cas9 is inactive in the absence of the 2 guide RNAs (gRNA). Cas9 recognizes a 3'-G-rich protospacer adjacent motif (PAM, TGGTG in this organism) 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. When the CRISPR3/cas system consisting of cas9-cas1-cas2-csn2-CRISPR3 or just cas9-CRISPR3 is expressed in E.coli it prevents plasmids homologous to spacers 1 or 2 from transforming. Endonuclease activity on target DNA requires Mg(2+). Only has nuclease activity when bound to both gRNAs (crRNA plus tracrRNA). Monomer (Probable). Binds crRNA and tracrRNA. Has 2 endonuclease domains. The discontinuous RuvC-like domain cleaves the target DNA noncomplementary to crRNA while the HNH nuclease domain cleaves the target DNA complementary to crRNA. Plasmid transformation is restored. The simplicity of the Cas9-gRNAs RNA-directed DNA endonuclease activity may be used to target and modify a DNA sequence of interest. This strain encodes 4 CRISPR-Cas systems; this is CRISPR3. Belongs to the CRISPR-associated protein Cas9 family. Subtype II-A subfamily. It is uncertain whether Met-1 or Met-22 is the initiator. Truncated N-terminus.