{"entryType":"UniProtKB reviewed (Swiss-Prot)","primaryAccession":"Q99ZW2","uniProtkbId":"CAS9_STRP1","entryAudit":{"firstPublicDate":"2012-07-11","lastAnnotationUpdateDate":"2026-09-02","lastSequenceUpdateDate":"2001-06-01","entryVersion":148,"sequenceVersion":1},"annotationScore":5.0,"organism":{"scientificName":"Streptococcus pyogenes serotype M1","taxonId":301447,"lineage":["Bacteria","Bacillati","Bacillota","Bacilli","Lactobacillales","Streptococcaceae","Streptococcus"]},"proteinExistence":"1: Evidence at protein level","proteinDescription":{"recommendedName":{"fullName":{"evidences":[{"evidenceCode":"ECO:0000255","source":"HAMAP-Rule","id":"MF_01480"}],"value":"CRISPR-associated endonuclease Cas9/Csn1"},"ecNumbers":[{"evidences":[{"evidenceCode":"ECO:0000255","source":"HAMAP-Rule","id":"MF_01480"}],"value":"3.1.-.-"}]},"alternativeNames":[{"fullName":{"evidences":[{"evidenceCode":"ECO:0000303","source":"PubMed","id":"23287718"}],"value":"SpCas9"}},{"fullName":{"evidences":[{"evidenceCode":"ECO:0000303","source":"PubMed","id":"24505130"}],"value":"SpyCas9"}}]},"genes":[{"geneName":{"evidences":[{"evidenceCode":"ECO:0000255","source":"HAMAP-Rule","id":"MF_01480"},{"evidenceCode":"ECO:0000303","source":"PubMed","id":"22745249"}],"value":"cas9"},"synonyms":[{"evidences":[{"evidenceCode":"ECO:0000303","source":"PubMed","id":"21455174"}],"value":"csn1"}],"orderedLocusNames":[{"value":"SPy_1046"}]}],"comments":[{"texts":[{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"21455174"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"22745249"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"24270795"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"24476820"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"24505130"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"24529477"}],"value":"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) (PubMed:21455174). 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; Cas9 only stabilizes the pre-crRNA:tracrRNA interaction and has no catalytic function in RNA processing (PubMed:24270795). 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). The target strand not complementary to crRNA is first cut endonucleolytically, then trimmed 3'-5' exonucleolytically. DNA-binding requires protein and both gRNAs, as does nuclease activity. 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. DNA strand separation and heteroduplex formation starts at PAM sites; PAM recognition is required for catalytic activity (PubMed:24476820). Confers immunity against a plasmid with homology to the appropriate CRISPR spacer sequences (CRISPR interference) (PubMed:21455174)"}],"commentType":"FUNCTION"},{"commentType":"COFACTOR","cofactors":[{"name":"Mg(2+)","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"22745249"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"24505130"}],"cofactorCrossReference":{"database":"ChEBI","id":"CHEBI:18420"}}],"note":{"texts":[{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"22745249"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"24505130"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"25079318"}],"value":"Endonuclease activity on target dsDNA requires Mg(2+) (PubMed:22745249). The RuvC-like nuclease domain should have 2 divalent cations, while the HNH domain should have 1. Crystals are often soaked in MgCl(2) or MnCl(2+)."}]}},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"22745249"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"24476820"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"24505130"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"26841432"}],"value":"Only has nuclease activity when bound to both gRNAs (crRNA plus tracrRNA), which results in conformational changes in the protein and formation of a central channel which binds target DNA (PubMed:24505130). Also requires interaction with PAM to trigger catalytic activity (PubMed:24476820). Nuclease activity is inhibited by EDTA (PubMed:26841432)"}],"commentType":"ACTIVITY REGULATION"},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000255","source":"HAMAP-Rule","id":"MF_01480"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"24505130"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"24529477"}],"value":"Monomer. Binds crRNA and tracrRNA"}],"commentType":"SUBUNIT"},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"22745249"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"24529477"}],"value":"Has 2 endonuclease domains. The discontinuous RuvC-like domain (approximately residues 1-62, 718-765 and 925-1102) recognizes and cleaves the target DNA noncomplementary to crRNA while the HNH nuclease domain (residues 810-872) cleaves the target DNA complementary to crRNA (PubMed:22745249, PubMed:24529477)"}],"commentType":"DOMAIN"},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"24505130"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"24529477"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"26113724"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"26841432"}],"value":"Has a bilobed architecture with a recognition lobe (REC, residues 60-718) and a discontinuous nuclease lobe (NUC, residues 1-59 and 719-1368) (PubMed:24505130, PubMed:24529477). The crRNA-target DNA lies in a channel between the 2 lobes (PubMed:24529477, PubMed:26841432). Binding of sgRNA induces large conformational changes further enhanced by target DNA binding (PubMed:26113724, PubMed:26841432). REC recognizes and binds differing regions of an artificial sgRNA in a sequence-independent manner. Deletions of parts of this lobe abolish nuclease activity (PubMed:24529477)"}],"commentType":"DOMAIN"},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"24529477"}],"value":"The PAM-interacting domain (PI domain, approximately residues 1099-1368) recognizes the PAM motif; swapping the PI domain of this enzyme with that from S.thermophilus St3Cas9 (AC Q03JI6) prevents cleavage of DNA with the endogenous PAM site (5'-NGG-3') but confers the ability to cleave DNA with the PAM site specific for St3 CRISPRs"}],"commentType":"DOMAIN"},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"21455174"}],"value":"Loss of correct processing of pre-crRNA and tracrRNA. Loss of immunity against a plasmid with homology to CRISPR spacer sequences"}],"commentType":"DISRUPTION PHENOTYPE"},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"23287718"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"23287722"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"23360964"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"23360965"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"23360966"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"23386978"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"26098369"}],"value":"Coexpression of Cas9 with an artificial single guide RNA (sgRNA) which fuses the crRNA with the tracrRNA in human cells has shown it is possible to target and modify DNA sequences of interest (PubMed:23287722, PubMed:23360966, PubMed:23386978). Cas9 plus the 2 sgRNAs have also been expressed individually in human and mouse cells to achieve DNA targeting; cleavage efficiencies of the artificial sgRNA were lower that those for systems with the 2 sgRNAs expressed separately (PubMed:23287718). Microinjection of Cas9-encoding mRNA and a synthetic sgRNA into zebrafish embryos induces targeted mutations (PubMed:23360964). In all cases introduction of multiple sgRNAs leads to multiplexed editing of genomic loci; DNA has also been inserted into a mammalian locus of interest. In S.pneumoniae and E.coli it has been used to generate markerless mutations; multiple changes can be made simultaneously (PubMed:23360965). Studies to make mutations that alter the PAM-specificity and thus recognition possibilities have been made, but are not annotated in this database (PubMed:26098369)"}],"commentType":"BIOTECHNOLOGY"},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000305"}],"value":"Belongs to the CRISPR-associated protein Cas9 family. Subtype II-A subfamily"}],"commentType":"SIMILARITY"}],"features":[{"type":"Chain","location":{"start":{"value":1,"modifier":"EXACT"},"end":{"value":1368,"modifier":"EXACT"}},"description":"CRISPR-associated endonuclease Cas9/Csn1","featureId":"PRO_0000418437"},{"type":"Domain","location":{"start":{"value":770,"modifier":"EXACT"},"end":{"value":921,"modifier":"EXACT"}},"description":"HNH Cas9-type","evidences":[{"evidenceCode":"ECO:0000255","source":"PROSITE-ProRule","id":"PRU01085"}]},{"type":"Region","location":{"start":{"value":1,"modifier":"EXACT"},"end":{"value":62,"modifier":"EXACT"}},"description":"RuvC-I","evidences":[{"evidenceCode":"ECO:0000303","source":"PubMed","id":"24505130"}]},{"type":"Region","location":{"start":{"value":56,"modifier":"EXACT"},"end":{"value":718,"modifier":"EXACT"}},"description":"Recognition lobe","evidences":[{"evidenceCode":"ECO:0000303","source":"PubMed","id":"24505130"}]},{"type":"Region","location":{"start":{"value":56,"modifier":"EXACT"},"end":{"value":73,"modifier":"EXACT"}},"description":"ARM","evidences":[{"evidenceCode":"ECO:0000303","source":"PubMed","id":"24505130"}]},{"type":"Region","location":{"start":{"value":718,"modifier":"EXACT"},"end":{"value":765,"modifier":"EXACT"}},"description":"RuvC-II","evidences":[{"evidenceCode":"ECO:0000303","source":"PubMed","id":"24505130"}]},{"type":"Region","location":{"start":{"value":925,"modifier":"EXACT"},"end":{"value":1102,"modifier":"EXACT"}},"description":"RuvC-III","evidences":[{"evidenceCode":"ECO:0000303","source":"PubMed","id":"24505130"}]},{"type":"Region","location":{"start":{"value":1099,"modifier":"EXACT"},"end":{"value":1368,"modifier":"EXACT"}},"description":"PAM-interacting domain (PI)","evidences":[{"evidenceCode":"ECO:0000303","source":"PubMed","id":"24529477"}]},{"type":"Motif","location":{"start":{"value":1333,"modifier":"EXACT"},"end":{"value":1335,"modifier":"EXACT"}},"description":"PAM substrate-binding","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"25079318"}]},{"type":"Active site","location":{"start":{"value":10,"modifier":"EXACT"},"end":{"value":10,"modifier":"EXACT"}},"description":"For RuvC-like nuclease domain","evidences":[{"evidenceCode":"ECO:0000305","source":"PubMed","id":"24529477"}]},{"type":"Active site","location":{"start":{"value":840,"modifier":"EXACT"},"end":{"value":840,"modifier":"EXACT"}},"description":"Proton acceptor for HNH nuclease domain","evidences":[{"evidenceCode":"ECO:0000305","source":"PubMed","id":"24529477"}]},{"type":"Binding 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Processes guide RNAs. In vivo, loss of Cas9-mediated CRISPR interference in plasmid transformation. Able to bind guide RNAs and target DNA but not cleave DNA; when associated with A-840.","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"22745249"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"24270795"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"24529477"}],"alternativeSequence":{"originalSequence":"D","alternativeSequences":["A"]}},{"type":"Mutagenesis","location":{"start":{"value":15,"modifier":"EXACT"},"end":{"value":15,"modifier":"EXACT"}},"description":"Decreased DNA cleavage.","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"24529477"}],"alternativeSequence":{"originalSequence":"S","alternativeSequences":["A"]}},{"type":"Mutagenesis","location":{"start":{"value":66,"modifier":"EXACT"},"end":{"value":66,"modifier":"EXACT"}},"description":"Significantly decreased DNA cleavage.","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"24529477"}],"alternativeSequence":{"originalSequence":"R","alternativeSequences":["A"]}},{"type":"Mutagenesis","location":{"start":{"value":70,"modifier":"EXACT"},"end":{"value":70,"modifier":"EXACT"}},"description":"No DNA cleavage.","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"24529477"}],"alternativeSequence":{"originalSequence":"R","alternativeSequences":["A"]}},{"type":"Mutagenesis","location":{"start":{"value":74,"modifier":"EXACT"},"end":{"value":74,"modifier":"EXACT"}},"description":"Significantly decreased DNA cleavage.","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"24529477"}],"alternativeSequence":{"originalSequence":"R","alternativeSequences":["A"]}},{"type":"Mutagenesis","location":{"start":{"value":78,"modifier":"EXACT"},"end":{"value":78,"modifier":"EXACT"}},"description":"Moderately decreased DNA cleavage.","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"24529477"}],"alternativeSequence":{"originalSequence":"R","alternativeSequences":["A"]}},{"type":"Mutagenesis","location":{"start":{"value":97,"modifier":"EXACT"},"end":{"value":150,"modifier":"EXACT"}},"description":"No nuclease activity.","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"24529477"}],"alternativeSequence":{}},{"type":"Mutagenesis","location":{"start":{"value":165,"modifier":"EXACT"},"end":{"value":165,"modifier":"EXACT"}},"description":"Moderately decreased DNA cleavage.","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"24529477"}],"alternativeSequence":{"originalSequence":"R","alternativeSequences":["A"]}},{"type":"Mutagenesis","location":{"start":{"value":175,"modifier":"EXACT"},"end":{"value":307,"modifier":"EXACT"}},"description":"About 50% nuclease activity.","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"24529477"}],"alternativeSequence":{}},{"type":"Mutagenesis","location":{"start":{"value":312,"modifier":"EXACT"},"end":{"value":409,"modifier":"EXACT"}},"description":"No nuclease activity.","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"24529477"}],"alternativeSequence":{}},{"type":"Mutagenesis","location":{"start":{"value":475,"modifier":"EXACT"},"end":{"value":477,"modifier":"EXACT"}},"description":"Slight decrease in target DNA cleavage and DNA-binding. Almost complete loss of DNA cleavage and binding; when associated with 1125-A--A-1127.","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"24505130"}],"alternativeSequence":{"originalSequence":"PWN","alternativeSequences":["AAA"]}},{"type":"Mutagenesis","location":{"start":{"value":762,"modifier":"EXACT"},"end":{"value":762,"modifier":"EXACT"}},"description":"Only cleaves 1 DNA strand, probably the noncomplementary strand. Processes guide RNAs correctly. In vivo, loss of Cas9-mediated CRISPR interference in plasmid transformation.","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"24270795"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"24529477"}],"alternativeSequence":{"originalSequence":"E","alternativeSequences":["A"]}},{"type":"Mutagenesis","location":{"start":{"value":840,"modifier":"EXACT"},"end":{"value":840,"modifier":"EXACT"}},"description":"Target DNA complementary to the crRNA is not cleaved; nickase activity. 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Almost complete loss of DNA cleavage and binding; when associated with 475-A--A-477.","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"24505130"}],"alternativeSequence":{"originalSequence":"DWD","alternativeSequences":["AAA"]}},{"type":"Mutagenesis","location":{"start":{"value":1132,"modifier":"EXACT"},"end":{"value":1132,"modifier":"EXACT"}},"description":"Probably inactivates protein.","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"23360965"}],"alternativeSequence":{"originalSequence":"G","alternativeSequences":["C"]}},{"type":"Mutagenesis","location":{"start":{"value":1333,"modifier":"EXACT"},"end":{"value":1335,"modifier":"EXACT"}},"description":"Nearly complete loss of target DNA 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