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CRISPR-associated endonuclease Cas9 2 (EC 3.1.-.-) (Cas9*) (St3Cas9)

 CAS9B_STRTD             Reviewed;        1388 AA.
Q03JI6;
06-MAR-2013, integrated into UniProtKB/Swiss-Prot.
14-NOV-2006, sequence version 1.
10-OCT-2018, entry version 69.
RecName: Full=CRISPR-associated endonuclease Cas9 2 {ECO:0000255|HAMAP-Rule:MF_01480};
EC=3.1.-.- {ECO:0000255|HAMAP-Rule:MF_01480};
AltName: Full=Cas9*;
AltName: Full=St3Cas9;
Name=cas9-2 {ECO:0000255|HAMAP-Rule:MF_01480}; Synonyms=csn1;
OrderedLocusNames=STER_1477;
Streptococcus thermophilus (strain ATCC BAA-491 / LMD-9).
Bacteria; Firmicutes; Bacilli; Lactobacillales; Streptococcaceae;
Streptococcus.
NCBI_TaxID=322159;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC BAA-491 / LMD-9;
PubMed=17030793; DOI=10.1073/pnas.0607117103;
Makarova K.S., Slesarev A., Wolf Y.I., Sorokin A., Mirkin B.,
Koonin E.V., Pavlov A., Pavlova N., Karamychev V., Polouchine N.,
Shakhova V., Grigoriev I., Lou Y., Rohksar D., Lucas S., Huang K.,
Goodstein D.M., Hawkins T., Plengvidhya V., Welker D., Hughes J.,
Goh Y., Benson A., Baldwin K., Lee J.-H., Diaz-Muniz I., Dosti B.,
Smeianov V., Wechter W., Barabote R., Lorca G., Altermann E.,
Barrangou R., Ganesan B., Xie Y., Rawsthorne H., Tamir D., Parker C.,
Breidt F., Broadbent J.R., Hutkins R., O'Sullivan D., Steele J.,
Unlu G., Saier M.H. Jr., Klaenhammer T., Richardson P., Kozyavkin S.,
Weimer B.C., Mills D.A.;
"Comparative genomics of the lactic acid bacteria.";
Proc. Natl. Acad. Sci. U.S.A. 103:15611-15616(2006).
[2]
FUNCTION AS AN DNA ENDONUCLEASE, SUBUNIT, AND RNA-BINDING.
STRAIN=ATCC BAA-491 / LMD-9;
PubMed=22745249; DOI=10.1126/science.1225829;
Jinek M., Chylinski K., Fonfara I., Hauer M., Doudna J.A.,
Charpentier E.;
"A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial
immunity.";
Science 337:816-821(2012).
[3]
BIOTECHNOLOGY.
STRAIN=ATCC BAA-491 / LMD-9;
PubMed=23287718; DOI=10.1126/science.1231143;
Cong L., Ran F.A., Cox D., Lin S., Barretto R., Habib N., Hsu P.D.,
Wu X., Jiang W., Marraffini L.A., Zhang F.;
"Multiplex genome engineering using CRISPR/Cas systems.";
Science 339:819-823(2013).
[4]
FUNCTION AS AN ENDONUCLEASE, AND FUNCTION IN GUIDE RNA PROCESSING.
STRAIN=ATCC BAA-491 / LMD-9;
PubMed=24270795; DOI=10.1093/nar/gkt1074;
Fonfara I., Le Rhun A., Chylinski K., Makarova K.S., Lecrivain A.L.,
Bzdrenga J., Koonin E.V., Charpentier E.;
"Phylogeny of Cas9 determines functional exchangeability of dual-RNA
and Cas9 among orthologous type II CRISPR-Cas systems.";
Nucleic Acids Res. 42:2577-2590(2014).
[5]
FUNCTION, AND DOMAIN.
PubMed=24505130; DOI=10.1126/science.1247997;
Jinek M., Jiang F., Taylor D.W., Sternberg S.H., Kaya E., Ma E.,
Anders C., Hauer M., Zhou K., Lin S., Kaplan M., Iavarone A.T.,
Charpentier E., Nogales E., Doudna J.A.;
"Structures of Cas9 endonucleases reveal RNA-mediated conformational
activation.";
Science 343:1247997-1247997(2014).
-!- FUNCTION: 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 (By
similarity). 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 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, GGG 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. Complements
the gRNA coprocessing defect in a cas9 deletion in S.pyogenes
strain 370, and cuts target DNA in Cas9:gRNAs mixing experiments
with S.mutans strain UA159. {ECO:0000255|HAMAP-Rule:MF_01480,
ECO:0000269|PubMed:22745249, ECO:0000269|PubMed:24270795,
ECO:0000269|PubMed:24505130}.
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000305};
Note=Endonuclease activity on target dsDNA requires Mg(2+).
{ECO:0000305};
-!- SUBUNIT: Monomer (By similarity). Binds crRNA and tracrRNA.
{ECO:0000255|HAMAP-Rule:MF_01480, ECO:0000269|PubMed:22745249}.
-!- DOMAIN: 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.
{ECO:0000255|HAMAP-Rule:MF_01480}.
-!- DOMAIN: The PAM-interacting domain (PI domain, approximately
residues 1102-1388) recognizes the PAM motif; swapping the PI
domain of this enzyme with that from S.pyogenes Cas9 (AC Q99ZW2)
prevents cleavage of DNA with the endogenous PAM site but confers
the ability to cleave DNA with the PAM site specific for
S.pyogenes CRISPRs. {ECO:0000269|PubMed:24505130}.
-!- BIOTECHNOLOGY: Coexpression of Cas9 and both gRNAs in human cells
has shown it is possible to use this system to target and modify a
DNA sequence of interest in situ. {ECO:0000269|PubMed:23287718}.
-!- SIMILARITY: Belongs to the CRISPR-associated protein Cas9 family.
Subtype II-A subfamily. {ECO:0000255|HAMAP-Rule:MF_01480,
ECO:0000305}.
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EMBL; CP000419; ABJ66636.1; -; Genomic_DNA.
RefSeq; WP_011681470.1; NC_008532.1.
ProteinModelPortal; Q03JI6; -.
SMR; Q03JI6; -.
PRIDE; Q03JI6; -.
EnsemblBacteria; ABJ66636; ABJ66636; STER_1477.
KEGG; ste:STER_1477; -.
HOGENOM; HOG000071789; -.
KO; K09952; -.
OMA; TDRHSIK; -.
GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
GO; GO:0004519; F:endonuclease activity; IEA:UniProtKB-UniRule.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-UniRule.
GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
GO; GO:0051607; P:defense response to virus; IEA:UniProtKB-UniRule.
GO; GO:0043571; P:maintenance of CRISPR repeat elements; IEA:UniProtKB-UniRule.
HAMAP; MF_01480; Cas9; 1.
InterPro; IPR028629; Cas9.
InterPro; IPR032239; Cas9-BH.
InterPro; IPR032237; Cas9_PI.
InterPro; IPR032240; Cas9_REC.
InterPro; IPR033114; HNH_CAS9.
InterPro; IPR003615; HNH_nuc.
Pfam; PF16593; Cas9-BH; 1.
Pfam; PF16595; Cas9_PI; 1.
Pfam; PF16592; Cas9_REC; 1.
Pfam; PF13395; HNH_4; 1.
TIGRFAMs; TIGR01865; cas_Csn1; 1.
PROSITE; PS51749; HNH_CAS9; 1.
1: Evidence at protein level;
Antiviral defense; DNA-binding; Endonuclease; Hydrolase; Magnesium;
Manganese; Metal-binding; Nuclease; RNA-binding.
CHAIN 1 1388 CRISPR-associated endonuclease Cas9 2.
/FTId=PRO_0000421686.
DOMAIN 771 928 HNH Cas9-type. {ECO:0000255|PROSITE-
ProRule:PRU01085}.
REGION 1102 1388 PAM-interacting domain (PI).
ACT_SITE 10 10 For RuvC-like nuclease domain.
{ECO:0000255|HAMAP-Rule:MF_01480}.
ACT_SITE 847 847 Proton acceptor for HNH nuclease domain.
{ECO:0000255|HAMAP-Rule:MF_01480}.
METAL 10 10 Magnesium 1. {ECO:0000255|HAMAP-
Rule:MF_01480}.
METAL 10 10 Magnesium 2. {ECO:0000255|HAMAP-
Rule:MF_01480}.
METAL 763 763 Magnesium 1. {ECO:0000255|HAMAP-
Rule:MF_01480}.
METAL 767 767 Magnesium 1. {ECO:0000255|HAMAP-
Rule:MF_01480}.
METAL 767 767 Magnesium 2. {ECO:0000255|HAMAP-
Rule:MF_01480}.
METAL 990 990 Magnesium 2; via pros nitrogen.
{ECO:0000255|HAMAP-Rule:MF_01480}.
SEQUENCE 1388 AA; 161031 MW; B97BC4C953090235 CRC64;
MTKPYSIGLD IGTNSVGWAV TTDNYKVPSK KMKVLGNTSK KYIKKNLLGV LLFDSGITAE
GRRLKRTARR RYTRRRNRIL YLQEIFSTEM ATLDDAFFQR LDDSFLVPDD KRDSKYPIFG
NLVEEKAYHD EFPTIYHLRK YLADSTKKAD LRLVYLALAH MIKYRGHFLI EGEFNSKNND
IQKNFQDFLD TYNAIFESDL SLENSKQLEE IVKDKISKLE KKDRILKLFP GEKNSGIFSE
FLKLIVGNQA DFRKCFNLDE KASLHFSKES YDEDLETLLG YIGDDYSDVF LKAKKLYDAI
LLSGFLTVTD NETEAPLSSA MIKRYNEHKE DLALLKEYIR NISLKTYNEV FKDDTKNGYA
GYIDGKTNQE DFYVYLKKLL AEFEGADYFL EKIDREDFLR KQRTFDNGSI PYQIHLQEMR
AILDKQAKFY PFLAKNKERI EKILTFRIPY YVGPLARGNS DFAWSIRKRN EKITPWNFED
VIDKESSAEA FINRMTSFDL YLPEEKVLPK HSLLYETFNV YNELTKVRFI AESMRDYQFL
DSKQKKDIVR LYFKDKRKVT DKDIIEYLHA IYGYDGIELK GIEKQFNSSL STYHDLLNII
NDKEFLDDSS NEAIIEEIIH TLTIFEDREM IKQRLSKFEN IFDKSVLKKL SRRHYTGWGK
LSAKLINGIR DEKSGNTILD YLIDDGISNR NFMQLIHDDA LSFKKKIQKA QIIGDEDKGN
IKEVVKSLPG SPAIKKGILQ SIKIVDELVK VMGGRKPESI VVEMARENQY TNQGKSNSQQ
RLKRLEKSLK ELGSKILKEN IPAKLSKIDN NALQNDRLYL YYLQNGKDMY TGDDLDIDRL
SNYDIDHIIP QAFLKDNSID NKVLVSSASN RGKSDDVPSL EVVKKRKTFW YQLLKSKLIS
QRKFDNLTKA ERGGLSPEDK AGFIQRQLVE TRQITKHVAR LLDEKFNNKK DENNRAVRTV
KIITLKSTLV SQFRKDFELY KVREINDFHH AHDAYLNAVV ASALLKKYPK LEPEFVYGDY
PKYNSFRERK SATEKVYFYS NIMNIFKKSI SLADGRVIER PLIEVNEETG ESVWNKESDL
ATVRRVLSYP QVNVVKKVEE QNHGLDRGKP KGLFNANLSS KPKPNSNENL VGAKEYLDPK
KYGGYAGISN SFTVLVKGTI EKGAKKKITN VLEFQGISIL DRINYRKDKL NFLLEKGYKD
IELIIELPKY SLFELSDGSR RMLASILSTN NKRGEIHKGN QIFLSQKFVK LLYHAKRISN
TINENHRKYV ENHKKEFEEL FYYILEFNEN YVGAKKNGKL LNSAFQSWQN HSIDELCSSF
IGPTGSERKG LFELTSRGSA ADFEFLGVKI PRYRDYTPSS LLKDATLIHQ SVTGLYETRI
DLAKLGEG


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