CAS3_ECOLI
ID CAS3_ECOLI Reviewed; 888 AA.
AC P38036; Q2MA68; Q46902;
DT 01-OCT-1994, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 2.
DT 03-AUG-2022, entry version 149.
DE RecName: Full=CRISPR-associated endonuclease/helicase Cas3;
DE EC=3.1.-.-;
DE EC=3.6.4.-;
GN Name=ygcB; Synonyms=cas3; OrderedLocusNames=b2761, JW2731;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-335.
RC STRAIN=K12;
RX PubMed=2005873; DOI=10.1007/bf00269864;
RA Krone F.A., Westphal G., Schwenn J.D.;
RT "Characterisation of the gene cysH and of its product phospho-
RT adenylylsulphate reductase from Escherichia coli.";
RL Mol. Gen. Genet. 225:314-319(1991).
RN [4]
RP IDENTIFICATION.
RX PubMed=7984428; DOI=10.1093/nar/22.22.4756;
RA Borodovsky M., Rudd K.E., Koonin E.V.;
RT "Intrinsic and extrinsic approaches for detecting genes in a bacterial
RT genome.";
RL Nucleic Acids Res. 22:4756-4767(1994).
RN [5]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=18703739; DOI=10.1126/science.1159689;
RA Brouns S.J., Jore M.M., Lundgren M., Westra E.R., Slijkhuis R.J.,
RA Snijders A.P., Dickman M.J., Makarova K.S., Koonin E.V., van der Oost J.;
RT "Small CRISPR RNAs guide antiviral defense in prokaryotes.";
RL Science 321:960-964(2008).
RN [6]
RP FUNCTION AS A HELICASE, FUNCTION IN FORMING R-LOOPS, COFACTOR, DNA-BINDING,
RP AND MUTAGENESIS OF HIS-74; ASP-75; LYS-78; 317-GLY-SER-318; LYS-320 AND
RP HIS-455.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=21699496; DOI=10.1042/bj20110901;
RA Howard J.A., Delmas S., Ivancic-Bace I., Bolt E.L.;
RT "Helicase dissociation and annealing of RNA-DNA hybrids by Escherichia coli
RT Cas3 protein.";
RL Biochem. J. 439:85-95(2011).
RN [7]
RP FUNCTION AS AN ENDONUCLEASE, FUNCTION AS AN EXONUCLEASE, COFACTOR,
RP INTERACTION WITH CASA, AND MUTAGENESIS OF HIS-74; ASP-75; LYS-78; LYS-320;
RP ASP-452 AND 483-SER--THR-485.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=22521689; DOI=10.1016/j.molcel.2012.03.018;
RA Westra E.R., van Erp P.B., Kunne T., Wong S.P., Staals R.H., Seegers C.L.,
RA Bollen S., Jore M.M., Semenova E., Severinov K., de Vos W.M., Dame R.T.,
RA de Vries R., Brouns S.J., van der Oost J.;
RT "CRISPR immunity relies on the consecutive binding and degradation of
RT negatively supercoiled invader DNA by Cascade and Cas3.";
RL Mol. Cell 46:595-605(2012).
CC -!- FUNCTION: CRISPR (clustered regularly interspaced short palindromic
CC repeat), is an adaptive immune system that provides protection against
CC mobile genetic elements (viruses, transposable elements and conjugative
CC plasmids). CRISPR clusters contain sequences complementary to
CC antecedent mobile elements and target invading nucleic acids. CRISPR
CC clusters are transcribed and processed into CRISPR RNA (crRNA). Cas3
CC plus Cascade participate in CRISPR interference, the third stage of
CC CRISPR immunity.
CC -!- FUNCTION: Acts as an endonuclease, a 3'-5'exonuclease, and an ATP-
CC dependent dsDNA helicase. Anneals and unwinds R-loops (in which crRNA
CC binds the target DNA, displacing the noncomplementary strand).
CC Unwinding requires ATP, annealing does not. Required along with the
CC Cascade complex for resistance to bacteriophage lambda infection as
CC well as the ability to cure CRISPR-encoding high-copy number plasmid. A
CC Cas3-CasA fusion protein purified with the Cascade complex nicks target
CC plasmid in the presence but not absence of Mg(2+), and degrades plasmid
CC fully in the presence of Mg(2+) and ATP, suggesting the helicase
CC activity is required for complete degradation.
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:21699496, ECO:0000269|PubMed:22521689};
CC -!- SUBUNIT: Interacts with the CasA subunit of Cascade once Cascade has
CC recognized target DNA. {ECO:0000269|PubMed:22521689}.
CC -!- DOMAIN: Proteins of this family have an N-terminal nuclease domain and
CC a C-terminal helicase/ATPase domain. In some CRISPR/Cas systems the
CC domains are swapped, in others they are encoded separately.
CC -!- DISRUPTION PHENOTYPE: Loss of plasmid silencing.
CC {ECO:0000269|PubMed:18703739}.
CC -!- SIMILARITY: In the N-terminal section; belongs to the CRISPR-associated
CC nuclease Cas3-HD family. {ECO:0000305}.
CC -!- SIMILARITY: In the central section; belongs to the CRISPR-associated
CC helicase Cas3 family. {ECO:0000305}.
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DR EMBL; U29579; AAA69271.1; -; Genomic_DNA.
DR EMBL; U00096; AAC75803.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE76838.1; -; Genomic_DNA.
DR EMBL; Y07525; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR PIR; E65057; E65057.
DR RefSeq; NP_417241.1; NC_000913.3.
DR RefSeq; WP_000433152.1; NZ_LN832404.1.
DR AlphaFoldDB; P38036; -.
DR SMR; P38036; -.
DR BioGRID; 4260740; 78.
DR IntAct; P38036; 7.
DR STRING; 511145.b2761; -.
DR PaxDb; P38036; -.
DR PRIDE; P38036; -.
DR EnsemblBacteria; AAC75803; AAC75803; b2761.
DR EnsemblBacteria; BAE76838; BAE76838; BAE76838.
DR GeneID; 947229; -.
DR KEGG; ecj:JW2731; -.
DR KEGG; eco:b2761; -.
DR PATRIC; fig|1411691.4.peg.3976; -.
DR EchoBASE; EB2516; -.
DR eggNOG; COG1203; Bacteria.
DR HOGENOM; CLU_013924_2_0_6; -.
DR InParanoid; P38036; -.
DR OMA; CVCWIRN; -.
DR PhylomeDB; P38036; -.
DR BioCyc; EcoCyc:EG12634-MON; -.
DR PRO; PR:P38036; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0008296; F:3'-5'-exodeoxyribonuclease activity; IDA:EcoCyc.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0033677; F:DNA/RNA helicase activity; IDA:EcoCyc.
DR GO; GO:0097098; F:DNA/RNA hybrid annealing activity; IDA:EcoCyc.
DR GO; GO:0003690; F:double-stranded DNA binding; IDA:EcoCyc.
DR GO; GO:0000287; F:magnesium ion binding; EXP:EcoCyc.
DR GO; GO:0003723; F:RNA binding; IBA:GO_Central.
DR GO; GO:0003724; F:RNA helicase activity; IBA:GO_Central.
DR GO; GO:0033592; F:RNA strand annealing activity; IBA:GO_Central.
DR GO; GO:0000014; F:single-stranded DNA endodeoxyribonuclease activity; IDA:EcoCyc.
DR GO; GO:0051607; P:defense response to virus; IDA:EcoCyc.
DR GO; GO:0000737; P:DNA catabolic process, endonucleolytic; IDA:EcoCyc.
DR GO; GO:0000738; P:DNA catabolic process, exonucleolytic; IDA:EcoCyc.
DR GO; GO:0000027; P:ribosomal large subunit assembly; IBA:GO_Central.
DR Gene3D; 1.10.3210.30; -; 1.
DR Gene3D; 3.40.50.300; -; 2.
DR InterPro; IPR006483; CRISPR-assoc_Cas3_HD.
DR InterPro; IPR038257; CRISPR-assoc_Cas3_HD_sf.
DR InterPro; IPR011545; DEAD/DEAH_box_helicase_dom.
DR InterPro; IPR014001; Helicase_ATP-bd.
DR InterPro; IPR001650; Helicase_C.
DR InterPro; IPR006474; Helicase_Cas3_CRISPR-ass_core.
DR InterPro; IPR027417; P-loop_NTPase.
DR Pfam; PF00270; DEAD; 1.
DR Pfam; PF18019; HD_6; 1.
DR Pfam; PF00271; Helicase_C; 1.
DR SMART; SM00487; DEXDc; 1.
DR SMART; SM00490; HELICc; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR TIGRFAMs; TIGR01587; cas3_core; 1.
DR TIGRFAMs; TIGR01596; cas3_HD; 1.
DR PROSITE; PS51643; HD_CAS3; 1.
DR PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
DR PROSITE; PS51194; HELICASE_CTER; 1.
PE 1: Evidence at protein level;
KW Antiviral defense; ATP-binding; DNA-binding; Endonuclease; Exonuclease;
KW Helicase; Hydrolase; Magnesium; Metal-binding; Nuclease;
KW Nucleotide-binding; Reference proteome.
FT CHAIN 1..888
FT /note="CRISPR-associated endonuclease/helicase Cas3"
FT /id="PRO_0000207308"
FT DOMAIN 20..231
FT /note="HD Cas3-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00974"
FT DOMAIN 301..504
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 556..735
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT MOTIF 452..455
FT /note="DEAH box"
FT BINDING 75
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255"
FT BINDING 160
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255"
FT BINDING 314..321
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT MUTAGEN 74
FT /note="H->A: Loss of CRISPR immunity to lambda DNA and of
FT CRISPR-mediated plasmid curing."
FT /evidence="ECO:0000269|PubMed:21699496,
FT ECO:0000269|PubMed:22521689"
FT MUTAGEN 74
FT /note="H->G: 75% R-loop formation."
FT /evidence="ECO:0000269|PubMed:21699496,
FT ECO:0000269|PubMed:22521689"
FT MUTAGEN 75
FT /note="D->A: Loss of CRISPR immunity to lambda DNA and of
FT CRISPR-mediated plasmid curing."
FT /evidence="ECO:0000269|PubMed:21699496,
FT ECO:0000269|PubMed:22521689"
FT MUTAGEN 75
FT /note="D->G: 10% R-loop formation."
FT /evidence="ECO:0000269|PubMed:21699496,
FT ECO:0000269|PubMed:22521689"
FT MUTAGEN 78
FT /note="K->A: Loss of CRISPR immunity to lambda DNA and of
FT CRISPR-mediated plasmid curing."
FT /evidence="ECO:0000269|PubMed:21699496,
FT ECO:0000269|PubMed:22521689"
FT MUTAGEN 78
FT /note="K->L: Less than 5% R-loop formation, binds DNA
FT normally. 100-fold greater sensitivity to bacteriophage
FT lambda. No effect on R-loop formation; when associated with
FT L-320."
FT /evidence="ECO:0000269|PubMed:21699496,
FT ECO:0000269|PubMed:22521689"
FT MUTAGEN 317..318
FT /note="GS->SY: No effect on R-loop formation. Impaired R-
FT loop unwinding."
FT /evidence="ECO:0000269|PubMed:21699496"
FT MUTAGEN 320
FT /note="K->L: Double R-loop formation. 2-4 fold decreased
FT ATPase. No effect on R-loop formation; when associated with
FT L-78."
FT /evidence="ECO:0000269|PubMed:21699496,
FT ECO:0000269|PubMed:22521689"
FT MUTAGEN 320
FT /note="K->N: Loss of CRISPR immunity to lambda DNA and of
FT CRISPR-mediated plasmid curing. Nicks target plasmid DNA
FT but does not degrade it."
FT /evidence="ECO:0000269|PubMed:21699496,
FT ECO:0000269|PubMed:22521689"
FT MUTAGEN 452
FT /note="D->N: Loss of CRISPR immunity to lambda DNA and of
FT CRISPR-mediated plasmid curing."
FT /evidence="ECO:0000269|PubMed:22521689"
FT MUTAGEN 455
FT /note="H->L: Loss of R-loop unwinding."
FT /evidence="ECO:0000269|PubMed:21699496"
FT MUTAGEN 483..485
FT /note="SAT->AAA: Retains CRISPR immunity to lambda DNA and
FT CRISPR-mediated plasmid curing."
FT /evidence="ECO:0000269|PubMed:22521689"
FT CONFLICT 118
FT /note="G -> R (in Ref. 3; Y07525)"
FT /evidence="ECO:0000305"
FT CONFLICT 334..335
FT /note="QQ -> PL (in Ref. 3; Y07525)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 888 AA; 100545 MW; 4CA3F5371B1BF0F2 CRC64;
MEPFKYICHY WGKSSKSLTK GNDIHLLIYH CLDVAAVADC WWDQSVVLQN TFCRNEMLSK
QRVKAWLLFF IALHDIGKFD IRFQYKSAES WLKLNPATPS LNGPSTQMCR KFNHGAAGLY
WFNQDSLSEQ SLGDFFSFFD AAPHPYESWF PWVEAVTGHH GFILHSQDQD KSRWEMPASL
ASYAAQDKQA REEWISVLEA LFLTPAGLSI NDIPPDCSSL LAGFCSLADW LGSWTTTNTF
LFNEDAPSDI NALRTYFQDR QQDASRVLEL SGLVSNKRCY EGVHALLDNG YQPRQLQVLV
DALPVAPGLT VIEAPTGSGK TETALAYAWK LIDQQIADSV IFALPTQATA NAMLTRMEAS
ASHLFSSPNL ILAHGNSRFN HLFQSIKSRA ITEQGQEEAW VQCCQWLSQS NKKVFLGQIG
VCTIDQVLIS VLPVKHRFIR GLGIGRSVLI VDEVHAYDTY MNGLLEAVLK AQADVGGSVI
LLSATLPMKQ KQKLLDTYGL HTDPVENNSA YPLINWRGVN GAQRFDLLAH PEQLPPRFSI
QPEPICLADM LPDLTMLERM IAAANAGAQV CLICNLVDVA QVCYQRLKEL NNTQVDIDLF
HARFTLNDRR EKENRVISNF GKNGKRNVGR ILVATQVVEQ SLDVDFDWLI TQHCPADLLF
QRLGRLHRHH RKYRPAGFEI PVATILLPDG EGYGRHEHIY SNVRVMWRTQ QHIEELNGAS
LFFPDAYRQW LDSIYDDAEM DEPEWVGNGM DKFESAECEK RFKARKVLQW AEEYSLQDND
ETILAVTRDG EMSLPLLPYV QTSSGKQLLD GQVYEDLSHE QQYEALALNR VNVPFTWKRS
FSEVVDEDGL LWLEGKQNLD GWVWQGNSIV ITYTGDEGMT RVIPANPK
