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Protein

CRISPR-associated endonuclease/helicase Cas3

Gene

ygcB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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 sequences complementary to antecedent mobile elements and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). Cas3 plus Cascade participate in CRISPR interference, the third stage of CRISPR immunity.
Acts as an endonuclease, a 3'-5'exonuclease, and an ATP-dependent dsDNA helicase. Anneals and unwinds R-loops (in which crRNA binds the target DNA, displacing the noncomplementary strand). Unwinding requires ATP, annealing does not. Required along with the Cascade complex for resistance to bacteriophage lambda infection as well as the ability to cure CRISPR-encoding high-copy number plasmid. A Cas3-CasA fusion protein purified with the Cascade complex nicks target plasmid in the presence but not absence of Mg2+, and degrades plasmid fully in the presence of Mg2+ and ATP, suggesting the helicase activity is required for complete degradation.

Cofactori

Mg2+2 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi75 – 751MagnesiumSequence analysis
Metal bindingi160 – 1601MagnesiumSequence analysis

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi314 – 3218ATPPROSITE-ProRule annotation

GO - Molecular functioni

  • 3'-5'-exodeoxyribonuclease activity Source: EcoCyc
  • ATP binding Source: UniProtKB-KW
  • ATP-dependent DNA/RNA helicase activity Source: EcoCyc
  • ATP-dependent RNA helicase activity Source: GO_Central
  • DNA/RNA hybrid annealing activity Source: EcoCyc
  • double-stranded DNA binding Source: EcoCyc
  • magnesium ion binding Source: EcoCyc
  • single-stranded DNA endodeoxyribonuclease activity Source: EcoCyc

GO - Biological processi

  • defense response to virus Source: EcoCyc
  • DNA catabolic process, endonucleolytic Source: EcoCyc
  • DNA catabolic process, exonucleolytic Source: EcoCyc
  • RNA secondary structure unwinding Source: GO_Central
Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Exonuclease, Helicase, Hydrolase, Nuclease

Keywords - Biological processi

Antiviral defense

Keywords - Ligandi

ATP-binding, DNA-binding, Magnesium, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG12634-MONOMER.
ECOL316407:JW2731-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
CRISPR-associated endonuclease/helicase Cas3 (EC:3.1.-.-, EC:3.6.4.-)
Gene namesi
Name:ygcB
Synonyms:cas3
Ordered Locus Names:b2761, JW2731
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG12634. ygcB.

Pathology & Biotechi

Disruption phenotypei

Loss of plasmid silencing.1 Publication

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi74 – 741H → A: Loss of CRISPR immunity to lambda DNA and of CRISPR-mediated plasmid curing. 2 Publications
Mutagenesisi74 – 741H → G: 75% R-loop formation. 2 Publications
Mutagenesisi75 – 751D → A: Loss of CRISPR immunity to lambda DNA and of CRISPR-mediated plasmid curing. 2 Publications
Mutagenesisi75 – 751D → G: 10% R-loop formation. 2 Publications
Mutagenesisi78 – 781K → A: Loss of CRISPR immunity to lambda DNA and of CRISPR-mediated plasmid curing. 2 Publications
Mutagenesisi78 – 781K → L: Less than 5% R-loop formation, binds DNA normally. 100-fold greater senstivity to bacteriophage lambda. No effect on R-loop formation; when associated with L-320. 2 Publications
Mutagenesisi317 – 3182GS → SY: No effect on R-loop formation. Impaired R-loop unwinding. 1 Publication
Mutagenesisi320 – 3201K → L: Double R-loop formation. 2-4 fold decreased ATPase. No effect on R-loop formation; when associated with L-78. 2 Publications
Mutagenesisi320 – 3201K → N: Loss of CRISPR immunity to lambda DNA and of CRISPR-mediated plasmid curing. Nicks target plasmid DNA but does not degrade it. 2 Publications
Mutagenesisi452 – 4521D → N: Loss of CRISPR immunity to lambda DNA and of CRISPR-mediated plasmid curing. 1 Publication
Mutagenesisi455 – 4551H → L: Loss of R-loop unwinding. 1 Publication
Mutagenesisi483 – 4853SAT → AAA: Retains CRISPR immunity to lambda DNA and CRISPR-mediated plasmid curing. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 888888CRISPR-associated endonuclease/helicase Cas3PRO_0000207308Add
BLAST

Proteomic databases

PaxDbiP38036.
PRIDEiP38036.

Interactioni

Subunit structurei

Interacts with the CasA subunit of Cascade once Cascade has recognized target DNA.1 Publication

Protein-protein interaction databases

BioGridi4260740. 48 interactions.
IntActiP38036. 7 interactions.
STRINGi511145.b2761.

Structurei

3D structure databases

ProteinModelPortaliP38036.
SMRiP38036. Positions 25-777.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini20 – 231212HD Cas3-typePROSITE-ProRule annotationAdd
BLAST
Domaini301 – 504204Helicase ATP-bindingPROSITE-ProRule annotationAdd
BLAST
Domaini556 – 735180Helicase C-terminalPROSITE-ProRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi452 – 4554DEAH box

Domaini

Proteins of this family have an N-terminal nuclease domain and a C-terminal helicase/ATPase domain. In some CRISPR/Cas systems the domains are swapped, in others they are encoded separately.

Sequence similaritiesi

In the N-terminal section; belongs to the CRISPR-associated nuclease Cas3-HD family.Curated
In the central section; belongs to the CRISPR-associated helicase Cas3 family.Curated
Contains 1 HD Cas3-type domain.PROSITE-ProRule annotation
Contains 1 helicase ATP-binding domain.PROSITE-ProRule annotation
Contains 1 helicase C-terminal domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiENOG4105DTT. Bacteria.
COG1203. LUCA.
HOGENOMiHOG000224183.
InParanoidiP38036.
KOiK07012.
OMAiCWIRNTV.
OrthoDBiEOG6QCD7N.
PhylomeDBiP38036.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR006483. CRISPR-assoc_Cas3_HD.
IPR011545. DEAD/DEAH_box_helicase_dom.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR006474. Helicase_Cas3_CRISPR-ass_core.
IPR027417. P-loop_NTPase.
[Graphical view]
PfamiPF00270. DEAD. 1 hit.
PF00271. Helicase_C. 1 hit.
[Graphical view]
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 3 hits.
TIGRFAMsiTIGR01587. cas3_core. 1 hit.
TIGR01596. cas3_HD. 1 hit.
PROSITEiPS51643. HD_CAS3. 1 hit.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P38036-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEPFKYICHY WGKSSKSLTK GNDIHLLIYH CLDVAAVADC WWDQSVVLQN
60 70 80 90 100
TFCRNEMLSK QRVKAWLLFF IALHDIGKFD IRFQYKSAES WLKLNPATPS
110 120 130 140 150
LNGPSTQMCR KFNHGAAGLY WFNQDSLSEQ SLGDFFSFFD AAPHPYESWF
160 170 180 190 200
PWVEAVTGHH GFILHSQDQD KSRWEMPASL ASYAAQDKQA REEWISVLEA
210 220 230 240 250
LFLTPAGLSI NDIPPDCSSL LAGFCSLADW LGSWTTTNTF LFNEDAPSDI
260 270 280 290 300
NALRTYFQDR QQDASRVLEL SGLVSNKRCY EGVHALLDNG YQPRQLQVLV
310 320 330 340 350
DALPVAPGLT VIEAPTGSGK TETALAYAWK LIDQQIADSV IFALPTQATA
360 370 380 390 400
NAMLTRMEAS ASHLFSSPNL ILAHGNSRFN HLFQSIKSRA ITEQGQEEAW
410 420 430 440 450
VQCCQWLSQS NKKVFLGQIG VCTIDQVLIS VLPVKHRFIR GLGIGRSVLI
460 470 480 490 500
VDEVHAYDTY MNGLLEAVLK AQADVGGSVI LLSATLPMKQ KQKLLDTYGL
510 520 530 540 550
HTDPVENNSA YPLINWRGVN GAQRFDLLAH PEQLPPRFSI QPEPICLADM
560 570 580 590 600
LPDLTMLERM IAAANAGAQV CLICNLVDVA QVCYQRLKEL NNTQVDIDLF
610 620 630 640 650
HARFTLNDRR EKENRVISNF GKNGKRNVGR ILVATQVVEQ SLDVDFDWLI
660 670 680 690 700
TQHCPADLLF QRLGRLHRHH RKYRPAGFEI PVATILLPDG EGYGRHEHIY
710 720 730 740 750
SNVRVMWRTQ QHIEELNGAS LFFPDAYRQW LDSIYDDAEM DEPEWVGNGM
760 770 780 790 800
DKFESAECEK RFKARKVLQW AEEYSLQDND ETILAVTRDG EMSLPLLPYV
810 820 830 840 850
QTSSGKQLLD GQVYEDLSHE QQYEALALNR VNVPFTWKRS FSEVVDEDGL
860 870 880
LWLEGKQNLD GWVWQGNSIV ITYTGDEGMT RVIPANPK
Length:888
Mass (Da):100,545
Last modified:November 1, 1997 - v2
Checksum:i4CA3F5371B1BF0F2
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti118 – 1181G → R in Y07525 (PubMed:2005873).Curated
Sequence conflicti334 – 3352QQ → PL in Y07525 (PubMed:2005873).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U29579 Genomic DNA. Translation: AAA69271.1.
U00096 Genomic DNA. Translation: AAC75803.1.
AP009048 Genomic DNA. Translation: BAE76838.1.
Y07525 Genomic DNA. No translation available.
PIRiE65057.
RefSeqiNP_417241.1. NC_000913.3.
WP_000433152.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC75803; AAC75803; b2761.
BAE76838; BAE76838; BAE76838.
GeneIDi947229.
KEGGiecj:JW2731.
eco:b2761.
PATRICi32120934. VBIEscCol129921_2859.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U29579 Genomic DNA. Translation: AAA69271.1.
U00096 Genomic DNA. Translation: AAC75803.1.
AP009048 Genomic DNA. Translation: BAE76838.1.
Y07525 Genomic DNA. No translation available.
PIRiE65057.
RefSeqiNP_417241.1. NC_000913.3.
WP_000433152.1. NZ_LN832404.1.

3D structure databases

ProteinModelPortaliP38036.
SMRiP38036. Positions 25-777.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4260740. 48 interactions.
IntActiP38036. 7 interactions.
STRINGi511145.b2761.

Proteomic databases

PaxDbiP38036.
PRIDEiP38036.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75803; AAC75803; b2761.
BAE76838; BAE76838; BAE76838.
GeneIDi947229.
KEGGiecj:JW2731.
eco:b2761.
PATRICi32120934. VBIEscCol129921_2859.

Organism-specific databases

EchoBASEiEB2516.
EcoGeneiEG12634. ygcB.

Phylogenomic databases

eggNOGiENOG4105DTT. Bacteria.
COG1203. LUCA.
HOGENOMiHOG000224183.
InParanoidiP38036.
KOiK07012.
OMAiCWIRNTV.
OrthoDBiEOG6QCD7N.
PhylomeDBiP38036.

Enzyme and pathway databases

BioCyciEcoCyc:EG12634-MONOMER.
ECOL316407:JW2731-MONOMER.

Miscellaneous databases

PROiP38036.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR006483. CRISPR-assoc_Cas3_HD.
IPR011545. DEAD/DEAH_box_helicase_dom.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR006474. Helicase_Cas3_CRISPR-ass_core.
IPR027417. P-loop_NTPase.
[Graphical view]
PfamiPF00270. DEAD. 1 hit.
PF00271. Helicase_C. 1 hit.
[Graphical view]
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 3 hits.
TIGRFAMsiTIGR01587. cas3_core. 1 hit.
TIGR01596. cas3_HD. 1 hit.
PROSITEiPS51643. HD_CAS3. 1 hit.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  2. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  3. "Characterisation of the gene cysH and of its product phospho-adenylylsulphate reductase from Escherichia coli."
    Krone F.A., Westphal G., Schwenn J.D.
    Mol. Gen. Genet. 225:314-319(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-335.
    Strain: K12.
  4. "Intrinsic and extrinsic approaches for detecting genes in a bacterial genome."
    Borodovsky M., Rudd K.E., Koonin E.V.
    Nucleic Acids Res. 22:4756-4767(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION.
  5. Cited for: FUNCTION, DISRUPTION PHENOTYPE.
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  6. "Helicase dissociation and annealing of RNA-DNA hybrids by Escherichia coli Cas3 protein."
    Howard J.A., Delmas S., Ivancic-Bace I., Bolt E.L.
    Biochem. J. 439:85-95(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION AS A HELICASE, FUNCTION IN FORMING R-LOOPS, COFACTOR, DNA-BINDING, MUTAGENESIS OF HIS-74; ASP-75; LYS-78; 317-GLY-SER-318; LYS-320 AND HIS-455.
    Strain: K12 / MG1655 / ATCC 47076.
  7. "CRISPR immunity relies on the consecutive binding and degradation of negatively supercoiled invader DNA by Cascade and Cas3."
    Westra E.R., van Erp P.B., Kunne T., Wong S.P., Staals R.H., Seegers C.L., Bollen S., Jore M.M., Semenova E., Severinov K., de Vos W.M., Dame R.T., de Vries R., Brouns S.J., van der Oost J.
    Mol. Cell 46:595-605(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION AS AN ENDONUCLEASE, FUNCTION AS AN EXONUCLEASE, COFACTOR, INTERACTION WITH CASA, MUTAGENESIS OF HIS-74; ASP-75; LYS-78; LYS-320; ASP-452 AND 483-SER--THR-485.
    Strain: K12 / MG1655 / ATCC 47076.

Entry informationi

Entry nameiCAS3_ECOLI
AccessioniPrimary (citable) accession number: P38036
Secondary accession number(s): Q2MA68, Q46902
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1994
Last sequence update: November 1, 1997
Last modified: March 16, 2016
This is version 120 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.