CAS5_ECOLI
ID CAS5_ECOLI Reviewed; 224 AA.
AC Q46898; Q2MA72;
DT 01-DEC-2000, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2000, sequence version 2.
DT 03-AUG-2022, entry version 128.
DE RecName: Full=CRISPR system Cascade subunit CasD;
GN Name=casD; Synonyms=cas5, ygcI; OrderedLocusNames=b2757, JW5844;
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 SUBUNIT, 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 [4]
RP OPERON STRUCTURE, AND INDUCTION BY LEUO.
RC STRAIN=K12 / BW25113;
RX PubMed=19429622; DOI=10.1128/jb.00108-09;
RA Shimada T., Yamamoto K., Ishihama A.;
RT "Involvement of the leucine response transcription factor LeuO in
RT regulation of the genes for sulfa drug efflux.";
RL J. Bacteriol. 191:4562-4571(2009).
RN [5]
RP INDUCTION BY H-NS.
RC STRAIN=K12;
RX PubMed=20132443; DOI=10.1111/j.1365-2958.2010.07073.x;
RA Pul U., Wurm R., Arslan Z., Geissen R., Hofmann N., Wagner R.;
RT "Identification and characterization of E. coli CRISPR-cas promoters and
RT their silencing by H-NS.";
RL Mol. Microbiol. 75:1495-1512(2010).
RN [6]
RP INTERACTION WITH CASC, SUBUNIT, INDUCTION BY BAER, ROLE IN PLASMID
RP SILENCING, AND DISRUPTION PHENOTYPE.
RC STRAIN=K12 / BW25113;
RX PubMed=21255106; DOI=10.1111/j.1365-2958.2010.07482.x;
RA Perez-Rodriguez R., Haitjema C., Huang Q., Nam K.H., Bernardis S., Ke A.,
RA DeLisa M.P.;
RT "Envelope stress is a trigger of CRISPR RNA-mediated DNA silencing in
RT Escherichia coli.";
RL Mol. Microbiol. 79:584-599(2011).
RN [7]
RP FUNCTION IN CASCADE, MASS SPECTROMETRY, SUBUNIT, STRUCTURE BY ELECTRON
RP MICROSCOPY, INTERACTION WITH CASD, AND DISRUPTION PHENOTYPE.
RC STRAIN=K12;
RX PubMed=21460843; DOI=10.1038/nsmb.2019;
RA Jore M.M., Lundgren M., van Duijn E., Bultema J.B., Westra E.R.,
RA Waghmare S.P., Wiedenheft B., Pul U., Wurm R., Wagner R., Beijer M.R.,
RA Barendregt A., Zhou K., Snijders A.P., Dickman M.J., Doudna J.A.,
RA Boekema E.J., Heck A.J., van der Oost J., Brouns S.J.;
RT "Structural basis for CRISPR RNA-guided DNA recognition by Cascade.";
RL Nat. Struct. Mol. Biol. 18:529-536(2011).
RN [8]
RP STRUCTURE BY ELECTRON MICROSCOPY OF CASCADE WITH AND WITHOUT TARGET RNA,
RP AND INTERACTION WITH CASA AND CASC.
RC STRAIN=K12;
RX PubMed=21938068; DOI=10.1038/nature10402;
RA Wiedenheft B., Lander G.C., Zhou K., Jore M.M., Brouns S.J.,
RA van der Oost J., Doudna J.A., Nogales E.;
RT "Structures of the RNA-guided surveillance complex from a bacterial immune
RT system.";
RL Nature 477:486-489(2011).
RN [9]
RP FUNCTION IN R-LOOP FORMATION, AND SUBUNIT.
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 [10]
RP SUBUNIT, AND CASCADE DNA-BINDING.
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).
CC -!- FUNCTION: A component of Cascade, which participates in CRISPR
CC interference, the third stage of CRISPR immunity. Cascade binds both
CC crRNA and in a sequence-specific manner negatively supercoiled dsDNA
CC target. This leads to the formation of an R-loop in which the crRNA
CC binds the target DNA, displacing the noncomplementary strand. Cas3 is
CC recruited to Cascade, nicks target DNA and then unwinds and cleaves the
CC target, leading to DNA degradation and invader neutralization. CasCDE
CC alone is also able to form R-loops.
CC -!- SUBUNIT: Part of the Cascade ribonucleoprotein complex, with
CC stoichiometry CasA(1),CasB(2),CasC(6),CasD(1),CasE(1)-crRNA(1).
CC Interacts directly with CasA and CasC. Stable subcomplexes of CasBCDE-
CC crRNA and CasCDE-crRNA also form, both of which are able to bind target
CC dsDNA, and at least CasCDE is able to form R-loops. CasCDE and CasCE
CC complexes have endonuclease activity. Binding of target ssRNA or dsDNA
CC causes a conformational change in the Cascade complex.
CC {ECO:0000269|PubMed:18703739, ECO:0000269|PubMed:21255106,
CC ECO:0000269|PubMed:21460843, ECO:0000269|PubMed:21699496,
CC ECO:0000269|PubMed:21938068, ECO:0000269|PubMed:22521689}.
CC -!- INDUCTION: Repressed by H-NS, activated by LeuO. Activated by the BaeSR
CC two-component regulatory system, possibly due to envelope stress. Part
CC of the casABCDE-ygbT-ygbF operon. {ECO:0000269|PubMed:19429622,
CC ECO:0000269|PubMed:20132443, ECO:0000269|PubMed:21255106}.
CC -!- MASS SPECTROMETRY: Mass=25210.4; Mass_error=3.8; Method=Unknown;
CC Evidence={ECO:0000269|PubMed:21460843};
CC -!- DISRUPTION PHENOTYPE: Loss of resistance to bacteriophage lambda
CC infection, loss of plasmid silencing. Decreased levels of crRNA.
CC {ECO:0000269|PubMed:18703739, ECO:0000269|PubMed:21255106,
CC ECO:0000269|PubMed:21460843}.
CC -!- SIMILARITY: Belongs to the CRISPR-associated protein Cas5 family.
CC Subtype I-E/Ecoli subfamily. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAA69267.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; U29579; AAA69267.1; ALT_INIT; Genomic_DNA.
DR EMBL; U00096; AAC75799.2; -; Genomic_DNA.
DR EMBL; AP009048; BAE76834.1; -; Genomic_DNA.
DR PIR; A65057; A65057.
DR RefSeq; NP_417237.2; NC_000913.3.
DR RefSeq; WP_001334996.1; NZ_LN832404.1.
DR PDB; 4QYZ; X-ray; 3.03 A; J=1-224.
DR PDB; 4TVX; X-ray; 3.24 A; H/T=1-224.
DR PDB; 4U7U; X-ray; 3.00 A; K/W=1-224.
DR PDB; 5CD4; X-ray; 3.20 A; H/T=1-224.
DR PDB; 5H9E; X-ray; 3.21 A; J=1-224.
DR PDB; 5H9F; X-ray; 2.45 A; J=1-224.
DR PDBsum; 4QYZ; -.
DR PDBsum; 4TVX; -.
DR PDBsum; 4U7U; -.
DR PDBsum; 5CD4; -.
DR PDBsum; 5H9E; -.
DR PDBsum; 5H9F; -.
DR AlphaFoldDB; Q46898; -.
DR SMR; Q46898; -.
DR BioGRID; 4261109; 689.
DR ComplexPortal; CPX-1005; Cascade complex.
DR DIP; DIP-12125N; -.
DR IntAct; Q46898; 4.
DR STRING; 511145.b2757; -.
DR PaxDb; Q46898; -.
DR PRIDE; Q46898; -.
DR EnsemblBacteria; AAC75799; AAC75799; b2757.
DR EnsemblBacteria; BAE76834; BAE76834; BAE76834.
DR GeneID; 947225; -.
DR KEGG; ecj:JW5844; -.
DR KEGG; eco:b2757; -.
DR PATRIC; fig|1411691.4.peg.3981; -.
DR EchoBASE; EB2917; -.
DR eggNOG; ENOG502ZBPB; Bacteria.
DR HOGENOM; CLU_084726_0_0_6; -.
DR InParanoid; Q46898; -.
DR OMA; EGICYWD; -.
DR PhylomeDB; Q46898; -.
DR BioCyc; EcoCyc:G7427-MON; -.
DR BioCyc; MetaCyc:G7427-MON; -.
DR PRO; PR:Q46898; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0032991; C:protein-containing complex; IDA:EcoCyc.
DR GO; GO:0071667; F:DNA/RNA hybrid binding; IDA:EcoCyc.
DR GO; GO:0003723; F:RNA binding; IDA:EcoCyc.
DR GO; GO:0099048; P:CRISPR-cas system; IDA:ComplexPortal.
DR GO; GO:0051607; P:defense response to virus; IDA:EcoCyc.
DR GO; GO:0043571; P:maintenance of CRISPR repeat elements; IEA:InterPro.
DR InterPro; IPR021124; CRISPR-assoc_prot_Cas5.
DR InterPro; IPR013422; CRISPR-assoc_prot_Cas5_N.
DR InterPro; IPR010147; CRISPR-assoc_prot_CasD.
DR Pfam; PF09704; Cas_Cas5d; 1.
DR TIGRFAMs; TIGR01868; casD_Cas5e; 1.
DR TIGRFAMs; TIGR02593; CRISPR_cas5; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Antiviral defense; Reference proteome.
FT CHAIN 1..224
FT /note="CRISPR system Cascade subunit CasD"
FT /id="PRO_0000013896"
FT STRAND 2..14
FT /evidence="ECO:0007829|PDB:5H9F"
FT STRAND 22..25
FT /evidence="ECO:0007829|PDB:5H9F"
FT HELIX 33..43
FT /evidence="ECO:0007829|PDB:5H9F"
FT HELIX 51..60
FT /evidence="ECO:0007829|PDB:5H9F"
FT STRAND 61..68
FT /evidence="ECO:0007829|PDB:5H9F"
FT STRAND 70..72
FT /evidence="ECO:0007829|PDB:5H9F"
FT STRAND 75..77
FT /evidence="ECO:0007829|PDB:5H9F"
FT STRAND 80..89
FT /evidence="ECO:0007829|PDB:5H9F"
FT STRAND 92..98
FT /evidence="ECO:0007829|PDB:5H9F"
FT STRAND 102..122
FT /evidence="ECO:0007829|PDB:5H9F"
FT HELIX 130..138
FT /evidence="ECO:0007829|PDB:5H9F"
FT STRAND 146..148
FT /evidence="ECO:0007829|PDB:5H9F"
FT STRAND 157..166
FT /evidence="ECO:0007829|PDB:5H9F"
FT HELIX 167..171
FT /evidence="ECO:0007829|PDB:5H9F"
FT STRAND 174..176
FT /evidence="ECO:0007829|PDB:5H9F"
FT STRAND 181..185
FT /evidence="ECO:0007829|PDB:5H9F"
FT STRAND 193..201
FT /evidence="ECO:0007829|PDB:5H9F"
FT STRAND 202..204
FT /evidence="ECO:0007829|PDB:5CD4"
FT STRAND 207..216
FT /evidence="ECO:0007829|PDB:5H9F"
SQ SEQUENCE 224 AA; 25209 MW; 1C42CC009B317D68 CRC64;
MRSYLILRLA GPMQAWGQPT FEGTRPTGRF PTRSGLLGLL GACLGIQRDD TSSLQALSES
VQFAVRCDEL ILDDRRVSVT GLRDYHTVLG AREDYRGLKS HETIQTWREY LCDASFTVAL
WLTPHATMVI SELEKAVLKP RYTPYLGRRS CPLTHPLFLG TCQASDPQKA LLNYEPVGGD
IYSEESVTGH HLKFTARDEP MITLPRQFAS REWYVIKGGM DVSQ
