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Protein

CRISPR system Cascade subunit CasD

Gene

casD

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).
A component of Cascade, which participates in CRISPR interference, the third stage of CRISPR immunity. Cascade binds both crRNA and in a sequence-specific manner negatively supercoiled dsDNA target. This leads to the formation of an R-loop in which the crRNA binds the target DNA, displacing the noncomplementary strand. Cas3 is recruited to Cascade, nicks target DNA and then unwinds and cleaves the target, leading to DNA degradation and invader neutralization. CasCDE alone is also able to form R-loops.

GO - Molecular functioni

  • DNA/RNA hybrid binding Source: EcoCyc
  • RNA binding Source: EcoCyc

GO - Biological processi

  • defense response to virus Source: EcoCyc
  • maintenance of CRISPR repeat elements Source: InterPro
Complete GO annotation...

Keywords - Biological processi

Antiviral defense

Enzyme and pathway databases

BioCyciEcoCyc:G7427-MONOMER.
ECOL316407:JW5844-MONOMER.
MetaCyc:G7427-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
CRISPR system Cascade subunit CasD
Gene namesi
Name:casD
Synonyms:cas5, ygcI
Ordered Locus Names:b2757, JW5844
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG13116. casD.

Subcellular locationi

GO - Cellular componenti

  • protein complex Source: EcoCyc
Complete GO annotation...

Pathology & Biotechi

Disruption phenotypei

Loss of resistance to bacteriophage lambda infection, loss of plasmid silencing. Decreased levels of crRNA.3 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 224224CRISPR system Cascade subunit CasDPRO_0000013896Add
BLAST

Proteomic databases

PaxDbiQ46898.

Expressioni

Inductioni

Repressed by H-NS, activated by LeuO. Activated by the BaeSR two-component regulatory system, possibly due to envelope stress. Part of the casABCDE-ygbT-ygbF operon.3 Publications

Interactioni

Subunit structurei

Part of the Cascade ribonucleoprotein complex, with stoichiometry CasA1,CasB2,CasC6,CasD1,CasE(1)-crRNA1. Interacts directly with CasA and CasC. Stable subcomplexes of CasBCDE-crRNA and CasCDE-crRNA also form, both of which are able to bind target dsDNA, and at least CasCDE is able to form R-loops. CasCDE and CasCE complexes have endonuclease activity. Binding of target ssRNA or dsDNA causes a conformational change in the Cascade complex.6 Publications

Protein-protein interaction databases

BioGridi4261109. 689 interactions.
DIPiDIP-12125N.
STRINGi511145.b2757.

Structurei

Secondary structure

1
224
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 1413Combined sources
Beta strandi22 – 254Combined sources
Helixi33 – 4311Combined sources
Helixi51 – 6010Combined sources
Beta strandi61 – 688Combined sources
Beta strandi70 – 723Combined sources
Beta strandi75 – 773Combined sources
Beta strandi80 – 8910Combined sources
Beta strandi92 – 987Combined sources
Beta strandi102 – 12221Combined sources
Helixi130 – 1389Combined sources
Beta strandi146 – 1483Combined sources
Beta strandi157 – 16610Combined sources
Helixi167 – 1715Combined sources
Beta strandi174 – 1763Combined sources
Beta strandi181 – 1855Combined sources
Beta strandi193 – 2019Combined sources
Beta strandi202 – 2043Combined sources
Beta strandi207 – 21610Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4QYZX-ray3.03J1-224[»]
4TVXX-ray3.24H/T1-224[»]
4U7UX-ray3.00K/W1-224[»]
5CD4X-ray3.20H/T1-224[»]
5H9EX-ray3.21J1-224[»]
5H9FX-ray2.45J1-224[»]
ProteinModelPortaliQ46898.
SMRiQ46898. Positions 1-218.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4108VWQ. Bacteria.
ENOG4111JEJ. LUCA.
HOGENOMiHOG000015840.
InParanoidiQ46898.
KOiK19125.
OMAiEGICYWD.
OrthoDBiEOG6WX4S7.

Family and domain databases

InterProiIPR021124. CRISPR-assoc_prot_Cas5.
IPR013422. CRISPR-assoc_prot_Cas5_N.
IPR010147. CRISPR-assoc_prot_CasD.
[Graphical view]
PfamiPF09704. Cas_Cas5d. 1 hit.
[Graphical view]
TIGRFAMsiTIGR01868. casD_Cas5e. 1 hit.
TIGR02593. CRISPR_cas5. 1 hit.

Sequencei

Sequence statusi: Complete.

Q46898-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRSYLILRLA GPMQAWGQPT FEGTRPTGRF PTRSGLLGLL GACLGIQRDD
60 70 80 90 100
TSSLQALSES VQFAVRCDEL ILDDRRVSVT GLRDYHTVLG AREDYRGLKS
110 120 130 140 150
HETIQTWREY LCDASFTVAL WLTPHATMVI SELEKAVLKP RYTPYLGRRS
160 170 180 190 200
CPLTHPLFLG TCQASDPQKA LLNYEPVGGD IYSEESVTGH HLKFTARDEP
210 220
MITLPRQFAS REWYVIKGGM DVSQ
Length:224
Mass (Da):25,209
Last modified:December 1, 2000 - v2
Checksum:i1C42CC009B317D68
GO

Sequence cautioni

The sequence AAA69267.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Mass spectrometryi

Molecular mass is 25210.4±3.8 Da from positions 1 - 224. 1 Publication

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U29579 Genomic DNA. Translation: AAA69267.1. Different initiation.
U00096 Genomic DNA. Translation: AAC75799.2.
AP009048 Genomic DNA. Translation: BAE76834.1.
PIRiA65057.
RefSeqiNP_417237.2. NC_000913.3.
WP_001334996.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC75799; AAC75799; b2757.
BAE76834; BAE76834; BAE76834.
GeneIDi947225.
KEGGiecj:JW5844.
eco:b2757.
PATRICi32120924. VBIEscCol129921_2854.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U29579 Genomic DNA. Translation: AAA69267.1. Different initiation.
U00096 Genomic DNA. Translation: AAC75799.2.
AP009048 Genomic DNA. Translation: BAE76834.1.
PIRiA65057.
RefSeqiNP_417237.2. NC_000913.3.
WP_001334996.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4QYZX-ray3.03J1-224[»]
4TVXX-ray3.24H/T1-224[»]
4U7UX-ray3.00K/W1-224[»]
5CD4X-ray3.20H/T1-224[»]
5H9EX-ray3.21J1-224[»]
5H9FX-ray2.45J1-224[»]
ProteinModelPortaliQ46898.
SMRiQ46898. Positions 1-218.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4261109. 689 interactions.
DIPiDIP-12125N.
STRINGi511145.b2757.

Proteomic databases

PaxDbiQ46898.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75799; AAC75799; b2757.
BAE76834; BAE76834; BAE76834.
GeneIDi947225.
KEGGiecj:JW5844.
eco:b2757.
PATRICi32120924. VBIEscCol129921_2854.

Organism-specific databases

EchoBASEiEB2917.
EcoGeneiEG13116. casD.

Phylogenomic databases

eggNOGiENOG4108VWQ. Bacteria.
ENOG4111JEJ. LUCA.
HOGENOMiHOG000015840.
InParanoidiQ46898.
KOiK19125.
OMAiEGICYWD.
OrthoDBiEOG6WX4S7.

Enzyme and pathway databases

BioCyciEcoCyc:G7427-MONOMER.
ECOL316407:JW5844-MONOMER.
MetaCyc:G7427-MONOMER.

Miscellaneous databases

PROiQ46898.

Family and domain databases

InterProiIPR021124. CRISPR-assoc_prot_Cas5.
IPR013422. CRISPR-assoc_prot_Cas5_N.
IPR010147. CRISPR-assoc_prot_CasD.
[Graphical view]
PfamiPF09704. Cas_Cas5d. 1 hit.
[Graphical view]
TIGRFAMsiTIGR01868. casD_Cas5e. 1 hit.
TIGR02593. CRISPR_cas5. 1 hit.
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. Cited for: SUBUNIT, DISRUPTION PHENOTYPE.
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  4. "Involvement of the leucine response transcription factor LeuO in regulation of the genes for sulfa drug efflux."
    Shimada T., Yamamoto K., Ishihama A.
    J. Bacteriol. 191:4562-4571(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: OPERON STRUCTURE, INDUCTION BY LEUO.
    Strain: K12 / BW25113.
  5. "Identification and characterization of E. coli CRISPR-cas promoters and their silencing by H-NS."
    Pul U., Wurm R., Arslan Z., Geissen R., Hofmann N., Wagner R.
    Mol. Microbiol. 75:1495-1512(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: INDUCTION BY H-NS.
    Strain: K12.
  6. "Envelope stress is a trigger of CRISPR RNA-mediated DNA silencing in Escherichia coli."
    Perez-Rodriguez R., Haitjema C., Huang Q., Nam K.H., Bernardis S., Ke A., DeLisa M.P.
    Mol. Microbiol. 79:584-599(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH CASC, SUBUNIT, INDUCTION BY BAER, ROLE IN PLASMID SILENCING, DISRUPTION PHENOTYPE.
    Strain: K12 / BW25113.
  7. Cited for: FUNCTION IN CASCADE, MASS SPECTROMETRY, SUBUNIT, STRUCTURE BY ELECTRON MICROSCOPY, INTERACTION WITH CASD, DISRUPTION PHENOTYPE.
    Strain: K12.
  8. "Structures of the RNA-guided surveillance complex from a bacterial immune system."
    Wiedenheft B., Lander G.C., Zhou K., Jore M.M., Brouns S.J., van der Oost J., Doudna J.A., Nogales E.
    Nature 477:486-489(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY ELECTRON MICROSCOPY OF CASCADE WITH AND WITHOUT TARGET RNA, INTERACTION WITH CASA AND CASC.
    Strain: K12.
  9. "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 IN R-LOOP FORMATION, SUBUNIT.
    Strain: K12 / MG1655 / ATCC 47076.
  10. "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: SUBUNIT, CASCADE DNA-BINDING.
    Strain: K12 / MG1655 / ATCC 47076.

Entry informationi

Entry nameiCAS5_ECOLI
AccessioniPrimary (citable) accession number: Q46898
Secondary accession number(s): Q2MA72
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 1, 2000
Last sequence update: December 1, 2000
Last modified: July 6, 2016
This is version 99 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.