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Protein

CRISPR system Cascade subunit CasD

Gene

casD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: -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

Keywordsi

Biological processAntiviral defense

Enzyme and pathway databases

BioCyciEcoCyc:G7427-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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi

Organism-specific databases

EcoGeneiEG13116 casD

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)DescriptionActionsGraphical viewLength
ChainiPRO_00000138961 – 224CRISPR system Cascade subunit CasDAdd BLAST224

Proteomic databases

PaxDbiQ46898
PRIDEiQ46898

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,CasE1-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 interactors
DIPiDIP-12125N
IntActiQ46898, 4 interactors
STRINGi316385.ECDH10B_2925

Structurei

Secondary structure

1224
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi2 – 14Combined sources13
Beta strandi22 – 25Combined sources4
Helixi33 – 43Combined sources11
Helixi51 – 60Combined sources10
Beta strandi61 – 68Combined sources8
Beta strandi70 – 72Combined sources3
Beta strandi75 – 77Combined sources3
Beta strandi80 – 89Combined sources10
Beta strandi92 – 98Combined sources7
Beta strandi102 – 122Combined sources21
Helixi130 – 138Combined sources9
Beta strandi146 – 148Combined sources3
Beta strandi157 – 166Combined sources10
Helixi167 – 171Combined sources5
Beta strandi174 – 176Combined sources3
Beta strandi181 – 185Combined sources5
Beta strandi193 – 201Combined sources9
Beta strandi202 – 204Combined sources3
Beta strandi207 – 216Combined sources10

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4108VWQ Bacteria
ENOG4111JEJ LUCA
HOGENOMiHOG000015840
InParanoidiQ46898
KOiK19125
OMAiEGICYWD

Family and domain databases

InterProiView protein in InterPro
IPR021124 CRISPR-assoc_prot_Cas5
IPR013422 CRISPR-assoc_prot_Cas5_N
IPR010147 CRISPR-assoc_prot_CasD
PfamiView protein in Pfam
PF09704 Cas_Cas5d, 1 hit
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 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
PATRICifig|1411691.4.peg.3981

Entry informationi

Entry nameiCAS5_ECOLI
AccessioniPrimary (citable) accession number: Q46898
Secondary accession number(s): Q2MA72
Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 1, 2000
Last sequence update: December 1, 2000
Last modified: April 25, 2018
This is version 108 of the entry and version 2 of the sequence. See 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

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