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Protein

CRISPR-associated endoribonuclease Cas2

Gene

ygbF

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) (PubMed:21255106, PubMed:24920831, PubMed:24793649). CRISPR clusters contain sequences complementary to antecedent mobile elements and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). The Cas1-Cas2 complex is involved in CRISPR adaptation, the first stage of CRISPR immunity, being required for the addition/removal of CRISPR spacers at the leader end of the CRISPR locus (PubMed:24920831, PubMed:25707795, PubMed:24793649). The Cas1-Cas2 complex introduces staggered nicks into both strands of the CRISPR array near the leader repeat and joins the 5'-ends of the repeat strands with the 3'-ends of the new spacer sequence (PubMed:24920831). Spacer DNA integration requires supercoiled target DNA and 3'-OH ends on the inserted (spacer) DNA and probably initiates with a nucleophilic attack of the C 3'-OH end of the protospacer on the minus strand of the first repeat sequence (PubMed:25707795). Expression of Cas1-Cas2 in a strain lacking both genes permits spacer acquisition (PubMed:24793649, PubMed:24920831). Cas2 not seen to bind DNA alone; the Cas1-Cas2 complex preferentially binds CRISPR-locus DNA (PubMed:24793649). Highest binding is seen to a dual forked DNA complex with 3'-overhangs and a protospacer-adjacent motif-complement specifically positioned (PubMed:26478180). The protospacer DNA lies across a flat surface extending from 1 Cas1 dimer, across the Cas2 dimer and contacting the other Cas1 dimer; the 23 bp-long ds section of the DNA is bracketed by 1 Tyr-22 from each of the Cas1 dimers (PubMed:26478180, PubMed:26503043). Cas1 cuts within the 3'-overhang, to generate a 33-nucleotide DNA that is probably incorporated into the CRISPR leader by a cut-and-paste mechanism (PubMed:26478180). This subunit's probable nuclease activity is not required for spacer acquisition (PubMed:24793649).4 Publications

GO - Molecular functioni

GO - Biological processi

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

Keywords - Molecular functioni

Endonuclease, Hydrolase, Nuclease

Keywords - Biological processi

Antiviral defense

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG12845-MONOMER.
ECOL316407:JW5438-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
CRISPR-associated endoribonuclease Cas2 (EC:3.1.-.-)
Gene namesi
Name:ygbF
Synonyms:cas2
Ordered Locus Names:b2754, JW5438
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG12845. ygbF.

Pathology & Biotechi

Disruption phenotypei

Loss of plasmid silencing (PubMed:21255106).1 Publication

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi9E → A or R: No effect on spacer acquisition, Cas1-Cas2 complex formation or CRISPR DNA-binding by complex. 2 Publications1
Mutagenesisi10N → A: No effect on spacer acquisition. 1 Publication1
Mutagenesisi14 – 16RLR → ALA: No in vivspacer acquisition, significantly decreased protospacer binding. 1 Publication3
Mutagenesisi14R → A: Slight decrease in spacer acquisition. 1 Publication1
Mutagenesisi16R → A: Slight decrease in spacer acquisition. 1 Publication1
Mutagenesisi16R → E: Dramatically decreased spacer acquisition in vivo. 1 Publication1
Mutagenesisi18R → A: Very little spacer acquisition. 1 Publication1
Mutagenesisi27R → A: Slight decrease in spacer acquisition. 1 Publication1
Mutagenesisi38 – 40KIR → AIA: Very little in vivo spacer acquisition. 1 Publication3
Mutagenesisi65E → A: No effect on spacer acquisition. 1 Publication1
Mutagenesisi65E → R: Slight decrease in spacer acquisition, Cas1-Cas2 complex formation or CRISPR DNA-binding by complex. Loss of spacer acquisition; when associated with R-84. 1 Publication1
Mutagenesisi77 – 78RR → AA: No spacer acquisition, significantly decreased protospacer binding. 1 Publication2
Mutagenesisi77R → E: No change in spacer acquisition in vivo. 1 Publication1
Mutagenesisi78R → E: Dramatically decreased spacer acquisition in vivo. 1 Publication1
Mutagenesisi79 – 94Missing : Loss of spacer acquisition, no Cas1-Cas2 complex formation, loss of CRISPR DNA-binding by complex (beta6-beta7 deletion). 2 PublicationsAdd BLAST16
Mutagenesisi84D → A: No effect on spacer acquisition. 1 Publication1
Mutagenesisi84D → R: Slight decrease in spacer acquisition. Loss of spacer acquisition; when associated with R-65. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001693121 – 94CRISPR-associated endoribonuclease Cas2Add BLAST94

Proteomic databases

PaxDbiP45956.
PRIDEiP45956.

Expressioni

Inductioni

Repressed by H-NS (PubMed:20132443). Activated by LeuO (PubMed:19429622). Activated by the BaeSR two-component regulatory system, possibly due to envelope stress (PubMed:21255106). Part of the casABCDE-ygbT-ygbF operon (PubMed:19429622).3 Publications

Interactioni

Subunit structurei

Homodimer (Ref. 10). Part of the Cas1-Cas2 complex (PubMed:24920831, PubMed:24793649, PubMed:25707795, Ref. 12, PubMed:26478180, PubMed:26503043). Forms a hexamer with 2 Cas1 dimers sandwiching a Cas2 dimer (PubMed:24793649). The DNA lies across a flat surface extending from 1 Cas1 dimer, across the Cas2 dimer and contacting the other Cas1 dimer. Only 1 Cas1 protein from each dimer is catalytic, the other interacts with the Cas2 dimer and possibly target DNA (PubMed:26478180, PubMed:26503043).2 Publications5 Publications

Protein-protein interaction databases

BioGridi4259585. 137 interactors.
DIPiDIP-12109N.
IntActiP45956. 2 interactors.
STRINGi511145.b2754.

Structurei

Secondary structure

194
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi3 – 10Combined sources8
Helixi13 – 22Combined sources10
Beta strandi23 – 27Combined sources5
Beta strandi30 – 34Combined sources5
Helixi37 – 50Combined sources14
Beta strandi55 – 61Combined sources7
Beta strandi63 – 66Combined sources4
Beta strandi68 – 73Combined sources6
Beta strandi79 – 83Combined sources5
Beta strandi86 – 91Combined sources6

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4MAKX-ray1.10A/B1-94[»]
4P6IX-ray2.30A/B1-94[»]
4QDLX-ray2.70E/F1-94[»]
5DLJX-ray2.60E/F1-78[»]
5DQTX-ray3.10E/F/M/N1-94[»]
5DQUX-ray4.50E/F1-94[»]
5DQZX-ray2.70E/F1-94[»]
5DS4X-ray3.20E/F1-94[»]
5DS5X-ray2.95E/F1-94[»]
5DS6X-ray3.35E/F1-94[»]
ProteinModelPortaliP45956.
SMRiP45956.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domaini

Substrate DNA-binding induces large structural changes that generate a surface for DNA-binding across the Cas2 dimer and formation of an optimal catalytic site (PubMed:26478180).1 Publication

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4105PWE. Bacteria.
ENOG4111VHR. LUCA.
HOGENOMiHOG000015873.
InParanoidiP45956.
KOiK09951.
OMAiGENRRMP.

Family and domain databases

InterProiIPR010152. CRISPR-assoc_prot_Cas2_sub.
[Graphical view]
PfamiPF09707. Cas_Cas2CT1978. 1 hit.
[Graphical view]
TIGRFAMsiTIGR01873. cas_CT1978. 1 hit.

Sequencei

Sequence statusi: Complete.

P45956-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSMLVVVTEN VPPRLRGRLA IWLLEVRAGV YVGDVSAKIR EMIWEQIAGL
60 70 80 90
AEEGNVVMAW ATNTETGFEF QTFGLNRRTP VDLDGLRLVS FLPV
Length:94
Mass (Da):10,518
Last modified:May 30, 2000 - v2
Checksum:iD1C159D924B477B4
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M27059 Unassigned DNA. No translation available.
U29579 Genomic DNA. Translation: AAA69264.1.
U00096 Genomic DNA. Translation: AAC75796.2.
AP009048 Genomic DNA. Translation: BAE76831.1.
PIRiF65056.
RefSeqiNP_417234.2. NC_000913.3.
WP_001381369.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC75796; AAC75796; b2754.
BAE76831; BAE76831; BAE76831.
GeneIDi947213.
KEGGiecj:JW5438.
eco:b2754.
PATRICi32120918. VBIEscCol129921_2851.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M27059 Unassigned DNA. No translation available.
U29579 Genomic DNA. Translation: AAA69264.1.
U00096 Genomic DNA. Translation: AAC75796.2.
AP009048 Genomic DNA. Translation: BAE76831.1.
PIRiF65056.
RefSeqiNP_417234.2. NC_000913.3.
WP_001381369.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4MAKX-ray1.10A/B1-94[»]
4P6IX-ray2.30A/B1-94[»]
4QDLX-ray2.70E/F1-94[»]
5DLJX-ray2.60E/F1-78[»]
5DQTX-ray3.10E/F/M/N1-94[»]
5DQUX-ray4.50E/F1-94[»]
5DQZX-ray2.70E/F1-94[»]
5DS4X-ray3.20E/F1-94[»]
5DS5X-ray2.95E/F1-94[»]
5DS6X-ray3.35E/F1-94[»]
ProteinModelPortaliP45956.
SMRiP45956.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4259585. 137 interactors.
DIPiDIP-12109N.
IntActiP45956. 2 interactors.
STRINGi511145.b2754.

Proteomic databases

PaxDbiP45956.
PRIDEiP45956.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75796; AAC75796; b2754.
BAE76831; BAE76831; BAE76831.
GeneIDi947213.
KEGGiecj:JW5438.
eco:b2754.
PATRICi32120918. VBIEscCol129921_2851.

Organism-specific databases

EchoBASEiEB2694.
EcoGeneiEG12845. ygbF.

Phylogenomic databases

eggNOGiENOG4105PWE. Bacteria.
ENOG4111VHR. LUCA.
HOGENOMiHOG000015873.
InParanoidiP45956.
KOiK09951.
OMAiGENRRMP.

Enzyme and pathway databases

BioCyciEcoCyc:EG12845-MONOMER.
ECOL316407:JW5438-MONOMER.

Miscellaneous databases

PROiP45956.

Family and domain databases

InterProiIPR010152. CRISPR-assoc_prot_Cas2_sub.
[Graphical view]
PfamiPF09707. Cas_Cas2CT1978. 1 hit.
[Graphical view]
TIGRFAMsiTIGR01873. cas_CT1978. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiCAS2_ECOLI
AccessioniPrimary (citable) accession number: P45956
Secondary accession number(s): Q2MA75
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: May 30, 2000
Last modified: November 2, 2016
This is version 104 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.