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CRISPR-associated endoribonuclease Cas2 (EC 3.1.-.-)

 CAS2_ECOLI              Reviewed;          94 AA.
P45956; Q2MA75;
01-NOV-1995, integrated into UniProtKB/Swiss-Prot.
30-MAY-2000, sequence version 2.
28-MAR-2018, entry version 111.
RecName: Full=CRISPR-associated endoribonuclease Cas2;
EC=3.1.-.-;
Name=ygbF; Synonyms=cas2; OrderedLocusNames=b2754, JW5438;
Escherichia coli (strain K12).
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
Enterobacteriaceae; Escherichia.
NCBI_TaxID=83333;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=K12;
PubMed=2656660; DOI=10.1128/jb.171.6.3553-3556.1989;
Nakata A., Amemura M., Makino K.;
"Unusual nucleotide arrangement with repeated sequences in the
Escherichia coli K-12 chromosome.";
J. Bacteriol. 171:3553-3556(1989).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=9278503; DOI=10.1126/science.277.5331.1453;
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J.,
Mau B., Shao Y.;
"The complete genome sequence of Escherichia coli K-12.";
Science 277:1453-1462(1997).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=16738553; DOI=10.1038/msb4100049;
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
"Highly accurate genome sequences of Escherichia coli K-12 strains
MG1655 and W3110.";
Mol. Syst. Biol. 2:E1-E5(2006).
[4]
IDENTIFICATION.
PubMed=7567469; DOI=10.1093/nar/23.17.3554;
Borodovsky M., McIninch J., Koonin E.V., Rudd K.E., Medigue C.,
Danchin A.;
"Detection of new genes in a bacterial genome using Markov models for
three gene classes.";
Nucleic Acids Res. 23:3554-3562(1995).
[5]
OPERON STRUCTURE, AND INDUCTION BY LEUO.
STRAIN=K12 / BW25113;
PubMed=19429622; DOI=10.1128/JB.00108-09;
Shimada T., Yamamoto K., Ishihama A.;
"Involvement of the leucine response transcription factor LeuO in
regulation of the genes for sulfa drug efflux.";
J. Bacteriol. 191:4562-4571(2009).
[6]
REPRESSION BY H-NS.
STRAIN=K12;
PubMed=20132443; DOI=10.1111/j.1365-2958.2010.07073.x;
Pul U., Wurm R., Arslan Z., Geissen R., Hofmann N., Wagner R.;
"Identification and characterization of E. coli CRISPR-cas promoters
and their silencing by H-NS.";
Mol. Microbiol. 75:1495-1512(2010).
[7]
INDUCTION BY BAER, ROLE IN PLASMID SILENCING, AND DISRUPTION
PHENOTYPE.
STRAIN=K12 / BW25113;
PubMed=21255106; DOI=10.1111/j.1365-2958.2010.07482.x;
Perez-Rodriguez R., Haitjema C., Huang Q., Nam K.H., Bernardis S.,
Ke A., DeLisa M.P.;
"Envelope stress is a trigger of CRISPR RNA-mediated DNA silencing in
Escherichia coli.";
Mol. Microbiol. 79:584-599(2011).
[8]
FUNCTION AS A SPACER INTEGRASE, AND SUBUNIT.
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=24920831; DOI=10.1093/nar/gku510;
Arslan Z., Hermanns V., Wurm R., Wagner R., Pul U.;
"Detection and characterization of spacer integration intermediates in
type I-E CRISPR-Cas system.";
Nucleic Acids Res. 42:7884-7893(2014).
[9]
FUNCTION, SUBUNIT, AND MUTAGENESIS OF GLU-9 AND 79-THR--VAL-94.
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=25707795; DOI=10.1038/nature14237;
Nunez J.K., Lee A.S., Engelman A., Doudna J.A.;
"Integrase-mediated spacer acquisition during CRISPR-Cas adaptive
immunity.";
Nature 519:193-198(2015).
[10]
X-RAY CRYSTALLOGRAPHY (1.1 ANGSTROMS).
Nocek B., Skarina T., Brown G., Yakunin A., Joachimiak A.;
"Crystal structure of a putative ssRNA endonuclease Cas2, CRISPR
adaptation protein from E.coli.";
Submitted (AUG-2013) to the PDB data bank.
[11]
X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) IN COMPLEX WITH CAS1, FUNCTION
IN SPACER ACQUISITION, INTERACTION WITH CAS1 (YGBT), SUBUNIT, AND
MUTAGENESIS OF GLU-9; ASN-10; ARG-14; ARG-16; ARG-18; ARG-27; GLU-65;
79-THR--VAL-94 AND ASP-84.
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=24793649; DOI=10.1038/nsmb.2820;
Nunez J.K., Kranzusch P.J., Noeske J., Wright A.V., Davies C.W.,
Doudna J.A.;
"Cas1-Cas2 complex formation mediates spacer acquisition during
CRISPR-Cas adaptive immunity.";
Nat. Struct. Mol. Biol. 21:528-534(2014).
[12]
X-RAY CRYSTALLOGRAPHY (2.70 ANGSTROMS) IN COMPLEX WITH CAS1, AND
SUBUNIT.
Tamulaitiene G., Sinkunas T., Silanskas A., Gasiunas G., Grazulis S.,
Siksnys V.;
"Crystal structure of E.coli Cas1-Cas2 complex.";
Submitted (MAY-2014) to the PDB data bank.
[13]
X-RAY CRYSTALLOGRAPHY (2.60 ANGSTROMS) OF 1-78 IN COMPLEX WITH CAS1
AND DNA, FUNCTION, SUBUNIT, DOMAIN, DNA-BINDING, AND MUTAGENESIS OF
14-ARG--ARG-16; 38-LYS--ARG-40 AND 77-ARG-ARG-78.
STRAIN=K12;
PubMed=26478180; DOI=10.1016/j.cell.2015.10.008;
Wang J., Li J., Zhao H., Sheng G., Wang M., Yin M., Wang Y.;
"Structural and mechanistic basis of PAM-dependent spacer acquisition
in CRISPR-Cas systems.";
Cell 163:840-853(2015).
[14]
X-RAY CRYSTALLOGRAPHY (2.95 ANGSTROMS) IN COMPLEX WITH CAS1 AND DNA,
FUNCTION, SUBUNIT, DNA-BINDING, AND MUTAGENESIS OF ARG-16; ARG-77 AND
ARG-78.
PubMed=26503043; DOI=10.1038/nature15760;
Nunez J.K., Harrington L.B., Kranzusch P.J., Engelman A.N.,
Doudna J.A.;
"Foreign DNA capture during CRISPR-Cas adaptive immunity.";
Nature 527:535-538(2015).
-!- FUNCTION: 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).
{ECO:0000269|PubMed:21255106, ECO:0000269|PubMed:24793649,
ECO:0000269|PubMed:24920831, ECO:0000269|PubMed:26478180}.
-!- SUBUNIT: 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).
{ECO:0000269|PubMed:24793649, ECO:0000269|PubMed:24920831,
ECO:0000269|PubMed:25707795, ECO:0000269|PubMed:26478180,
ECO:0000269|PubMed:26503043, ECO:0000305|Ref.10,
ECO:0000305|Ref.12}.
-!- INTERACTION:
Q46896:ygbT; NbExp=8; IntAct=EBI-9150552, EBI-1130209;
-!- INDUCTION: 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).
{ECO:0000269|PubMed:19429622, ECO:0000269|PubMed:20132443,
ECO:0000269|PubMed:21255106}.
-!- DOMAIN: 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).
{ECO:0000269|PubMed:26478180}.
-!- DISRUPTION PHENOTYPE: Loss of plasmid silencing (PubMed:21255106).
{ECO:0000269|PubMed:21255106}.
-!- SIMILARITY: Belongs to the CRISPR-associated endoribonuclease Cas2
protein family. E.coli-subtype subfamily. {ECO:0000305}.
-----------------------------------------------------------------------
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-----------------------------------------------------------------------
EMBL; M27059; -; NOT_ANNOTATED_CDS; Unassigned_DNA.
EMBL; U29579; AAA69264.1; -; Genomic_DNA.
EMBL; U00096; AAC75796.2; -; Genomic_DNA.
EMBL; AP009048; BAE76831.1; -; Genomic_DNA.
PIR; F65056; F65056.
RefSeq; NP_417234.2; NC_000913.3.
RefSeq; WP_001381369.1; NZ_LN832404.1.
PDB; 4MAK; X-ray; 1.10 A; A/B=1-94.
PDB; 4P6I; X-ray; 2.30 A; A/B=1-94.
PDB; 4QDL; X-ray; 2.70 A; E/F=1-94.
PDB; 5DLJ; X-ray; 2.60 A; E/F=1-78.
PDB; 5DQT; X-ray; 3.10 A; E/F/M/N=1-94.
PDB; 5DQU; X-ray; 4.50 A; E/F=1-94.
PDB; 5DQZ; X-ray; 2.70 A; E/F=1-94.
PDB; 5DS4; X-ray; 3.20 A; E/F=1-94.
PDB; 5DS5; X-ray; 2.95 A; E/F=1-94.
PDB; 5DS6; X-ray; 3.35 A; E/F=1-94.
PDB; 5VVJ; X-ray; 3.89 A; E/F=1-94.
PDB; 5VVK; X-ray; 2.90 A; E/F=1-94.
PDB; 5VVL; X-ray; 3.31 A; E/F=1-94.
PDB; 5WFE; EM; 3.64 A; E/F=1-94.
PDBsum; 4MAK; -.
PDBsum; 4P6I; -.
PDBsum; 4QDL; -.
PDBsum; 5DLJ; -.
PDBsum; 5DQT; -.
PDBsum; 5DQU; -.
PDBsum; 5DQZ; -.
PDBsum; 5DS4; -.
PDBsum; 5DS5; -.
PDBsum; 5DS6; -.
PDBsum; 5VVJ; -.
PDBsum; 5VVK; -.
PDBsum; 5VVL; -.
PDBsum; 5WFE; -.
ProteinModelPortal; P45956; -.
SMR; P45956; -.
BioGrid; 4259585; 139.
DIP; DIP-12109N; -.
IntAct; P45956; 3.
STRING; 316385.ECDH10B_2922; -.
PaxDb; P45956; -.
PRIDE; P45956; -.
EnsemblBacteria; AAC75796; AAC75796; b2754.
EnsemblBacteria; BAE76831; BAE76831; BAE76831.
GeneID; 947213; -.
KEGG; ecj:JW5438; -.
KEGG; eco:b2754; -.
PATRIC; fig|1411691.4.peg.3984; -.
EchoBASE; EB2694; -.
EcoGene; EG12845; ygbF.
eggNOG; ENOG4105PWE; Bacteria.
eggNOG; ENOG4111VHR; LUCA.
HOGENOM; HOG000015873; -.
InParanoid; P45956; -.
KO; K09951; -.
OMA; TNNEQGF; -.
BioCyc; EcoCyc:EG12845-MONOMER; -.
PRO; PR:P45956; -.
Proteomes; UP000000318; Chromosome.
Proteomes; UP000000625; Chromosome.
GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
GO; GO:0004519; F:endonuclease activity; IEA:UniProtKB-KW.
GO; GO:0051607; P:defense response to virus; IEA:UniProtKB-KW.
GO; GO:0043571; P:maintenance of CRISPR repeat elements; IMP:EcoCyc.
InterPro; IPR010152; CRISPR-assoc_prot_Cas2_sub.
Pfam; PF09707; Cas_Cas2CT1978; 1.
TIGRFAMs; TIGR01873; cas_CT1978; 1.
1: Evidence at protein level;
3D-structure; Antiviral defense; Complete proteome; DNA-binding;
Endonuclease; Hydrolase; Nuclease; Reference proteome.
CHAIN 1 94 CRISPR-associated endoribonuclease Cas2.
/FTId=PRO_0000169312.
MUTAGEN 9 9 E->A,R: No effect on spacer acquisition,
Cas1-Cas2 complex formation or CRISPR
DNA-binding by complex.
{ECO:0000269|PubMed:24793649,
ECO:0000269|PubMed:25707795}.
MUTAGEN 10 10 N->A: No effect on spacer acquisition.
{ECO:0000269|PubMed:24793649}.
MUTAGEN 14 16 RLR->ALA: No in vivspacer acquisition,
significantly decreased protospacer
binding. {ECO:0000269|PubMed:26478180}.
MUTAGEN 14 14 R->A: Slight decrease in spacer
acquisition.
{ECO:0000269|PubMed:24793649}.
MUTAGEN 16 16 R->A: Slight decrease in spacer
acquisition.
{ECO:0000269|PubMed:24793649}.
MUTAGEN 16 16 R->E: Dramatically decreased spacer
acquisition in vivo.
{ECO:0000269|PubMed:26503043}.
MUTAGEN 18 18 R->A: Very little spacer acquisition.
{ECO:0000269|PubMed:24793649}.
MUTAGEN 27 27 R->A: Slight decrease in spacer
acquisition.
{ECO:0000269|PubMed:24793649}.
MUTAGEN 38 40 KIR->AIA: Very little in vivo spacer
acquisition.
{ECO:0000269|PubMed:26478180}.
MUTAGEN 65 65 E->A: No effect on spacer acquisition.
{ECO:0000269|PubMed:24793649}.
MUTAGEN 65 65 E->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. {ECO:0000269|PubMed:24793649}.
MUTAGEN 77 78 RR->AA: No spacer acquisition,
significantly decreased protospacer
binding. {ECO:0000269|PubMed:26478180}.
MUTAGEN 77 77 R->E: No change in spacer acquisition in
vivo. {ECO:0000269|PubMed:26503043}.
MUTAGEN 78 78 R->E: Dramatically decreased spacer
acquisition in vivo.
{ECO:0000269|PubMed:26503043}.
MUTAGEN 79 94 Missing: Loss of spacer acquisition, no
Cas1-Cas2 complex formation, loss of
CRISPR DNA-binding by complex (beta6-
beta7 deletion).
{ECO:0000269|PubMed:24793649,
ECO:0000269|PubMed:25707795}.
MUTAGEN 84 84 D->A: No effect on spacer acquisition.
{ECO:0000269|PubMed:24793649}.
MUTAGEN 84 84 D->R: Slight decrease in spacer
acquisition. Loss of spacer acquisition;
when associated with R-65.
{ECO:0000269|PubMed:24793649}.
STRAND 3 10 {ECO:0000244|PDB:4MAK}.
HELIX 13 22 {ECO:0000244|PDB:4MAK}.
STRAND 23 27 {ECO:0000244|PDB:4MAK}.
STRAND 30 34 {ECO:0000244|PDB:4MAK}.
HELIX 37 50 {ECO:0000244|PDB:4MAK}.
STRAND 55 61 {ECO:0000244|PDB:4MAK}.
STRAND 63 66 {ECO:0000244|PDB:4MAK}.
STRAND 68 73 {ECO:0000244|PDB:4MAK}.
STRAND 79 83 {ECO:0000244|PDB:4P6I}.
STRAND 86 91 {ECO:0000244|PDB:4P6I}.
SEQUENCE 94 AA; 10518 MW; D1C159D924B477B4 CRC64;
MSMLVVVTEN VPPRLRGRLA IWLLEVRAGV YVGDVSAKIR EMIWEQIAGL AEEGNVVMAW
ATNTETGFEF QTFGLNRRTP VDLDGLRLVS FLPV


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