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CRISPR-associated endonuclease Cas6/Csy4 (EC 3.1.-.-)

 CAS6_PSEAB              Reviewed;         187 AA.
Q02MM2;
13-JUN-2012, integrated into UniProtKB/Swiss-Prot.
13-JUN-2012, sequence version 2.
25-OCT-2017, entry version 49.
RecName: Full=CRISPR-associated endonuclease Cas6/Csy4;
EC=3.1.-.-;
Name=cas6f; Synonyms=csy4; OrderedLocusNames=PA14_33300;
Pseudomonas aeruginosa (strain UCBPP-PA14).
Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
Pseudomonadaceae; Pseudomonas.
NCBI_TaxID=208963;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=UCBPP-PA14;
PubMed=17038190; DOI=10.1186/gb-2006-7-10-r90;
Lee D.G., Urbach J.M., Wu G., Liberati N.T., Feinbaum R.L., Miyata S.,
Diggins L.T., He J., Saucier M., Deziel E., Friedman L., Li L.,
Grills G., Montgomery K., Kucherlapati R., Rahme L.G., Ausubel F.M.;
"Genomic analysis reveals that Pseudomonas aeruginosa virulence is
combinatorial.";
Genome Biol. 7:R90.1-R90.14(2006).
[2]
FUNCTION IN CRRNA FORMATION, FUNCTION IN INHIBITION OF BIOFILM
FORMATION, DISRUPTION PHENOTYPE, AND MUTAGENESIS OF HIS-29.
STRAIN=UCBPP-PA14;
PubMed=21398535; DOI=10.1128/JB.01411-10;
Cady K.C., O'Toole G.A.;
"Non-identity-mediated CRISPR-bacteriophage interaction mediated via
the Csy and Cas3 proteins.";
J. Bacteriol. 193:3433-3445(2011).
[3]
NO ROLE IN PHAGE PROTECTION, AND DISRUPTION PHENOTYPE.
STRAIN=UCBPP-PA14;
PubMed=21081758; DOI=10.1099/mic.0.045732-0;
Cady K.C., White A.S., Hammond J.H., Abendroth M.D., Karthikeyan R.S.,
Lalitha P., Zegans M.E., O'Toole G.A.;
"Prevalence, conservation and functional analysis of Yersinia and
Escherichia CRISPR regions in clinical Pseudomonas aeruginosa
isolates.";
Microbiology 157:430-437(2011).
[4]
SUBUNIT, RNA-BINDING, AND MASS SPECTROMETRY.
STRAIN=UCBPP-PA14;
PubMed=21536913; DOI=10.1073/pnas.1102716108;
Wiedenheft B., van Duijn E., Bultema J.B., Waghmare S.P., Zhou K.,
Barendregt A., Westphal W., Heck A.J., Boekema E.J., Dickman M.J.,
Doudna J.A.;
"RNA-guided complex from a bacterial immune system enhances target
recognition through seed sequence interactions.";
Proc. Natl. Acad. Sci. U.S.A. 108:10092-10097(2011).
[5]
X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS), FUNCTION AS AN ENDONUCLEASE,
COFACTOR, RNA-BINDING, AND MUTAGENESIS OF HIS-29; ARG-102; GLN-104;
SER-148 AND PHE-155.
STRAIN=UCBPP-PA14;
PubMed=20829488; DOI=10.1126/science.1192272;
Haurwitz R.E., Jinek M., Wiedenheft B., Zhou K., Doudna J.A.;
"Sequence- and structure-specific RNA processing by a CRISPR
endonuclease.";
Science 329:1355-1358(2010).
[6]
X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEX WITH RNA, FUNCTION IN
CRRNA FORMATION, SUBUNIT, RNA-BINDING, AND MUTAGENESIS OF HIS-29;
SER-148; SER-150; THR-151 AND TYR-176.
STRAIN=UCBPP-PA14;
PubMed=22522703; DOI=10.1038/emboj.2012.107;
Haurwitz R.E., Sternberg S.H., Doudna J.A.;
"Csy4 relies on an unusual catalytic dyad to position and cleave
CRISPR RNA.";
EMBO J. 31:2824-2832(2012).
-!- 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). CRISPR clusters contain
sequences complementary to antecedent mobile elements and target
invading nucleic acids. CRISPR clusters are transcribed and
processed into CRISPR RNA (crRNA). Processes pre-crRNA into
individual crRNA units. Absolutely required for crRNA production
or stability. Upon expression in E.coli endonucleolytically
processes pre-crRNA, although disruption and reconstitution
experiments indicate that in situ other genes are also required
for processing. Yields 5'-hydroxy and 3'-phosphate groups. The Csy
ribonucleoprotein complex binds target ssDNA with high affinity
but target dsDNA with much lower affinity.
{ECO:0000269|PubMed:20829488, ECO:0000269|PubMed:21398535,
ECO:0000269|PubMed:22522703}.
-!- COFACTOR:
Note=Metal-ion independent. Binds processed crRNA.
{ECO:0000269|PubMed:20829488};
-!- SUBUNIT: Part of the Csy ribonucleoprotein complex with a probable
stoichiometry of Csy1(1),Csy2(1),Csy3(6),Cas6/Csy4(1)-crRNA(1). A
Csy3(6),Cas6/Csy4(1)-crRNA(1) subcomplex is also formed.
{ECO:0000269|PubMed:21536913, ECO:0000269|PubMed:22522703}.
-!- INTERACTION:
Q02MM1:csy3; NbExp=12; IntAct=EBI-15924852, EBI-15924841;
-!- MASS SPECTROMETRY: Mass=21533.8; Mass_error=1.9;
Method=Electrospray; Range=1-187;
Evidence={ECO:0000269|PubMed:21536913};
-!- DISRUPTION PHENOTYPE: Infection with phage DMS3 inhibits biofilm
formation; disrupting this gene restores biofilm formation despite
DMS3 infection. Normal biofilm formation in the absence of phage
infection. Loss of production of crRNA in the presence or absence
of phage. Disruption of the entire Y.pestis-subtype CRISPR region
disrupts crRNA production but does not alter phage resistance
(possibly OLNs PA14_33350 to PA14_33310, plus the flanking CRISPR
loci), indicating this CRISPR is not involved in phage resistance.
{ECO:0000269|PubMed:21081758, ECO:0000269|PubMed:21398535}.
-!- MISCELLANEOUS: In this bacteria, Y.pestis-subtype CRISPRs do not
confer resistance to phage DMS3 or MP22, but instead are required
for DMS3-dependent inhibition of biofilm formation and possibly
motility.
-!- SIMILARITY: Belongs to the CRISPR-associated endoribonuclease Cas6
family. Cas6f/Csy4, subtype I-F/Ypest subfamily. {ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=ABJ11605.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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-----------------------------------------------------------------------
EMBL; CP000438; ABJ11605.1; ALT_INIT; Genomic_DNA.
RefSeq; WP_016254196.1; NC_008463.1.
PDB; 2XLI; X-ray; 2.33 A; A=1-187.
PDB; 2XLJ; X-ray; 2.60 A; A=1-187.
PDB; 2XLK; X-ray; 1.80 A; A/B=1-187.
PDB; 4AL5; X-ray; 2.00 A; A=1-187.
PDB; 4AL6; X-ray; 2.63 A; A=1-187.
PDB; 4AL7; X-ray; 2.32 A; A=1-187.
PDB; 5UZ9; EM; 3.40 A; L=1-187.
PDBsum; 2XLI; -.
PDBsum; 2XLJ; -.
PDBsum; 2XLK; -.
PDBsum; 4AL5; -.
PDBsum; 4AL6; -.
PDBsum; 4AL7; -.
PDBsum; 5UZ9; -.
SMR; Q02MM2; -.
DIP; DIP-59681N; -.
IntAct; Q02MM2; 6.
EnsemblBacteria; ABJ11605; ABJ11605; PA14_33300.
KEGG; pau:PA14_33300; -.
HOGENOM; HOG000118359; -.
KO; K19130; -.
Proteomes; UP000000653; Chromosome.
GO; GO:0004519; F:endonuclease activity; IEA:UniProtKB-KW.
GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
GO; GO:0043571; P:maintenance of CRISPR repeat elements; IEA:InterPro.
InterPro; IPR013396; CRISPR-assoc_prot_Csy4.
Pfam; PF09618; Cas_Csy4; 1.
TIGRFAMs; TIGR02563; cas_Csy4; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; Endonuclease; Hydrolase; Nuclease;
RNA-binding.
CHAIN 1 187 CRISPR-associated endonuclease Cas6/Csy4.
/FTId=PRO_0000417882.
ACT_SITE 29 29 Proton acceptor. {ECO:0000305}.
SITE 148 148 Substrate binding.
MUTAGEN 29 29 H->A: No pre-crRNA cleavage, still binds
crRNA. Does not support formation of the
Csy ribonucleoprotein complex.
{ECO:0000269|PubMed:20829488,
ECO:0000269|PubMed:21398535,
ECO:0000269|PubMed:22522703}.
MUTAGEN 29 29 H->D: Cleaves pre-crRNA 910-fold slower.
{ECO:0000269|PubMed:20829488,
ECO:0000269|PubMed:21398535,
ECO:0000269|PubMed:22522703}.
MUTAGEN 29 29 H->K: Cleaves pre-crRNA 130-fold slower.
{ECO:0000269|PubMed:20829488,
ECO:0000269|PubMed:21398535,
ECO:0000269|PubMed:22522703}.
MUTAGEN 49 49 E->A: No biofilm formation upon phage
infection, no crRNA formed.
MUTAGEN 49 49 E->K: Restores biofilm formation upon
phage infection, crRNA forms.
MUTAGEN 102 102 R->A: Loss of pre-crRNA cleavage, still
binds crRNA.
{ECO:0000269|PubMed:20829488}.
MUTAGEN 104 104 Q->A: No loss of pre-crRNA cleavage,
still binds crRNA.
{ECO:0000269|PubMed:20829488}.
MUTAGEN 148 148 S->A: Cleaves pre-crRNA 8300-fold slower.
{ECO:0000269|PubMed:20829488,
ECO:0000269|PubMed:22522703}.
MUTAGEN 148 148 S->C: No pre-crRNA cleavage, still binds
crRNA. {ECO:0000269|PubMed:20829488,
ECO:0000269|PubMed:22522703}.
MUTAGEN 150 150 S->A: Cleaves pre-crRNA 350-fold slower.
{ECO:0000269|PubMed:22522703}.
MUTAGEN 151 151 T->A: Cleaves pre-crRNA 380-fold slower.
{ECO:0000269|PubMed:22522703}.
MUTAGEN 155 155 F->A: Very little pre-crRNA cleavage,
still binds crRNA.
{ECO:0000269|PubMed:20829488}.
MUTAGEN 176 176 Y->A: Cleaves pre-crRNA 130-fold slower.
{ECO:0000269|PubMed:22522703}.
MUTAGEN 176 176 Y->F: Cleaves pre-crRNA 13-fold slower.
{ECO:0000269|PubMed:22522703}.
STRAND 3 9 {ECO:0000244|PDB:2XLK}.
STRAND 13 15 {ECO:0000244|PDB:2XLK}.
HELIX 17 35 {ECO:0000244|PDB:2XLK}.
STRAND 41 43 {ECO:0000244|PDB:2XLK}.
TURN 49 52 {ECO:0000244|PDB:2XLK}.
STRAND 56 62 {ECO:0000244|PDB:2XLK}.
HELIX 64 71 {ECO:0000244|PDB:2XLK}.
HELIX 74 76 {ECO:0000244|PDB:4AL5}.
HELIX 77 82 {ECO:0000244|PDB:2XLK}.
STRAND 83 85 {ECO:0000244|PDB:4AL5}.
STRAND 100 103 {ECO:0000244|PDB:2XLK}.
HELIX 109 120 {ECO:0000244|PDB:2XLK}.
HELIX 124 130 {ECO:0000244|PDB:2XLK}.
HELIX 133 135 {ECO:0000244|PDB:4AL5}.
STRAND 143 147 {ECO:0000244|PDB:2XLK}.
TURN 149 151 {ECO:0000244|PDB:2XLK}.
STRAND 154 161 {ECO:0000244|PDB:2XLK}.
STRAND 165 167 {ECO:0000244|PDB:2XLK}.
STRAND 179 181 {ECO:0000244|PDB:2XLK}.
SEQUENCE 187 AA; 21391 MW; 0C4A370883007481 CRC64;
MDHYLDIRLR PDPEFPPAQL MSVLFGKLHQ ALVAQGGDRI GVSFPDLDES RSRLGERLRI
HASADDLRAL LARPWLEGLR DHLQFGEPAV VPHPTPYRQV SRVQAKSNPE RLRRRLMRRH
DLSEEEARKR IPDTVARALD LPFVTLRSQS TGQHFRLFIR HGPLQVTAEE GGFTCYGLSK
GGFVPWF


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