CMR4_PYRFU
ID CMR4_PYRFU Reviewed; 295 AA.
AC Q8U1S9;
DT 11-JUL-2012, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2002, sequence version 1.
DT 25-MAY-2022, entry version 94.
DE RecName: Full=CRISPR system Cmr endoribonuclease Cmr4 {ECO:0000303|PubMed:25280103};
DE EC=3.1.-.-;
DE AltName: Full=CRISPR type III-B/RAMP module RAMP protein Cmr4;
DE AltName: Full=Target RNase Cmr4;
GN Name=cmr4 {ECO:0000303|PubMed:19945378}; OrderedLocusNames=PF1126;
OS Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Pyrococcus.
OX NCBI_TaxID=186497;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43587 / DSM 3638 / JCM 8422 / Vc1;
RX PubMed=10430560; DOI=10.1093/genetics/152.4.1299;
RA Maeder D.L., Weiss R.B., Dunn D.M., Cherry J.L., Gonzalez J.M.,
RA DiRuggiero J., Robb F.T.;
RT "Divergence of the hyperthermophilic archaea Pyrococcus furiosus and P.
RT horikoshii inferred from complete genomic sequences.";
RL Genetics 152:1299-1305(1999).
RN [2]
RP IDENTIFICATION BY MASS SPECTROMETRY, FUNCTION IN CMR COMPLEX, SUBCELLULAR
RP LOCATION, AND SUBUNIT.
RC STRAIN=ATCC 43587 / DSM 3638 / JCM 8422 / Vc1;
RX PubMed=19945378; DOI=10.1016/j.cell.2009.07.040;
RA Hale C.R., Zhao P., Olson S., Duff M.O., Graveley B.R., Wells L.,
RA Terns R.M., Terns M.P.;
RT "RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex.";
RL Cell 139:945-956(2009).
RN [3]
RP INTERACTION WITH CMR5, AND SUBUNIT.
RC STRAIN=ATCC 43587 / DSM 3638 / JCM 8422 / Vc1;
RX PubMed=23370277; DOI=10.1016/j.febslet.2013.01.029;
RA Park J.H., Sun J., Park S.Y., Hwang H.J., Park M.Y., Shin M., Kim J.S.;
RT "Crystal structure of Cmr5 from Pyrococcus furiosus and its functional
RT implications.";
RL FEBS Lett. 587:562-568(2013).
RN [4]
RP STRUCTURE BY ELECTRON MICROSCOPY (12.0 ANGSTROMS) OF WHOLE CMR COMPLEX WITH
RP TARGET RNA, SUBUNIT, AND RNA-BINDING.
RC STRAIN=ATCC 43587 / DSM 3638 / JCM 8422 / Vc1;
RX PubMed=24119404; DOI=10.1016/j.molcel.2013.09.008;
RA Spilman M., Cocozaki A., Hale C., Shao Y., Ramia N., Terns R., Terns M.,
RA Li H., Stagg S.;
RT "Structure of an RNA silencing complex of the CRISPR-Cas immune system.";
RL Mol. Cell 52:146-152(2013).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS), FUNCTION, INTERACTION WITH CMR2;
RP CMR3; CMR5 AND CMR6, SUBUNIT, AND MUTAGENESIS OF HIS-15; ASP-26; GLU-227
RP AND TYR-229.
RC STRAIN=ATCC 43587 / DSM 3638 / JCM 8422 / Vc1;
RX PubMed=25280103; DOI=10.1016/j.molcel.2014.09.002;
RA Benda C., Ebert J., Scheltema R.A., Schiller H.B., Baumgaertner M.,
RA Bonneau F., Mann M., Conti E.;
RT "Structural model of a CRISPR RNA-silencing complex reveals the RNA-target
RT cleavage activity in Cmr4.";
RL Mol. Cell 56:43-54(2014).
CC -!- FUNCTION: CRISPR (clustered regularly interspaced short palindromic
CC repeat), is an adaptive immune system that provides protection against
CC mobile genetic elements (viruses, transposable elements and conjugative
CC plasmids). CRISPR clusters contain sequences complementary to
CC antecedent mobile elements and target invading nucleic acids. CRISPR
CC clusters are transcribed and processed into CRISPR RNA (crRNA),
CC formerly called psiRNA (prokaryotic silencing) in this organism. Part
CC of the Cmr ribonucleoprotein complex which has divalent cation-
CC dependent endoribonuclease activity specific for ssRNA complementary to
CC the crRNA (target RNA), generating 5' hydroxy- and 3' phosphate or 2'-
CC 3' cyclic phosphate termini. This is probably the subunit that cleaves
CC the target RNA (PubMed:25280103). Cmr complex does not cleave ssDNA
CC complementary to the crRNA. Cleavage of target RNA is guided by the
CC crRNA; substrate cleavage occurs a fixed distance (14 nt) from the 3'
CC end of the crRNA. In vitro reconstitution shows Cmr1-2 and Cmr5 are not
CC absolutely necessary for target cleavage (PubMed:19945378).
CC {ECO:0000269|PubMed:19945378, ECO:0000269|PubMed:25280103}.
CC -!- SUBUNIT: Forms oligomers in isolation (PubMed:23370277). Part of the
CC type III-B Cmr ribonucleoprotein (RNP) complex, an elongated RNP with
CC Cmr2 and Cmr3 as the base, with Cmr4 and Cmr5 forming a helical core
CC along the mature crRNA (39 or 45 nt in length), while the complex is
CC capped by Cmr6 and Cmr1. The 5' end of the crRNA is bound to Cmr2 and
CC Cmr3, while Cmr6 and a Cmr1 subunit (Cmr1-1 or Cmr1-2) cap the 3' end
CC of the crRNA. The target RNA lies anti-parallel to the crRNA, with its
CC 5' end near Cmr1 and Cmr6 and its 3' end near Cmr2 and Cmr3; major
CC target RNA cleavage occurs nears the junction of Cmr1/Cmr6 and
CC Cmr4/Cmr5, with minor cleavage occurring at 6 nt intervals which
CC coincide with the proposed spacing of Cmr4 subunits (PubMed:24119404,
CC PubMed:25280103). Interacts with Cmr5 (PubMed:23370277). Interacts with
CC Cmr2, Cmr3, Cmr5 and Cmr6 (PubMed:25280103).
CC {ECO:0000269|PubMed:19945378, ECO:0000269|PubMed:23370277,
CC ECO:0000269|PubMed:24119404, ECO:0000269|PubMed:25280103}.
CC -!- INTERACTION:
CC Q8U1S9; Q8U1T0: cmr5; NbExp=2; IntAct=EBI-2504950, EBI-2504964;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:19945378}.
CC -!- SIMILARITY: Belongs to the CRISPR system Cmr4 family. {ECO:0000305}.
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DR EMBL; AE009950; AAL81250.1; -; Genomic_DNA.
DR RefSeq; WP_011012266.1; NZ_CP023154.1.
DR PDB; 4RDP; X-ray; 2.85 A; A/B=2-295.
DR PDB; 4W8W; X-ray; 2.80 A; A/B/C/D=1-295.
DR PDB; 4WNZ; X-ray; 2.80 A; A/B=1-295.
DR PDBsum; 4RDP; -.
DR PDBsum; 4W8W; -.
DR PDBsum; 4WNZ; -.
DR AlphaFoldDB; Q8U1S9; -.
DR SMR; Q8U1S9; -.
DR DIP; DIP-54367N; -.
DR IntAct; Q8U1S9; 4.
DR MINT; Q8U1S9; -.
DR STRING; 186497.PF1126; -.
DR PRIDE; Q8U1S9; -.
DR DNASU; 1468995; -.
DR EnsemblBacteria; AAL81250; AAL81250; PF1126.
DR GeneID; 41712935; -.
DR KEGG; pfu:PF1126; -.
DR PATRIC; fig|186497.12.peg.1187; -.
DR eggNOG; arCOG02657; Archaea.
DR HOGENOM; CLU_047795_0_0_2; -.
DR OMA; FAWITCP; -.
DR OrthoDB; 111027at2157; -.
DR PhylomeDB; Q8U1S9; -.
DR Proteomes; UP000001013; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0004519; F:endonuclease activity; IEA:UniProtKB-KW.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0051607; P:defense response to virus; IEA:UniProtKB-KW.
DR InterPro; IPR013410; CRISPR-assoc_RAMP_Cmr4.
DR InterPro; IPR005537; RAMP_III_fam.
DR PANTHER; PTHR36700; PTHR36700; 1.
DR Pfam; PF03787; RAMPs; 1.
DR TIGRFAMs; TIGR02580; cas_RAMP_Cmr4; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Antiviral defense; Cytoplasm; Endonuclease; Hydrolase;
KW Nuclease; Reference proteome; RNA-binding.
FT CHAIN 1..295
FT /note="CRISPR system Cmr endoribonuclease Cmr4"
FT /id="PRO_0000418077"
FT MUTAGEN 15
FT /note="H->A: Significant decrease in cleavage of target RNA
FT in the whole Cmr complex."
FT /evidence="ECO:0000269|PubMed:25280103"
FT MUTAGEN 26
FT /note="D->A: Nearly complete loss of cleavage of target RNA
FT in the whole Cmr complex."
FT /evidence="ECO:0000269|PubMed:25280103"
FT MUTAGEN 227
FT /note="E->A: Significant decrease in cleavage of target RNA
FT in the whole Cmr complex."
FT /evidence="ECO:0000269|PubMed:25280103"
FT MUTAGEN 229
FT /note="Y->A: Moderate decrease in cleavage of target RNA in
FT the whole Cmr complex."
FT /evidence="ECO:0000269|PubMed:25280103"
FT STRAND 3..12
FT /evidence="ECO:0007829|PDB:4WNZ"
FT TURN 33..35
FT /evidence="ECO:0007829|PDB:4WNZ"
FT STRAND 38..40
FT /evidence="ECO:0007829|PDB:4W8W"
FT HELIX 42..55
FT /evidence="ECO:0007829|PDB:4WNZ"
FT HELIX 61..67
FT /evidence="ECO:0007829|PDB:4WNZ"
FT STRAND 82..84
FT /evidence="ECO:0007829|PDB:4WNZ"
FT STRAND 87..105
FT /evidence="ECO:0007829|PDB:4WNZ"
FT HELIX 107..119
FT /evidence="ECO:0007829|PDB:4WNZ"
FT STRAND 133..138
FT /evidence="ECO:0007829|PDB:4WNZ"
FT TURN 140..142
FT /evidence="ECO:0007829|PDB:4WNZ"
FT STRAND 145..150
FT /evidence="ECO:0007829|PDB:4WNZ"
FT STRAND 153..157
FT /evidence="ECO:0007829|PDB:4WNZ"
FT HELIX 164..176
FT /evidence="ECO:0007829|PDB:4WNZ"
FT HELIX 178..184
FT /evidence="ECO:0007829|PDB:4WNZ"
FT STRAND 187..190
FT /evidence="ECO:0007829|PDB:4WNZ"
FT HELIX 193..201
FT /evidence="ECO:0007829|PDB:4WNZ"
FT STRAND 203..205
FT /evidence="ECO:0007829|PDB:4W8W"
FT STRAND 228..230
FT /evidence="ECO:0007829|PDB:4RDP"
FT STRAND 235..242
FT /evidence="ECO:0007829|PDB:4WNZ"
FT HELIX 248..259
FT /evidence="ECO:0007829|PDB:4WNZ"
FT TURN 260..263
FT /evidence="ECO:0007829|PDB:4WNZ"
FT STRAND 265..267
FT /evidence="ECO:0007829|PDB:4WNZ"
FT TURN 272..275
FT /evidence="ECO:0007829|PDB:4WNZ"
FT STRAND 277..284
FT /evidence="ECO:0007829|PDB:4WNZ"
SQ SEQUENCE 295 AA; 32630 MW; FFF22879BB86CECE CRC64;
MKAYLVGLYT LTPTHPGSGT ELGVVDQPIQ RERHTGFPVI WGQSLKGVLR SYLKLVEKVD
EEKINKIFGP PTEKAHEQAG LISVGDAKIL FFPVRSLKGV YAYVTSPLVL NRFKRDLELA
GVKNFQTEIP ELTDTAIASE EITVDNKVIL EEFAILIQKD DKGILESVVK AIEQAFGNEM
AEKIKGRIAI IPDDVFRDLV ELSTEIVARI RINAETGTVE TGGLWYEEYI PSDTLFYSLI
LVTPRAKDND MALIKEVLGK INGKYLQIGG NETVGKGFVK VTLKEVTNNG GTHAK
