CMR3_PYRFU
ID CMR3_PYRFU Reviewed; 322 AA.
AC Q8U1S7;
DT 11-JUL-2012, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2002, sequence version 1.
DT 03-AUG-2022, entry version 91.
DE RecName: Full=CRISPR system Cmr subunit Cmr3;
DE AltName: Full=CRISPR type III-B/RAMP module-associated protein Cmr3;
GN Name=cmr3 {ECO:0000303|PubMed:19945378}; OrderedLocusNames=PF1128;
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 FUNCTION, INTERACTION WITH CMR2 AND CMR4, AND SUBUNIT.
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).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) IN COMPLEX WITH CMR2 AND NUCLEOTIDES,
RP SUBUNIT, AND POSSIBLE RNA-BINDING.
RC STRAIN=ATCC 43587 / DSM 3638 / JCM 8422 / Vc1;
RX PubMed=23583914; DOI=10.1016/j.jmb.2013.03.042;
RA Osawa T., Inanaga H., Numata T.;
RT "Crystal structure of the Cmr2-Cmr3 subcomplex in the CRISPR-Cas RNA
RT silencing effector complex.";
RL J. Mol. Biol. 425:3811-3823(2013).
RN [5]
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 [6]
RP X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF 215-871 IN COMPLEX WITH CMR3 AND
RP ATP, SUBUNIT, AND MUTAGENESIS OF ASP-10; 96-ASN--ILE-105; GLU-144; GLU-160;
RP 198-GLY--ARG-202; 198-GLY-GLY-199; GLU-200; 267-SER-LYS-277 AND TYR-313.
RC STRAIN=ATCC 43587 / DSM 3638 / JCM 8422 / Vc1;
RX PubMed=23395183; DOI=10.1016/j.str.2013.01.002;
RA Shao Y., Cocozaki A.I., Ramia N.F., Terns R.M., Terns M.P., Li H.;
RT "Structure of the Cmr2-Cmr3 subcomplex of the Cmr RNA silencing complex.";
RL Structure 21:376-384(2013).
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. Cmr4 is probably the subunit that cleaves
CC target RNA (PubMed:25280103). Cmr complex does not cleave ssDNA
CC complementary to the crRNA. Cleavage of invading 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. {ECO:0000269|PubMed:19945378,
CC ECO:0000269|PubMed:25280103}.
CC -!- SUBUNIT: Part of the type III-B Cmr ribonucleoprotein (RNP) complex, an
CC elongated RNP with Cmr2 and Cmr3 as the base, with Cmr4 and Cmr5
CC forming a helical core along the mature crRNA (39 or 45 nt in length),
CC while the complex is capped by Cmr6 and Cmr1. The 5' end of the crRNA
CC is bound to Cmr2 and Cmr3, while Cmr6 and a Cmr1 subunit (Cmr1-1 or
CC Cmr1-2) cap the 3' end of the crRNA. The target RNA lies antiparallel
CC to the crRNA, with its 5' end near Cmr1 and Cmr6 and its 3' end near
CC Cmr2 and Cmr3; major target cleavage occurs nears the junction of
CC Cmr1/Cmr6 and Cmr4/Cmr, with minor cleavage occurring at 6 nt intervals
CC which coincide with the proposed spacing of Cmr4 subunits
CC (PubMed:24119404, PubMed:25280103). Forms a 1:1 complex with Cmr2
CC (PubMed:23583914, PubMed:23395183, PubMed:23583914). Interacts with
CC Cmr4 (PubMed:25280103). The complex non-specifically binds ss-target
CC RNA and crRNA (PubMed:23583914). {ECO:0000269|PubMed:19945378,
CC ECO:0000269|PubMed:23395183, ECO:0000269|PubMed:23583914,
CC ECO:0000269|PubMed:24119404, ECO:0000269|PubMed:25280103}.
CC -!- INTERACTION:
CC Q8U1S7; Q8U1S6: cmr2; NbExp=6; IntAct=EBI-2504943, EBI-2504936;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:19945378}.
CC -!- SIMILARITY: Belongs to the CRISPR system Cmr3 family. {ECO:0000305}.
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DR EMBL; AE009950; AAL81252.1; -; Genomic_DNA.
DR RefSeq; WP_011012268.1; NZ_CP023154.1.
DR PDB; 3W2V; X-ray; 2.60 A; B=1-322.
DR PDB; 3W2W; X-ray; 2.50 A; B=1-322.
DR PDB; 3X1L; X-ray; 2.10 A; B=1-322.
DR PDB; 4H4K; X-ray; 2.80 A; A=1-322.
DR PDBsum; 3W2V; -.
DR PDBsum; 3W2W; -.
DR PDBsum; 3X1L; -.
DR PDBsum; 4H4K; -.
DR AlphaFoldDB; Q8U1S7; -.
DR SMR; Q8U1S7; -.
DR DIP; DIP-54365N; -.
DR IntAct; Q8U1S7; 3.
DR STRING; 186497.PF1128; -.
DR PRIDE; Q8U1S7; -.
DR EnsemblBacteria; AAL81252; AAL81252; PF1128.
DR GeneID; 41712937; -.
DR KEGG; pfu:PF1128; -.
DR PATRIC; fig|186497.12.peg.1189; -.
DR eggNOG; arCOG02663; Archaea.
DR HOGENOM; CLU_044328_1_0_2; -.
DR OMA; REEPECI; -.
DR OrthoDB; 127888at2157; -.
DR PhylomeDB; Q8U1S7; -.
DR Proteomes; UP000001013; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0000166; F:nucleotide binding; 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; IPR010165; CRISPR-assoc_prot_TM1793.
DR InterPro; IPR019117; CRISPR-assoc_protein_Cmr3.
DR Pfam; PF09700; Cas_Cmr3; 1.
DR TIGRFAMs; TIGR01888; cas_cmr3; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Antiviral defense; Cytoplasm; Nucleotide-binding;
KW Reference proteome; RNA-binding.
FT CHAIN 1..322
FT /note="CRISPR system Cmr subunit Cmr3"
FT /id="PRO_0000418075"
FT MUTAGEN 10
FT /note="D->N: Still cleaves target RNA when assembled in the
FT Cmr complex."
FT /evidence="ECO:0000269|PubMed:23395183"
FT MUTAGEN 96..105
FT /note="Missing: Loss of interaction with Cmr2, still
FT cleaves target RNA when assembled in the Cmr complex."
FT /evidence="ECO:0000269|PubMed:23395183"
FT MUTAGEN 144
FT /note="E->Q: Still cleaves target RNA when assembled in the
FT Cmr complex."
FT /evidence="ECO:0000269|PubMed:23395183"
FT MUTAGEN 160
FT /note="E->Q: Still cleaves target RNA when assembled in the
FT Cmr complex."
FT /evidence="ECO:0000269|PubMed:23395183"
FT MUTAGEN 198..202
FT /note="Missing: No cleavage of target RNA when assembled in
FT the Cmr complex."
FT /evidence="ECO:0000269|PubMed:23395183"
FT MUTAGEN 198..199
FT /note="GG->AA: Still cleaves target RNA when assembled in
FT the Cmr complex."
FT /evidence="ECO:0000269|PubMed:23395183"
FT MUTAGEN 200
FT /note="E->Q: Still cleaves target RNA when assembled in the
FT Cmr complex."
FT /evidence="ECO:0000269|PubMed:23395183"
FT MUTAGEN 267..277
FT /note="Missing: Loss of interaction with Cmr2, no cleavage
FT of target RNA when assembled in the Cmr complex."
FT /evidence="ECO:0000269|PubMed:23395183"
FT MUTAGEN 313
FT /note="Y->A: Still cleaves target RNA when assembled in the
FT Cmr complex."
FT /evidence="ECO:0000269|PubMed:23395183"
FT STRAND 2..10
FT /evidence="ECO:0007829|PDB:3X1L"
FT HELIX 22..26
FT /evidence="ECO:0007829|PDB:3W2W"
FT STRAND 27..30
FT /evidence="ECO:0007829|PDB:3X1L"
FT HELIX 35..49
FT /evidence="ECO:0007829|PDB:3X1L"
FT HELIX 52..55
FT /evidence="ECO:0007829|PDB:3X1L"
FT TURN 56..58
FT /evidence="ECO:0007829|PDB:3X1L"
FT STRAND 59..61
FT /evidence="ECO:0007829|PDB:3X1L"
FT STRAND 63..72
FT /evidence="ECO:0007829|PDB:3X1L"
FT STRAND 78..80
FT /evidence="ECO:0007829|PDB:3X1L"
FT STRAND 85..88
FT /evidence="ECO:0007829|PDB:3X1L"
FT STRAND 91..94
FT /evidence="ECO:0007829|PDB:3X1L"
FT STRAND 98..100
FT /evidence="ECO:0007829|PDB:3X1L"
FT STRAND 103..105
FT /evidence="ECO:0007829|PDB:3X1L"
FT STRAND 116..118
FT /evidence="ECO:0007829|PDB:3X1L"
FT HELIX 119..126
FT /evidence="ECO:0007829|PDB:3X1L"
FT STRAND 132..134
FT /evidence="ECO:0007829|PDB:3X1L"
FT HELIX 135..137
FT /evidence="ECO:0007829|PDB:3X1L"
FT STRAND 142..151
FT /evidence="ECO:0007829|PDB:3X1L"
FT TURN 153..155
FT /evidence="ECO:0007829|PDB:3X1L"
FT STRAND 157..170
FT /evidence="ECO:0007829|PDB:3X1L"
FT STRAND 172..179
FT /evidence="ECO:0007829|PDB:3X1L"
FT STRAND 181..183
FT /evidence="ECO:0007829|PDB:3X1L"
FT HELIX 185..191
FT /evidence="ECO:0007829|PDB:3X1L"
FT STRAND 193..196
FT /evidence="ECO:0007829|PDB:3X1L"
FT STRAND 203..210
FT /evidence="ECO:0007829|PDB:3X1L"
FT HELIX 214..217
FT /evidence="ECO:0007829|PDB:3X1L"
FT STRAND 222..232
FT /evidence="ECO:0007829|PDB:3X1L"
FT STRAND 234..236
FT /evidence="ECO:0007829|PDB:3X1L"
FT HELIX 238..248
FT /evidence="ECO:0007829|PDB:3X1L"
FT STRAND 253..259
FT /evidence="ECO:0007829|PDB:3X1L"
FT STRAND 264..266
FT /evidence="ECO:0007829|PDB:3X1L"
FT TURN 271..274
FT /evidence="ECO:0007829|PDB:3X1L"
FT STRAND 280..283
FT /evidence="ECO:0007829|PDB:3X1L"
FT STRAND 288..298
FT /evidence="ECO:0007829|PDB:3X1L"
FT STRAND 301..304
FT /evidence="ECO:0007829|PDB:3X1L"
FT TURN 312..314
FT /evidence="ECO:0007829|PDB:3W2W"
FT STRAND 315..320
FT /evidence="ECO:0007829|PDB:3X1L"
SQ SEQUENCE 322 AA; 36315 MW; 0097FC64CA296F03 CRC64;
MIEVTFTPYD VLLFRESRPF DAGSESVARS IIPLPQTVAG AIRTLLFYKG LKNCVGVGEE
EPEFTLVGIA IGTEKGRIYP LPFNIIKSEK FYKVVNPGRF LGKLILPPKG KYKSGYVTES
ILEKYLKGEL KEVEENKVIR IEKEKRIGIK LSREKKVVEE GMLYTVEFLR IEKIYAWIED
PGCGIKDILS SYEFLTLGGE SRVAFVEVDD KTPDIFNREL GSTKKALFYF STPTIGKVGE
IVQELEKRLN AKIDDYLLVS SRPTAISGWD MHEKKPKGTK FAIPPGSVLF VEFKEEVEVP
PYIKLGKLKK LGYGLALGGI WE
