CSM3_STRTR
ID CSM3_STRTR Reviewed; 220 AA.
AC A0A0A7HIF0;
DT 10-APR-2019, integrated into UniProtKB/Swiss-Prot.
DT 04-MAR-2015, sequence version 1.
DT 25-MAY-2022, entry version 31.
DE RecName: Full=CRISPR system Cms endoribonuclease Csm3;
DE Short=Csm3 RNase;
DE EC=3.1.-.- {ECO:0000269|PubMed:25458845};
DE AltName: Full=CRISPR type III A-associated RAMP protein Csm3;
GN Name=csm3 {ECO:0000303|PubMed:25458845};
OS Streptococcus thermophilus.
OC Bacteria; Firmicutes; Bacilli; Lactobacillales; Streptococcaceae;
OC Streptococcus.
OX NCBI_TaxID=1308;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION IN PHAGE RESISTANCE, TARGETS
RP SSRNA, FUNCTION AS AN ENDONUCLEASE, COFACTOR, ACTIVITY REGULATION, SUBUNIT,
RP MUTAGENESIS OF HIS-19; ASP-33; ASP-100; GLU-119; GLU-123 AND GLU-139, AND
RP ANTIVIRAL DEFENSE.
RC STRAIN=DGCC8004;
RX PubMed=25458845; DOI=10.1016/j.molcel.2014.09.027;
RA Tamulaitis G., Kazlauskiene M., Manakova E., Venclovas C., Nwokeoji A.O.,
RA Dickman M.J., Horvath P., Siksnys V.;
RT "Programmable RNA shredding by the type III-A CRISPR-Cas system of
RT Streptococcus thermophilus.";
RL Mol. Cell 56:506-517(2014).
RN [2]
RP FUNCTION, COFACTOR, SUBUNIT, AND MUTAGENESIS OF ASP-33.
RC STRAIN=DGCC8004;
RX PubMed=27105119; DOI=10.1016/j.molcel.2016.03.024;
RA Kazlauskiene M., Tamulaitis G., Kostiuk G., Venclovas C., Siksnys V.;
RT "Spatiotemporal control of type III-A CRISPR-Cas immunity: coupling DNA
RT degradation with the target RNA recognition.";
RL Mol. Cell 62:295-306(2016).
RN [3]
RP SUBUNIT.
RC STRAIN=DGCC8004;
RX PubMed=28663439; DOI=10.1126/science.aao0100;
RA Kazlauskiene M., Kostiuk G., Venclovas C., Tamulaitis G., Siksnys V.;
RT "A cyclic oligonucleotide signaling pathway in type III CRISPR-Cas
RT systems.";
RL Science 357:605-609(2017).
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 spacers, sequences complementary to
CC antecedent mobile elements, and target invading nucleic acids. CRISPR
CC clusters are transcribed and processed into CRISPR RNA (crRNA). The
CC type III-A Csm effector complex binds crRNA and acts as a crRNA-guided
CC RNase, DNase and cyclic oligoadenylate synthase; binding of target RNA
CC cognate to the crRNA is required for all activities. In a heterologous
CC host this Csm effector complex restricts ssRNA phage MS2, suggesting it
CC may target RNA viruses in vivo. {ECO:0000269|PubMed:25458845}.
CC -!- FUNCTION: Csm functions as a non-specific ssDNase. Base-pairing between
CC crRNA and target RNA to form a ternary Csm complex activates a ssDNase
CC activity; target RNA cleavage suppresses the ssDNase, a temporal
CC control that prevents uncontrolled DNA degradation. Viral RNA
CC transcripts probably tether the Csm complex to the viral genome,
CC recruiting Cas10 ssDNA activity which is able to degrade DNA in the
CC transcription bubble, spatially controlling the DNase activity.
CC {ECO:0000269|PubMed:27105119}.
CC -!- FUNCTION: This subunit has the target ssRNA endonuclease activity; it
CC cleaves multiple sites in the target RNA at 6 nucleotide intervals. The
CC number of cleavage sites in the target RNA correlates with the number
CC of Csm3 subunits in the Csm effector complex (PubMed:25458845). In the
CC Csm complex target RNA and ssDNA are cleaved simultaneously, although
CC RNase activity (of Csm3) is much faster. RNA cleavage by Csm3 is not
CC required for ssDNase activity as Csm complex with inactive Csm3 still
CC has ssDNase activity; however as the cleaved target RNA products
CC dissociate away ssDNase activity decreases (PubMed:27105119).
CC {ECO:0000269|PubMed:25458845, ECO:0000269|PubMed:27105119}.
CC -!- COFACTOR:
CC Name=a metal cation; Xref=ChEBI:CHEBI:25213;
CC Evidence={ECO:0000269|PubMed:25458845};
CC Note=Endonucleolytic cleavage of target ssRNA by the Csm complex
CC requires a divalent metal ion; Mg(2+) has the best activity in vitro,
CC but Mn(2+), Ca(2+), Zn(2+), Ni(2+), and Co(2+) also support cleavage.
CC {ECO:0000269|PubMed:25458845, ECO:0000305|PubMed:27105119};
CC -!- ACTIVITY REGULATION: Target ssRNase is inhibited by EDTA.
CC {ECO:0000269|PubMed:25458845}.
CC -!- SUBUNIT: Part of the Csm effector complex that includes at least
CC Cas10(1), Csm2(3), Csm3(5), Csm4(1), Csm5(1) and mature crRNA
CC (PubMed:25458845, PubMed:27105119, PubMed:28663439). The Csm complex is
CC elongated and slightly twisted with a maximal length of 215 Angstroms
CC and a diameter of 75-80 Angstroms (PubMed:25458845). It has been
CC modeled to have a central protein filamant of Csm3 subunits along which
CC the dsRNA helix of paired crRNA and target RNA binds. The filament is
CC capped at one end by Cas10 and Csm4 and at the other end by Csm5; ssDNA
CC is thought to bind to the N-terminal HD domain of Cas10 (Probable). Csm
CC with a precursor crRNA does not include Csm5, while Cas6, the enzyme
CC probably involved in pre-crRNA processing, is found associated with a
CC subset of the Csm complex (PubMed:25458845).
CC {ECO:0000269|PubMed:25458845, ECO:0000269|PubMed:27105119,
CC ECO:0000269|PubMed:28663439, ECO:0000305|PubMed:25458845,
CC ECO:0000305|PubMed:27105119}.
CC -!- MISCELLANEOUS: Encoded in a type III-A CRISPR locus.
CC {ECO:0000269|PubMed:25458845}.
CC -!- SIMILARITY: Belongs to the CRISPR-associated Csm3 family.
CC {ECO:0000305}.
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DR EMBL; KM222358; AIZ03606.1; -; Genomic_DNA.
DR RefSeq; WP_011681112.1; NZ_QFLC01000003.1.
DR PDB; 6NUD; EM; 3.50 A; C/E/N/O/P=1-220.
DR PDB; 6NUE; EM; 3.30 A; C/E/N/O/P=1-220.
DR PDBsum; 6NUD; -.
DR PDBsum; 6NUE; -.
DR AlphaFoldDB; A0A0A7HIF0; -.
DR SMR; A0A0A7HIF0; -.
DR STRING; 322159.STER_0975; -.
DR EnsemblBacteria; POO15348; POO15348; CDA68_00842.
DR PATRIC; fig|1308.45.peg.983; -.
DR eggNOG; COG1337; Bacteria.
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; IPR013412; CRISPR-assoc_RAMP_Csm3.
DR InterPro; IPR005537; RAMP_III_fam.
DR Pfam; PF03787; RAMPs; 1.
DR TIGRFAMs; TIGR02582; cas7_TM1809; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Antiviral defense; Endonuclease; Hydrolase; Nuclease;
KW RNA-binding.
FT CHAIN 1..220
FT /note="CRISPR system Cms endoribonuclease Csm3"
FT /id="PRO_0000446119"
FT MUTAGEN 19
FT /note="H->A: Wild-type degradation of target ssRNA by the
FT Csm complex."
FT /evidence="ECO:0000269|PubMed:25458845"
FT MUTAGEN 33
FT /note="D->A: No degradation of target ssRNA by the Csm
FT complex, complex assembles normally and binds ssRNA. 10(3)
FT to 10(4) decreased growth of an RNA phage in vivo. No
FT change in ssDNase activity of the ternary Csm complex."
FT /evidence="ECO:0000269|PubMed:25458845,
FT ECO:0000269|PubMed:27105119"
FT MUTAGEN 100
FT /note="D->A: Nearly wild-type degradation of target ssRNA
FT by the Csm complex, crRNA is shorter, Csm complex is
FT altered."
FT /evidence="ECO:0000269|PubMed:25458845"
FT MUTAGEN 119
FT /note="E->A: Wild-type degradation of target ssRNA by the
FT Csm complex."
FT /evidence="ECO:0000269|PubMed:25458845"
FT MUTAGEN 123
FT /note="E->A: Wild-type degradation of target ssRNA by the
FT Csm complex."
FT /evidence="ECO:0000269|PubMed:25458845"
FT MUTAGEN 139
FT /note="E->A: Wild-type degradation of target ssRNA by the
FT Csm complex."
FT /evidence="ECO:0000269|PubMed:25458845"
FT STRAND 5..16
FT /evidence="ECO:0007829|PDB:6NUE"
FT STRAND 23..25
FT /evidence="ECO:0007829|PDB:6NUE"
FT STRAND 27..30
FT /evidence="ECO:0007829|PDB:6NUE"
FT STRAND 40..42
FT /evidence="ECO:0007829|PDB:6NUE"
FT HELIX 50..60
FT /evidence="ECO:0007829|PDB:6NUE"
FT TURN 61..63
FT /evidence="ECO:0007829|PDB:6NUE"
FT STRAND 70..73
FT /evidence="ECO:0007829|PDB:6NUD"
FT TURN 77..79
FT /evidence="ECO:0007829|PDB:6NUE"
FT HELIX 80..83
FT /evidence="ECO:0007829|PDB:6NUE"
FT STRAND 95..97
FT /evidence="ECO:0007829|PDB:6NUE"
FT HELIX 105..107
FT /evidence="ECO:0007829|PDB:6NUE"
FT HELIX 109..112
FT /evidence="ECO:0007829|PDB:6NUE"
FT STRAND 117..122
FT /evidence="ECO:0007829|PDB:6NUE"
FT STRAND 128..133
FT /evidence="ECO:0007829|PDB:6NUE"
FT STRAND 137..141
FT /evidence="ECO:0007829|PDB:6NUE"
FT STRAND 149..154
FT /evidence="ECO:0007829|PDB:6NUE"
FT HELIX 163..177
FT /evidence="ECO:0007829|PDB:6NUE"
FT STRAND 183..185
FT /evidence="ECO:0007829|PDB:6NUE"
FT STRAND 187..189
FT /evidence="ECO:0007829|PDB:6NUD"
FT STRAND 193..204
FT /evidence="ECO:0007829|PDB:6NUE"
SQ SEQUENCE 220 AA; 24569 MW; AC361B95CB8A3DF8 CRC64;
MTFAKIKFSA QIRLETGLHI GGSDAFAAIG AIDSPVIKDP ITNIPIIPGS SLKGKMRTLL
AKVYNEKVAE KPSDDSDILS RLFGNSKDKR FKMGRLIFRD AFLSNADELD SLGVRSYTEV
KFENTIDRIT AEANPRQIER AIRNSTFDFE LIYEITDENE NQVEEDFKVI RDGLKLLELD
YLGGSGSRGY GKVAFEKLKA TTVFGNYDVK TLNELLTAEV
