Family Search for PF12469 (Cmr2_N)

April 2024: See Interactive Tools for Functional Annotation of Bacterial Genomes for advice on using these tools.

Running HMMer for PF12469

PF12469 hits 23 sequences in PaperBLAST's database above the trusted cutoff. Showing hits to curated sequences only. Or see all hits or try another family.

CMR2_PYRFU / Q8U1S6 CRISPR system Cmr subunit Cmr2; CRISPR-associated protein Cas10/Cmr2, subtype III-B from Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (see 7 papers)
Aligns to 221:331 / 871 (12.7%), covers 97.3% of PF12469, 111.9 bits

• 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), formerly called psiRNA (prokaryotic silencing) in this organism. Part of the Cmr ribonucleoprotein complex which has divalent cation- dependent endoribonuclease activity specific for ssRNA complementary to the crRNA (target RNA), generating 5' hydroxy- and 3' phosphate or 2'- 3' cyclic phosphate termini. Cmr4 is probably the subunit that cleaves target RNA (PubMed:25280103). Cmr complex does not cleave ssDNA complementary to the crRNA. Cleavage of target RNA is guided by the crRNA; substrate cleavage occurs a fixed distance (14 nt) from the 3' end of the crRNA. In vitro reconstitution shows Cmr1-2 and Cmr5 are not absolutely necessary for target cleavage (PubMed:19945378).
  cofactor: Ca(2+) (Binds 2 Ca(2+) per subunit, this may not be the physiological cation.)
  cofactor: Mn(2+) (Binds 4 Mn(2+) per subunit.)
  cofactor: Zn(2+) (Binds 1 Zn(2+) ion per subunit.)
  subunit: Part of the type III-B Cmr ribonucleoprotein (RNP) complex, an elongated RNP with Cmr2 and Cmr3 as the base, with Cmr4 and Cmr5 forming a helical core along the mature crRNA (39 or 45 nt in length), while the complex is capped by Cmr6 and Cmr1. The 5' end of the crRNA is bound to Cmr2 and Cmr3, while Cmr6 and a Cmr1 subunit (Cmr1-1 or Cmr1-2) cap the 3' end of the crRNA. The target RNA lies antiparallel to the crRNA, with its 5' end near Cmr1 and Cmr6 and its 3' end near Cmr2 and Cmr3; major target cleavage occurs nears the junction of Cmr1/Cmr6 and Cmr4/Cmr, with minor cleavage occurring at 6 nt intervals which coincide with the proposed spacing of Cmr4 subunits (PubMed:24119404, PubMed:25280103). Forms a 1:1 complex with Cmr3 (PubMed:23583914, PubMed:23395183). The Cmr2-Cmr3 complex non- specifically binds ss-target RNA and crRNA (PubMed:23583914). Interacts with Cmr3, Cmr4 and Cmr5 (PubMed:25280103).

CMR2_SACS2 / Q97WX0 CRISPR system CMR subunit Cmr2; CRISPR-associated protein Cas10/Cmr2, subtype III-B from Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (Sulfolobus solfataricus) (see paper)
Aligns to 204:354 / 1045 (14.4%), covers 100.0% of PF12469, 100.6 bits

• 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 spacers, sequences complementary to antecedent mobile elements, and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA) (By similarity). The CMR complex degrades RNA complementary to the crRNA (target RNA) within UA dinucleotides, generating 3'-OH and 5'-phosphate ends. Activity is dependent on the 8 nt long 5' tag in the crRNA, an unpaired 3' flag on the target RNA, and is stimulated by ATP. Some cleavage of the guide crRNA can also be observed.
  cofactor: Ca(2+) (Binds 2 Ca(2+) per subunit.)
  cofactor: Zn(2+) (Binds 1 Zn(2+) ion per subunit.)
  subunit: Part of the CMR ribonucleoprotein complex, consisting of crRNA plus Cmr1/Cmr2/Cmr3/Cmr4/Cmr5/Cmr6 at 1:1 and possibly 3 Cmr7 dimers. A Cmr2/Cmr3/Cmr7 subcomplex without crRNA can also be isolated. It does not cleave target RNA.

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