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Protein

CRISPR system Cmr endoribonuclease Cmr4

Gene

cmr4

Organism
Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

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. This is probably the subunit that cleaves the 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).2 Publications

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Hydrolase, Nuclease

Keywords - Biological processi

Antiviral defense

Keywords - Ligandi

RNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
CRISPR system Cmr endoribonuclease Cmr41 Publication (EC:3.1.-.-)
Alternative name(s):
CRISPR type III-B/RAMP module RAMP protein Cmr4
Target RNase Cmr4
Gene namesi
Name:cmr41 Publication
Ordered Locus Names:PF1126
OrganismiPyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
Taxonomic identifieri186497 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
Proteomesi
  • UP000001013 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi15 – 151H → A: Significant decrease in cleavage of target RNA in the whole Cmr complex. 1 Publication
Mutagenesisi26 – 261D → A: Nearly complete loss of cleavage of target RNA in the whole Cmr complex. 1 Publication
Mutagenesisi227 – 2271E → A: Significant decrease in cleavage of target RNA in the whole Cmr complex. 1 Publication
Mutagenesisi229 – 2291Y → A: Moderate decrease in cleavage of target RNA in the whole Cmr complex. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 295295CRISPR system Cmr endoribonuclease Cmr4PRO_0000418077Add
BLAST

Proteomic databases

PRIDEiQ8U1S9.

Interactioni

Subunit structurei

Forms oligomers in isolation (PubMed:23370277). 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 anti-parallel to the crRNA, with its 5' end near Cmr1 and Cmr6 and its 3' end near Cmr2 and Cmr3; major target RNA cleavage occurs nears the junction of Cmr1/Cmr6 and Cmr4/Cmr5, with minor cleavage occurring at 6 nt intervals which coincide with the proposed spacing of Cmr4 subunits (PubMed:24119404, PubMed:25280103). Interacts with Cmr5 (PubMed:23370277). Interacts with Cmr2, Cmr3, Cmr5 and Cmr6 (PubMed:25280103).4 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
cmr5Q8U1T02EBI-2504950,EBI-2504964

Protein-protein interaction databases

DIPiDIP-54367N.
IntActiQ8U1S9. 4 interactions.
MINTiMINT-8409090.
STRINGi186497.PF1126.

Structurei

Secondary structure

1
295
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 1210Combined sources
Turni33 – 353Combined sources
Beta strandi38 – 403Combined sources
Helixi42 – 5514Combined sources
Helixi61 – 677Combined sources
Beta strandi82 – 843Combined sources
Beta strandi87 – 10519Combined sources
Helixi107 – 11913Combined sources
Beta strandi133 – 1386Combined sources
Turni140 – 1423Combined sources
Beta strandi145 – 1506Combined sources
Beta strandi153 – 1575Combined sources
Helixi164 – 17613Combined sources
Helixi178 – 1847Combined sources
Beta strandi187 – 1904Combined sources
Helixi193 – 2019Combined sources
Beta strandi203 – 2053Combined sources
Beta strandi228 – 2303Combined sources
Beta strandi235 – 2428Combined sources
Helixi248 – 25912Combined sources
Turni260 – 2634Combined sources
Beta strandi265 – 2673Combined sources
Turni272 – 2754Combined sources
Beta strandi277 – 2848Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4RDPX-ray2.85A/B2-295[»]
4W8WX-ray2.80A/B/C/D1-295[»]
4WNZX-ray2.80A/B1-295[»]
ProteinModelPortaliQ8U1S9.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the CRISPR system Cmr4 family.Curated

Phylogenomic databases

eggNOGiarCOG02657. Archaea.
COG1336. LUCA.
HOGENOMiHOG000226211.
KOiK09000.
OMAiVFAWITC.

Family and domain databases

InterProiIPR013410. CRISPR-assoc_RAMP_Cmr4.
IPR005537. RAMP_III_fam.
[Graphical view]
PfamiPF03787. RAMPs. 1 hit.
[Graphical view]
TIGRFAMsiTIGR02580. cas_RAMP_Cmr4. 1 hit.

Sequencei

Sequence statusi: Complete.

Q8U1S9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKAYLVGLYT LTPTHPGSGT ELGVVDQPIQ RERHTGFPVI WGQSLKGVLR
60 70 80 90 100
SYLKLVEKVD EEKINKIFGP PTEKAHEQAG LISVGDAKIL FFPVRSLKGV
110 120 130 140 150
YAYVTSPLVL NRFKRDLELA GVKNFQTEIP ELTDTAIASE EITVDNKVIL
160 170 180 190 200
EEFAILIQKD DKGILESVVK AIEQAFGNEM AEKIKGRIAI IPDDVFRDLV
210 220 230 240 250
ELSTEIVARI RINAETGTVE TGGLWYEEYI PSDTLFYSLI LVTPRAKDND
260 270 280 290
MALIKEVLGK INGKYLQIGG NETVGKGFVK VTLKEVTNNG GTHAK
Length:295
Mass (Da):32,630
Last modified:June 1, 2002 - v1
Checksum:iFFF22879BB86CECE
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE009950 Genomic DNA. Translation: AAL81250.1.
RefSeqiWP_011012266.1. NC_003413.1.

Genome annotation databases

EnsemblBacteriaiAAL81250; AAL81250; PF1126.
GeneIDi1468995.
KEGGipfu:PF1126.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE009950 Genomic DNA. Translation: AAL81250.1.
RefSeqiWP_011012266.1. NC_003413.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4RDPX-ray2.85A/B2-295[»]
4W8WX-ray2.80A/B/C/D1-295[»]
4WNZX-ray2.80A/B1-295[»]
ProteinModelPortaliQ8U1S9.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-54367N.
IntActiQ8U1S9. 4 interactions.
MINTiMINT-8409090.
STRINGi186497.PF1126.

Proteomic databases

PRIDEiQ8U1S9.

Protocols and materials databases

DNASUi1468995.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAL81250; AAL81250; PF1126.
GeneIDi1468995.
KEGGipfu:PF1126.

Phylogenomic databases

eggNOGiarCOG02657. Archaea.
COG1336. LUCA.
HOGENOMiHOG000226211.
KOiK09000.
OMAiVFAWITC.

Family and domain databases

InterProiIPR013410. CRISPR-assoc_RAMP_Cmr4.
IPR005537. RAMP_III_fam.
[Graphical view]
PfamiPF03787. RAMPs. 1 hit.
[Graphical view]
TIGRFAMsiTIGR02580. cas_RAMP_Cmr4. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiCMR4_PYRFU
AccessioniPrimary (citable) accession number: Q8U1S9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 11, 2012
Last sequence update: June 1, 2002
Last modified: September 7, 2016
This is version 74 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.