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Entry version 25 (11 Dec 2019)
Sequence version 1 (04 Mar 2015)
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Protein

CRISPR system Cms endoribonuclease Csm3

Gene

csm3

Organism
Streptococcus thermophilus
Status
Reviewed-Annotation score:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>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 spacers, sequences complementary to antecedent mobile elements, and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). The type III-A Csm effector complex binds crRNA and acts as a crRNA-guided RNase, DNase and cyclic oligoadenylate synthase; binding of target RNA cognate to the crRNA is required for all activities. In a heterologous host this Csm effector complex restricts ssRNA phage MS2, suggesting it may target RNA viruses in vivo.1 Publication
Csm functions as a non-specific ssDNase. Base-pairing between crRNA and target RNA to form a ternary Csm complex activates a ssDNase activity; target RNA cleavage suppresses the ssDNase, a temporal control that prevents uncontrolled DNA degradation. Viral RNA transcripts probably tether the Csm complex to the viral genome, recruiting Cas10 ssDNA activity which is able to degrade DNA in the transcription bubble, spatially controlling the DNase activity.1 Publication
This subunit has the target ssRNA endonuclease activity; it cleaves multiple sites in the target RNA at 6 nucleotide intervals. The number of cleavage sites in the target RNA correlates with the number of Csm3 subunits in the Csm effector complex (PubMed:25458845). In the Csm complex target RNA and ssDNA are cleaved simultaneously, although RNase activity (of Csm3) is much faster. RNA cleavage by Csm3 is not required for ssDNase activity as Csm complex with inactive Csm3 still has ssDNase activity; however as the cleaved target RNA products dissociate away ssDNase activity decreases (PubMed:27105119).2 Publications

Miscellaneous

Encoded in a type III-A CRISPR locus.1 Publication

<p>This subsection of the ‘Function’ section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

a metal cation1 PublicationNote: Endonucleolytic cleavage of target ssRNA by the Csm complex requires a divalent metal ion; Mg2+ has the best activity in vitro, but Mn2+, Ca2+, Zn2+, Ni2+, and Co2+ also support cleavage.1 Publication1 Publication

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes regulatory mechanisms for enzymes, transporters or microbial transcription factors, and reports the components which regulate (by activation or inhibition) the reaction.<p><a href='/help/activity_regulation' target='_top'>More...</a></p>Activity regulationi

Target ssRNase is inhibited by EDTA.1 Publication

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionEndonuclease, Hydrolase, Nuclease, RNA-binding
Biological processAntiviral defense

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

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BioCyci
GCF_001663795:G1EVC-217-MONOMER
GCF_001855705:G1FB8-1892-MONOMER

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
CRISPR system Cms endoribonuclease Csm3 (EC:3.1.-.-1 Publication)
Short name:
Csm3 RNase
Alternative name(s):
CRISPR type III A-associated RAMP protein Csm3
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:csm31 Publication
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiStreptococcus thermophilus
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri1308 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesStreptococcaceaeStreptococcus

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/manual/pathology_and_biotech_section">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>Mutagenesisi19H → A: Wild-type degradation of target ssRNA by the Csm complex. 1 Publication1
Mutagenesisi33D → A: No degradation of target ssRNA by the Csm complex, complex assembles normally and binds ssRNA. 10(3) to 10(4) decreased growth of an RNA phage in vivo. No change in ssDNase activity of the ternary Csm complex. 2 Publications1
Mutagenesisi100D → A: Nearly wild-type degradation of target ssRNA by the Csm complex, crRNA is shorter, Csm complex is altered. 1 Publication1
Mutagenesisi119E → A: Wild-type degradation of target ssRNA by the Csm complex. 1 Publication1
Mutagenesisi123E → A: Wild-type degradation of target ssRNA by the Csm complex. 1 Publication1
Mutagenesisi139E → A: Wild-type degradation of target ssRNA by the Csm complex. 1 Publication1

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00004461191 – 220CRISPR system Cms endoribonuclease Csm3Add BLAST220

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Part of the Csm effector complex that includes at least Cas101, Csm23, Csm35, Csm41, Csm51 and mature crRNA (PubMed:25458845, PubMed:27105119, PubMed:28663439). The Csm complex is elongated and slightly twisted with a maximal length of 215 Angstroms and a diameter of 75-80 Angstroms (PubMed:25458845). It has been modeled to have a central protein filamant of Csm3 subunits along which the dsRNA helix of paired crRNA and target RNA binds. The filament is capped at one end by Cas10 and Csm4 and at the other end by Csm5; ssDNA is thought to bind to the N-terminal HD domain of Cas10 (Probable). Csm with a precursor crRNA does not include Csm5, while Cas6, the enzyme probably involved in pre-crRNA processing, is found associated with a subset of the Csm complex (PubMed:25458845).

2 Publications3 Publications

Protein-protein interaction databases

STRING: functional protein association networks

More...
STRINGi
322159.STER_0975

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

1220
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

Database of comparative protein structure models

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ModBasei
Search...

SWISS-MODEL Interactive Workspace

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SWISS-MODEL-Workspacei
Submit a new modelling project...

Protein Data Bank in Europe - Knowledge Base

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PDBe-KBi
Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

<p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the CRISPR-associated Csm3 family.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

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eggNOGi
ENOG4108W8W Bacteria
COG1337 LUCA

Family and domain databases

Integrated resource of protein families, domains and functional sites

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InterProi
View protein in InterPro
IPR013412 CRISPR-assoc_RAMP_Csm3
IPR005537 RAMP_III_fam

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF03787 RAMPs, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR02582 cas7_TM1809, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

A0A0A7HIF0-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MTFAKIKFSA QIRLETGLHI GGSDAFAAIG AIDSPVIKDP ITNIPIIPGS
60 70 80 90 100
SLKGKMRTLL AKVYNEKVAE KPSDDSDILS RLFGNSKDKR FKMGRLIFRD
110 120 130 140 150
AFLSNADELD SLGVRSYTEV KFENTIDRIT AEANPRQIER AIRNSTFDFE
160 170 180 190 200
LIYEITDENE NQVEEDFKVI RDGLKLLELD YLGGSGSRGY GKVAFEKLKA
210 220
TTVFGNYDVK TLNELLTAEV
Length:220
Mass (Da):24,569
Last modified:March 4, 2015 - v1
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:iAC361B95CB8A3DF8
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

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EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

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DDBJi
Links Updated
KM222358 Genomic DNA Translation: AIZ03606.1

NCBI Reference Sequences

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RefSeqi
WP_011681112.1, NZ_QFLC01000003.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
KPL37382; KPL37382; ADU38_883

Pathosystems Resource Integration Center (PATRIC)

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PATRICi
fig|1308.45.peg.983

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
KM222358 Genomic DNA Translation: AIZ03606.1
RefSeqiWP_011681112.1, NZ_QFLC01000003.1

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...
PDBei

Protein Data Bank RCSB

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RCSB PDBi

Protein Data Bank Japan

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PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
6NUDelectron microscopy3.50C/E/N/O/P1-220[»]
6NUEelectron microscopy3.30C/E/N/O/P1-220[»]
ModBaseiSearch...
SWISS-MODEL-WorkspaceiSubmit a new modelling project...
PDBe-KBiSearch...

Protein-protein interaction databases

STRINGi322159.STER_0975

Genome annotation databases

EnsemblBacteriaiKPL37382; KPL37382; ADU38_883
PATRICifig|1308.45.peg.983

Phylogenomic databases

eggNOGiENOG4108W8W Bacteria
COG1337 LUCA

Enzyme and pathway databases

BioCyciGCF_001663795:G1EVC-217-MONOMER
GCF_001855705:G1FB8-1892-MONOMER

Family and domain databases

InterProiView protein in InterPro
IPR013412 CRISPR-assoc_RAMP_Csm3
IPR005537 RAMP_III_fam
PfamiView protein in Pfam
PF03787 RAMPs, 1 hit
TIGRFAMsiTIGR02582 cas7_TM1809, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiCSM3_STRTR
<p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: A0A0A7HIF0
<p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 10, 2019
Last sequence update: March 4, 2015
Last modified: December 11, 2019
This is version 25 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

<p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure

Documents

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