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Entry version 72 (11 Dec 2019)
Sequence version 1 (20 Jan 2009)
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Protein

CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A)

Gene

csm1

Organism
Thermococcus onnurineus (strain NA1)
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.By similarity
A single-strand deoxyribonuclease (ssDNase) which digests linear and circular ssDNA; has 5'-3' and 3'-5' exonuclease activity as well as a less efficient endonuclease activity. Has a minimal size requirement; 100 nucleotide ssDNA (nt) is more efficiently digested than 50 or 25 nt ssDNA, while 14 nt ssDNA is not cleaved at all. It has no activity on dsDNA or ssRNA.1 Publication
ssDNase activity is stimulated in the ternary Csm effector complex; binding of cognate target RNA activates the ssDNase, as the target RNA is degraded ssDNA activity decreases.By similarity
When associated with the ternary Csm effector complex (the crRNA, Cas proteins and a cognate target ssRNA) synthesizes cyclic oligoadenylates (cOA) from ATP. cOAs are second messengers that stimulate the ssRNase activity of Csm6, inducing an antiviral state important for defense against invading nucleic acids.By similarity

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 divalent metal cation1 PublicationNote: Ni2+ and Mn2+, but not Mg2+, Ca2+, Zn2+, Co2+, or Cu2+, is required for ssDNase activity.1 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

ssDNase activity 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, Exonuclease, Hydrolase, Nuclease, Transferase
Biological processAntiviral defense
LigandATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
TONN523850:G1GAB-926-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 single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A)1 Publication (EC:3.1.-.-1 Publication)
Short name:
ssDNase Cas10
Alternative name(s):
Cyclic oligoadenylate synthase (EC:2.7.7.-By similarity)
ToCsm11 Publication
<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:csm11 Publication
Synonyms:cas10Curated
Ordered Locus Names:TON_0893
<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>OrganismiThermococcus onnurineus (strain NA1)
<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 identifieri523850 [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 lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaeThermococcus
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000002727 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome

<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>Mutagenesisi15D → N: Loss of ssDNase activity. 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_00004461141 – 777CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A)Add BLAST777

<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

Probably part of the Csm effector complex, that includes Cas10, Csm2, Csm3, Csm4, Csm5 and mature crRNA (By similarity). Will form a homodimer in solution, interacts with Csm4, which is a tighter, better association than the homodimeric Cas10 and uses the same interface for interaction (PubMed:25773141).

By similarity1 Publication

<p>This subsection of the '<a href="http://www.uniprot.org/help/interaction_section%27">Interaction</a> section provides information about binary protein-protein interactions. The data presented in this section are a quality-filtered subset of binary interactions automatically derived from the <a href="http://www.ebi.ac.uk/intact/">IntAct database</a>. It is updated on a monthly basis. Each binary interaction is displayed on a separate line.<p><a href='/help/binary_interactions' target='_top'>More...</a></p>Binary interactionsi

Show more details

GO - Molecular functioni

Protein-protein interaction databases

Database of interacting proteins

More...
DIPi
DIP-61404N

Protein interaction database and analysis system

More...
IntActi
B6YWB8, 1 interactor

STRING: functional protein association networks

More...
STRINGi
523850.TON_0893

<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

1777
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

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SMRi
B6YWB8

Database of comparative protein structure models

More...
ModBasei
Search...

Protein Data Bank in Europe - Knowledge Base

More...
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

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family_and_domains_section">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini1 – 106HDPROSITE-ProRule annotationAdd BLAST106
Domaini513 – 660GGDEFPROSITE-ProRule annotationAdd BLAST148

<p>This subsection of the ‘Family and domains’ section provides general information on the biological role of a domain. The term ‘domain’ is intended here in its wide acceptation, it may be a structural domain, a transmembrane region or a functional domain. Several domains are described in this subsection.<p><a href='/help/domain_cc' target='_top'>More...</a></p>Domaini

The N-terminal HD domain has ssDNase activity (PubMed:25773141). The C-terminal GGDEF domain has the cOA synthesis activity (By similarity).By similarity1 Publication

<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

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
arCOG02666 Archaea
COG1353 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000078204

KEGG Orthology (KO)

More...
KOi
K07016

Identification of Orthologs from Complete Genome Data

More...
OMAi
DYFFKGY

Database of Orthologous Groups

More...
OrthoDBi
21880at2157

Family and domain databases

Conserved Domains Database

More...
CDDi
cd09680 Cas10_III, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR013408 Cas10/Csm1
IPR041062 Csm1_B
IPR000160 GGDEF_dom
IPR003607 HD/PDEase_dom
IPR006674 HD_domain

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF18211 Csm1_B, 1 hit
PF01966 HD, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR02578 cas_TM1811_Csm1, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS50887 GGDEF, 1 hit
PS51831 HD, 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.

B6YWB8-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MEIDELTALG GLLHDIGKPV QRAGLYSGDH STQGARFLRD LAENTGRAEY
60 70 80 90 100
ELLSLFSEFH HKGHMKNDEL MIRRIKELSP ERFGLTMEDV LNALWIVYEA
110 120 130 140 150
DNLASGEREE GQPQASRPLY SVFNPGKAYP WAELDFEKEL PVPGDVFSIR
160 170 180 190 200
SQDYRELVKR LWEELSKAKL RSDRLLPVLE KYLTFVSSVT SEGNIISLYD
210 220 230 240 250
HMRMTSAIAL AMLRAGCTAE DVRSGRCRKE KRFLLIEGDF SGIQDFIYRV
260 270 280 290 300
SGKGTLKYLR ARSAYLELIG WDVVLEILSR LGLTRANVVF NAGGHFMIIA
310 320 330 340 350
QNTPDAVKEL EEIRAKAVEW LYREFESDLY LAIEWEPVSG REFGREGGKN
360 370 380 390 400
LFAEARKRLK HKLTVRKLKR FGEIKGLFEH GHTERLAECP VCGRELPEGK
410 420 430 440 450
LEPSASDPET KVCPTCNRLV SLGGNLPKLL GFGRTAKNDA GVLVEGPFSG
460 470 480 490 500
FVPYLQGGRP VGEQILVKNT LNPGEIPESA QFVPYFVADY FKKDPKGGVA
510 520 530 540 550
TFEELSMAST GTRRLGVMKG DVDRLGEFFS SMDSPSKLAT ASRFMDYFFK
560 570 580 590 600
GYIGAIIEGK FGYIIGDVPS LRDWPEEPDI VVVYAGGDDF FIVGAWDQIF
610 620 630 640 650
ELAFRVRRAF NAYTGGKLTL SVGLGYFDER TPIYRMADVV SERLDTAKDE
660 670 680 690 700
GRNRVFVVGR SRPLDGKHKL SYEWNHYEEL WRTYAPRIYA GNGRLKGKLE
710 720 730 740 750
SKKGLLWKLL EIRELYVRDP NDVRWAYLTA YLLGRHGLSD LFPELVGIDT
760 770
KAVERKEPQP VYWVDGVLKI VLMAVRR
Length:777
Mass (Da):88,009
Last modified:January 20, 2009 - 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:i0F28CCAD584FB779
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
CP000855 Genomic DNA Translation: ACJ16381.1

NCBI Reference Sequences

More...
RefSeqi
WP_012571853.1, NC_011529.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
ACJ16381; ACJ16381; TON_0893

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
7017196

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
ton:TON_0893

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|523850.10.peg.901

<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
CP000855 Genomic DNA Translation: ACJ16381.1
RefSeqiWP_012571853.1, NC_011529.1

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...
PDBei

Protein Data Bank RCSB

More...
RCSB PDBi

Protein Data Bank Japan

More...
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4UW2X-ray2.63A/B/C/D1-777[»]
6IQWelectron microscopy3.35A1-777[»]
6MUAX-ray2.91A1-777[»]
6MURelectron microscopy3.10A1-777[»]
6MUSelectron microscopy3.60A1-777[»]
6MUTelectron microscopy3.10A1-777[»]
6MUUelectron microscopy3.00A1-777[»]
6O73X-ray3.00A1-777[»]
6O74X-ray2.71A1-777[»]
6O75X-ray2.60A1-777[»]
6O78X-ray2.80A1-777[»]
6O79X-ray3.00A1-777[»]
6O7BX-ray2.40A1-777[»]
6O7DX-ray2.81A1-777[»]
6O7Eelectron microscopy3.20A1-777[»]
6O7Helectron microscopy2.90A1-777[»]
6O7Ielectron microscopy3.20A1-777[»]
SMRiB6YWB8
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

DIPiDIP-61404N
IntActiB6YWB8, 1 interactor
STRINGi523850.TON_0893

Genome annotation databases

EnsemblBacteriaiACJ16381; ACJ16381; TON_0893
GeneIDi7017196
KEGGiton:TON_0893
PATRICifig|523850.10.peg.901

Phylogenomic databases

eggNOGiarCOG02666 Archaea
COG1353 LUCA
HOGENOMiHOG000078204
KOiK07016
OMAiDYFFKGY
OrthoDBi21880at2157

Enzyme and pathway databases

BioCyciTONN523850:G1GAB-926-MONOMER

Family and domain databases

CDDicd09680 Cas10_III, 1 hit
InterProiView protein in InterPro
IPR013408 Cas10/Csm1
IPR041062 Csm1_B
IPR000160 GGDEF_dom
IPR003607 HD/PDEase_dom
IPR006674 HD_domain
PfamiView protein in Pfam
PF18211 Csm1_B, 1 hit
PF01966 HD, 1 hit
TIGRFAMsiTIGR02578 cas_TM1811_Csm1, 1 hit
PROSITEiView protein in PROSITE
PS50887 GGDEF, 1 hit
PS51831 HD, 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 nameiCAS10_THEON
<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: B6YWB8
<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: January 16, 2019
Last sequence update: January 20, 2009
Last modified: December 11, 2019
This is version 72 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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