Cas10 (Csm1) is the large catalytic subunit of the type III-A Csm effector complex of Streptococcus thermophilus, which assembles one copy of Cas10 and one of Csm4 at one end of a filament of five Csm3 subunits, with three copies of Csm2 and a single Csm5, around a mature CRISPR RNA. The complex is licensed not by invader DNA but by base-pairing of its crRNA to a nascent transcript of the invading element, and that recognition event switches on two chemically unrelated activities that lie in separate domains of Cas10. The N-terminal HD domain is a single-strand-specific deoxyribonuclease, active with Mn2+, Co2+ or Ni2+ but not Mg2+, which degrades the single-stranded DNA exposed in the transcription bubble of the locus being transcribed; because recognition is transcription-dependent, the nuclease destroys actively expressed invader DNA while leaving silent and host DNA untouched. The C-terminal Palm domain, recognised as a GGDEF-like fold, polymerises and cyclises ATP into cyclic oligoadenylates ranging from cyclic triadenylate to cyclic hexaadenylate with release of diphosphate, a reaction that needs a free 3'-OH ribose. These cyclic oligoadenylates are diffusible second messengers that leave the complex and allosterically activate the standalone ribonuclease Csm6 through its CARF domain, amplifying a single recognition event into indiscriminate RNA degradation. The two catalytic centres are independent: substituting the HD-domain aspartate at position 16 abolishes DNA degradation while leaving cyclic oligoadenylate synthesis intact, and substituting the Palm-domain aspartate pair at 575-576 does the reverse. Both outputs are self-limiting, because cleavage of the bound target RNA by Csm3 and its subsequent dissociation shut the complex down, and pairing of the crRNA 5' handle with the target's 3' flank suppresses the nuclease on self transcripts.
The preferred accession for this review is A0A0A7HFE1. These relationships are manually assessed.
REFERENCE PROTEOME CANDIDATE · Reviewed 2026-10-19
Reference proteome: UP000232434
Retain A0A0A7HFE1 as the primary Swiss-Prot accession. The full-length Cas10/Csm1 match is strong but nonidentical (94.61% global identity). The characterized protein is from strain DGCC8004. A shared genomic locus or operon correspondence across the source and reference strains has not been established; retain a candidate rather than assuming equivalent CRISPR complexes.
MMseqs2 searched 1,657 sequences across UP000232434 at E <= 1e-5 and sensitivity 7.5, returning 1 hits. Every returned sequence was globally aligned using BLOSUM62 with gap-open -10 and extension -0.5. Scores and sequences for all 1 returned candidates are retained, with 1 detailed alignment files. The heuristic search does not establish genomic absence or unique locus identity.
file:STRTR/cas10/cas10-record-evidence.yaml
target_sequence_count: 1657
file:STRTR/cas10/cas10-record-evidence.yaml
candidate_count: 1
A0ACM8UA39: 720 identities across 761 global-alignment columns (94.6124% identity including gaps), 35 substitutions and 6 gap columns. Query coverage is 99.6042%; target coverage is 99.6042%. Sequence similarity is interpreted in the manual rationale. Identity over paired residues is 95.3642% (720/755); gap columns are excluded from this denominator.
file:STRTR/cas10/cas10-record-evidence.yaml
query_length: 758 target_length: 758 alignment_columns: 761 identities: 720 mismatches: 35 gap_columns: 6 identity_percent: 94.6124 query_coverage_percent: 99.6042 target_coverage_percent: 99.6042
The primary accession is outside every searched exact-taxon reference proteome. Current UniProt records place A0ACM8UA39 in UP000232434 and give it the same taxon as the primary.
file:STRTR/cas10/cas10-record-evidence.yaml
primary_in_any_reference_proteome: false
file:STRTR/cas10/cas10-record-evidence.yaml
alternative_in_reference_proteome: true
file:STRTR/cas10/cas10-record-evidence.yaml
same_taxon: true
Sampled UniSave observations: 09-DEC-2015, entry version 3.: no Proteomes cross-reference; 07-OCT-2020, entry version 13.: no Proteomes cross-reference; 27-NOV-2024, entry version 27.: no Proteomes cross-reference. These dated observations do not establish uninterrupted membership/absence, the exact change date, or UniProt's motivation.
file:STRTR/cas10/cas10-record-evidence.yaml
entry_date: 09-DEC-2015, entry version 3. proteomes: []
file:STRTR/cas10/cas10-record-evidence.yaml
entry_date: 07-OCT-2020, entry version 13. proteomes: []
file:STRTR/cas10/cas10-record-evidence.yaml
entry_date: 27-NOV-2024, entry version 27. proteomes: []
Definition: Catalysis of the polymerisation and cyclisation of ATP into a cyclic oligoadenylate with release of diphosphate, for example 4 ATP = cyclic tetraadenylate + 4 diphosphate, or 6 ATP = cyclic hexaadenylate + 6 diphosphate. The product is a closed ring of three to six adenosine 5'-monophosphate units joined by 3'-5' phosphodiester bonds, which acts as a second messenger. The activity resides in the Palm (GGDEF-like) domains of the Cas10/Csm1 subunit of type III CRISPR-Cas effector complexes, where it is licensed by binding of a target RNA complementary to the complex's CRISPR RNA.
Justification: No GO molecular-function term describes the synthesis of cyclic oligoadenylate (cA3-cA6) second messengers, which is one of the two catalytic outputs of Cas10 and the step that makes type III CRISPR immunity a two-tier, amplifying response. GO:0001730 2'-5'-oligoadenylate synthetase activity must not be reused for it: that term is defined as "Catalysis of the reaction: ATP = pppA(2'p5'A)n oligomers. This reaction requires the binding of double-stranded RNA", which is the metazoan interferon-induced OAS enzyme. Its product is a linear 2'-5'-linked oligomer that retains a 5'-triphosphate, its trigger is free double-stranded RNA, and it sits under GO:0070566 adenylyltransferase activity. Cas10 instead makes a covalently closed ring of 3'-5'-linked AMP units, releases diphosphate at every step, and is triggered by crRNA-guided recognition of a target RNA inside a ribonucleoprotein complex; the requirement for a free 3'-OH ribose, measured on this very protein, is the direct chemical counter-indication to the 2'-5' term. The natural placement is alongside the bacterial cyclic-dinucleotide synthases, which GO already distinguishes at this granularity and places as direct children of GO:0016779 nucleotidyltransferase activity: GO:0106408 diadenylate cyclase activity ("Catalysis of the reaction: 2 ATP = 3',3'-c-di-AMP + 2 diphosphate") and GO:0052621 diguanylate cyclase activity. A cyclic oligoadenylate synthase term is the missing member of that series. UniProt already records the reaction for this entry with Rhea cross-references (RHEA:58276 for cA6, RHEA:58280 for cA4 in the Thermus orthologue) and ChEBI entities for the products, so the term can be given exact external mappings on creation. The module modules/crispr_cas_adaptive_immunity.yaml carries the Cas10 Palm-domain annoton with no GO id and records the gap, but a module cannot propose a term; this is that proposal. A matching biological-process term for cyclic oligoadenylate signalling, and a cyclic oligoadenylate ring nuclease activity term for the enzymes that destroy the signal, are the companion requests.
Parent term: nucleotidyltransferase activity
Mappings:
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000014 single-stranded DNA endonuclease activity | IDA PMID:27105119 Spatiotemporal Control of Type III-A CRISPR-Cas Immunity: Co... | NEW | Summary: The HD domain of Cas10 is the single-strand-specific DNase of the Csm complex, activated by crRNA:target-RNA base-pairing and cleaving ssDNA internally. Reason: GOA holds no annotations for A0A0A7HFE1, so this row is proposed rather than reviewed. The activity was measured directly on the purified complex and localised to the Cas10 HD domain, and the D16A substitution abolishes it while leaving cOA synthesis intact, so the row is coded IDA. GO:0000014 is preferred over the generic GO:0004536 DNA nuclease activity because both the single-strand specificity and the endonucleolytic mode are established; a separate row records the exonucleolytic mode, which is required to account for digestion of circular ssDNA. Supporting Evidence: PMID:27105119 ssDNase activity is confined to the HD-domain of Cas10 PMID:27105119 base-pairing between crRNA and target RNA activates single-stranded DNA (ssDNA) degradation by StCsm |
| GO:0008297 single-stranded DNA exodeoxyribonuclease activity | ISS UniProtKB:A0A0A7HFE1 | NEW | Summary: Cas10 also degrades single-stranded DNA processively from a free end, so it carries the exonucleolytic mode in addition to the endonucleolytic one. Reason: UniProt records digestion of both linear and circular ssDNA with both exo- and endonuclease activity, but assigns that particular statement by similarity (ECO:0000250|UniProtKB:B6YWB8) rather than from the Streptococcus work, so this row is coded ISS while the endonuclease row above is IDA. The distinction is kept rather than collapsed because the two modes have different evidence in this entry. Supporting Evidence: UniProtKB:A0A0A7HFE1 This subunit is a single-strand-specific deoxyribonuclease (ssDNase) which digests both linear and circular ssDNA; it has both exo- and endonuclease activity. |
| GO:0005524 ATP binding | IDA PMID:28663439 A cyclic oligonucleotide signaling pathway in type III CRISP... | NEW | Summary: ATP is the substrate of the Palm-domain cyclase, which binds it and polymerises it into cyclic oligoadenylate. Reason: The nucleotide specificity of the reaction was determined directly: synthesis proceeds with ATP, 2'dATP or 3'dATP but no other nucleotides, and requires a free 3'-OH ribose moiety. Retained as its own row because the catalytic activity has no GO term yet, so without it the ATP dependence of the protein appears nowhere in the annotation set. Supporting Evidence: PMID:28722012 its Cas10 subunit converts ATP into a cyclic oligoadenylate product UniProtKB:A0A0A7HFE1 Synthesis of cOA can occur with AMP plus ATP, 2'dATP or 3'dATP (but no other nucleotides), and requires a free 3'-OH ribose moiety. |
| GO:0046872 metal ion binding | IDA PMID:27105119 Spatiotemporal Control of Type III-A CRISPR-Cas Immunity: Co... | NEW | Summary: Both Cas10 activities are metal dependent, with different and partly non-overlapping sets of permissive divalent cations. Reason: Determined experimentally and recorded in the UniProt COFACTOR block with ECO:0000269 from both PubMed:27105119 and PubMed:28663439: ssDNA degradation requires Mn(2+), Co(2+) or Ni(2+) and is not supported by Mg(2+), Ca(2+) or Zn(2+), while cOA formation requires Mn(2+), Co(2+) or Zn(2+). The ssDNase is also inhibited by EDTA. Supporting Evidence: UniProtKB:A0A0A7HFE1 Note=Degradation of ssDNA requires Mn(2+), Co(2+) or Ni(2+); Mg(2+), Ca(2+) or Zn(2+) do not activate ssDNase activity (PubMed:27105119). Formation of cOA requires Mn(2+), Co(2+) or Zn(2+), Mg(2+) is not as efficient (PubMed:28663439). |
| GO:0032991 protein-containing complex | IDA PMID:25458845 Programmable RNA shredding by the type III-A CRISPR-Cas syst... | NEW | Summary: Cas10 is a single-copy subunit of the Csm effector complex, which also contains Csm2, Csm3, Csm4, Csm5 and a mature crRNA. Reason: Complex composition and stoichiometry were determined on purified material in three separate studies. GO has no cellular-component term for the Csm or Cmr effector complex, so membership is recorded at the generic GO:0032991 rather than by inventing an id; this matches the convention for the curated Escherichia coli K-12 Cascade subunits, which each carry GO:0032991 by IDA. The missing specific term is raised in suggested_questions. Supporting Evidence: PMID:25458845 When expressed in Escherichia coli, two complexes of different stoichiometry copurified with 40 and 72 nt crRNA species, respectively. UniProtKB:A0A0A7HFE1 Part of the Csm effector complex that includes at least Cas10(1), Csm2(3), Csm3(5), Csm4(1), Csm5(1) and mature crRNA |
| GO:0099048 CRISPR-cas system | IDA PMID:27105119 Spatiotemporal Control of Type III-A CRISPR-Cas Immunity: Co... | NEW | Summary: Cas10 carries out the target-interference stage of the type III-A CRISPR-Cas response, degrading invader DNA at transcribed loci and generating the second messenger that recruits accessory nucleases. Reason: The term's definition names target interference as one of the three stages of the process, and Cas10 catalyses steps of that stage, so it performs part of the work rather than merely being required. Comparator check: every curated Escherichia coli K-12 Cas protein in this repository carries GO:0099048 (casA, casB, casC, casD, casE, cas1/ygbT, cas2/ygbF; IDA, PMID:18703739), confirming that this is the conventional process term for a Cas subunit. Coded IDA from the reconstituted interference assays on the purified StCsm complex. Supporting Evidence: PMID:27105119 crRNA-guided StCsm binding to the emerging transcript recruits Cas10 DNase to the actively transcribed phage DNA, resulting in degradation of both the transcript and phage DNA, but not the host DNA |
| GO:0051607 defense response to virus | IC PMID:25458845 Programmable RNA shredding by the type III-A CRISPR-Cas syst... | NEW | Summary: The Csm system restricts invading phage, and the two Cas10 catalytic outputs are the DNA-destroying and signal-generating arms of that response. Reason: Coded IC rather than IMP, deliberately. The in vivo restriction that has been measured for this system is of MS2 RNA phage in a heterologous host, and that restriction was shown to depend on the Csm3 nuclease; no published experiment ablates Cas10 and measures a loss of immunity in Streptococcus thermophilus. The term is nonetheless justified by curator inference from the demonstrated activities: Cas10 degrades invader DNA and makes the second messenger that, per PMID:28663439, coordinates the system to prevent phage propagation. Comparator check: casA and casE of the Escherichia coli type I-E system carry GO:0051607 alongside GO:0099048, so pairing the two on a Cas subunit is conventional. Supporting Evidence: PMID:25458845 In the heterologous E. coli host, StCsm restricts MS2 RNA phage in a Csm3 nuclease-dependent manner. PMID:28663439 This cyclic oligoadenylate-based signaling pathway coordinates different components of CRISPR-Cas to prevent phage infection and propagation. |
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Download this section (compressed HTML)Q: Why does this enzyme produce a cA3 to cA6 mixture when its cognate receiver, Csm6, responds to one ring size? Is the distribution controlled by the complex, by ATP concentration, or trimmed afterwards by a ring nuclease?
Q: Does ablating Cas10 catalysis, as opposed to ablating Csm3, cause a measurable loss of phage immunity in Streptococcus thermophilus itself? Until that experiment exists, GO:0051607 for this subunit rests on curator inference rather than a phenotype.
Q: Should GO acquire a cellular-component term for the Csm/Cmr effector complex? Complex membership for every curated Cas subunit currently collapses onto the root term GO:0032991, which loses the distinction between Cascade, Csm and Cmr.
Q: Is a biological-process term for cyclic oligoadenylate signalling warranted, parallel to GO:0061939 c-di-GMP signaling, so that the producer, the CARF-domain receivers and the ring nucleases that terminate the signal can be linked in the ontology?
Experiment: Determine the ring-size distribution of the products as a function of ATP concentration, metal identity and target-RNA length by LC-MS, to establish whether the cA3-cA6 spectrum is a property of the active site or of the assay conditions.
Experiment: Build a cryo-EM structure of the StCsm complex with a bound target RNA and a non-hydrolysable ATP analogue in the Palm domains, to show how target recognition at the Csm3 filament is transmitted to the cyclase active site tens of angstroms away.
Experiment: Challenge Streptococcus thermophilus carrying wild-type, D16A and D575/D576A cas10 alleles with a protospacer-bearing phage, separating the contribution of invader-DNA degradation from that of cyclic oligoadenylate signalling to immunity in the native host.
Experiment: Measure the kinetics of cOA accumulation and decay in vivo after phage challenge, using a quantitative assay for cA4 and cA6, to test whether the host encodes a ring nuclease that terminates the signal.
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