id: A0A0A7HFE1 gene_symbol: cas10 product_type: PROTEIN status: COMPLETE taxon: id: NCBITaxon:1308 label: Streptococcus thermophilus description: >- 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. references: - id: file:STRTR/cas10/cas10-record-evidence.yaml title: Compact archived record and sequence evidence for A0A0A7HFE1 - id: UniProtKB:A0A0A7HFE1 title: UniProtKB entry for Streptococcus thermophilus Cas10/Csm1 (A0A0A7HFE1) publication_type: DATABASE findings: - statement: >- The N-terminal HD domain has ssDNase activity (ECO:0000269|PubMed:27105119) and the C-terminal GGDEF domain has the cOA synthesis activity (ECO:0000269|PubMed:28663439). reference_section_type: DATABASE_ENTRY - statement: >- The two catalytic centres are genetically separable: the D16A substitution dramatically decreases ssDNase activity but leaves wild-type cOA synthesis, and the D575-D576 to AA substitution leaves wild-type ssDNase activity but abolishes cOA synthesis. reference_section_type: DATABASE_ENTRY - statement: >- Experimentally determined catalytic activity 6 ATP = cyclic hexaadenylate + 6 diphosphate (Rhea:RHEA:58276), with cA3 to cA6 produced and cA6 the active species; synthesis requires a free 3'-OH ribose moiety and accepts 2'dATP or 3'dATP but no other nucleotides. reference_section_type: DATABASE_ENTRY - statement: >- Degradation of ssDNA requires Mn(2+), Co(2+) or Ni(2+) and is not activated by Mg(2+), Ca(2+) or Zn(2+); formation of cOA requires Mn(2+), Co(2+) or Zn(2+). ssDNase activity is inhibited by EDTA. reference_section_type: DATABASE_ENTRY - statement: >- Part of the Csm effector complex that includes at least Cas10(1), Csm2(3), Csm3(5), Csm4(1), Csm5(1) and mature crRNA; Cas10 and Csm4 cap one end of the Csm3 filament. reference_section_type: DATABASE_ENTRY reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- Reviewed Swiss-Prot entry whose FUNCTION, CATALYTIC ACTIVITY, COFACTOR, ACTIVITY REGULATION, SUBUNIT, DOMAIN and MUTAGEN blocks all carry ECO:0000269 experimental evidence from PubMed:25458845, PubMed:27105119 and PubMed:28663439. Statements used here were read off the cached cas10-uniprot.txt. - id: PMID:28663439 title: A cyclic oligonucleotide signaling pathway in type III CRISPR-Cas systems. full_text_unavailable: true findings: - statement: >- Target RNA binding by the Streptococcus thermophilus Csm effector complex triggers Cas10 to synthesise cyclic oligoadenylates through its Palm domains. supporting_text: >- target RNA binding by the Csm effector complex of Streptococcus thermophilus triggers Cas10 to synthesize cyclic oligoadenylates reference_section_type: ABSTRACT - statement: >- Cas10 contains an HD nuclease domain responsible for DNA degradation and two Palm domains. supporting_text: >- The Cas10 subunit of the complex contains an HD nuclease domain that is responsible for DNA degradation and two Palm domains with elusive functions. reference_section_type: ABSTRACT - statement: >- The cyclic oligoadenylates act as signalling molecules that bind Csm6 and switch on its nonspecific RNA degradation, coordinating the components of the system to prevent phage propagation. supporting_text: >- Acting as signaling molecules, cyclic oligoadenylates bind Csm6 to activate its nonspecific RNA degradation. reference_section_type: ABSTRACT reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- Cached record is abstract-only, but the abstract itself names Streptococcus thermophilus as the organism assayed, so the cOA-synthesis result is attributable to this entry rather than transferred to it. This is the demonstration paper for the activity; the Thermus orthologue Q53W19 carries the same function with ECO:0000305. - id: PMID:27105119 title: 'Spatiotemporal Control of Type III-A CRISPR-Cas Immunity: Coupling DNA Degradation with the Target RNA Recognition.' full_text_unavailable: true findings: - statement: >- Base-pairing between the crRNA and a target RNA activates single-stranded DNA degradation by the Streptococcus thermophilus Csm complex. supporting_text: >- base-pairing between crRNA and target RNA activates single-stranded DNA (ssDNA) degradation by StCsm reference_section_type: ABSTRACT - statement: The single-stranded DNase activity resides in the HD domain of Cas10. supporting_text: >- ssDNase activity is confined to the HD-domain of Cas10 reference_section_type: ABSTRACT - statement: >- Cleavage of the target RNA by Csm3 suppresses the Cas10 DNase, giving the DNA degradation a defined temporal window. supporting_text: >- target RNA cleavage by the Csm3 RNase suppresses Cas10 DNase activity, ensuring temporal control of DNA degradation reference_section_type: ABSTRACT - statement: >- Pairing of the crRNA 5' handle with the 3' flank of the target RNA inhibits the Cas10 ssDNase, preventing self-targeting. supporting_text: >- base-pairing between crRNA 5'-handle and target RNA 3'-flanking sequence inhibits Cas10 ssDNase to prevent self-targeting reference_section_type: ABSTRACT - statement: >- crRNA-guided binding to an emerging transcript recruits the Cas10 DNase to actively transcribed invader DNA, sparing host DNA. supporting_text: >- 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 reference_section_type: ABSTRACT reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- Cached record is abstract-only, but the abstract explicitly names the Streptococcus thermophilus type III-A system and StCsm, so the domain mapping and the regulatory logic are attributable to this entry directly. - id: PMID:25458845 title: Programmable RNA shredding by the type III-A CRISPR-Cas system of Streptococcus thermophilus. full_text_unavailable: true findings: - statement: >- Two Csm complexes of different stoichiometry were purified from a heterologous host, associated with 40 and 72 nucleotide crRNA species. supporting_text: >- When expressed in Escherichia coli, two complexes of different stoichiometry copurified with 40 and 72 nt crRNA species, respectively. reference_section_type: ABSTRACT - statement: >- The complex cleaves target RNA at 6 nucleotide intervals, and the Csm3 subunit is the endoribonuclease responsible. supporting_text: >- The Csm3 protein, present in multiple copies in both Csm complexes, acts as endoribonuclease. reference_section_type: ABSTRACT - statement: >- The system restricts MS2 RNA phage in a heterologous host, and in that assay the restriction depends on the Csm3 nuclease rather than on Cas10. supporting_text: >- In the heterologous E. coli host, StCsm restricts MS2 RNA phage in a Csm3 nuclease-dependent manner. reference_section_type: ABSTRACT reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: >- Cached record is abstract-only. Supports complex composition and the antiviral competence of the system; it attributes the measured restriction to Csm3, which is why GO:0051607 is coded IC for Cas10 rather than IMP. - id: PMID:28722012 title: Type III CRISPR-Cas systems produce cyclic oligoadenylate second messengers. full_text_unavailable: true findings: - statement: >- Independent demonstration that the Cas10 subunit converts ATP into a cyclic oligoadenylate on target RNA binding, and that the product activates Csm6 through its CARF domain. supporting_text: >- Upon target RNA binding by the interference complex, its Cas10 subunit converts ATP into a cyclic oligoadenylate product, which allosterically activates Csm6 by binding to its CRISPR-associated Rossmann fold (CARF) domain. reference_section_type: ABSTRACT reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- Cached record is abstract-only. Cited as the independent corroboration of the cyclase activity; the experiments in this paper are on the Staphylococcus epidermidis and Enterococcus italicus systems, so it is used for the general mechanism and not as a measurement on A0A0A7HFE1. alternative_records: - id: A0ACM8UA39 relationship: REFERENCE_PROTEOME_CANDIDATE reference_proteome: UP000232434 reviewed_on: '2026-10-19' reason: 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. evidence: - type: PROTEOME_SEARCH description: 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. supported_by: - reference_id: file:STRTR/cas10/cas10-record-evidence.yaml supporting_text: 'target_sequence_count: 1657' - reference_id: file:STRTR/cas10/cas10-record-evidence.yaml supporting_text: 'candidate_count: 1' - type: SEQUENCE_COMPARISON description: '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.' supported_by: - reference_id: file:STRTR/cas10/cas10-record-evidence.yaml supporting_text: |- 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 - type: PROTEOME_MEMBERSHIP description: 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. supported_by: - reference_id: file:STRTR/cas10/cas10-record-evidence.yaml supporting_text: 'primary_in_any_reference_proteome: false' - reference_id: file:STRTR/cas10/cas10-record-evidence.yaml supporting_text: 'alternative_in_reference_proteome: true' - reference_id: file:STRTR/cas10/cas10-record-evidence.yaml supporting_text: 'same_taxon: true' - type: RECORD_HISTORY description: '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.' supported_by: - reference_id: file:STRTR/cas10/cas10-record-evidence.yaml supporting_text: |- entry_date: 09-DEC-2015, entry version 3. proteomes: [] - reference_id: file:STRTR/cas10/cas10-record-evidence.yaml supporting_text: |- entry_date: 07-OCT-2020, entry version 13. proteomes: [] - reference_id: file:STRTR/cas10/cas10-record-evidence.yaml supporting_text: |- entry_date: 27-NOV-2024, entry version 27. proteomes: [] existing_annotations: - term: id: GO:0000014 label: single-stranded DNA endonuclease activity qualifier: enables evidence_type: IDA original_reference_id: PMID:27105119 review: 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. action: NEW 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. supported_by: - reference_id: PMID:27105119 supporting_text: >- ssDNase activity is confined to the HD-domain of Cas10 full_text_unavailable: true - reference_id: PMID:27105119 supporting_text: >- base-pairing between crRNA and target RNA activates single-stranded DNA (ssDNA) degradation by StCsm full_text_unavailable: true - term: id: GO:0008297 label: single-stranded DNA exodeoxyribonuclease activity qualifier: enables evidence_type: ISS original_reference_id: UniProtKB:A0A0A7HFE1 supporting_entities: - UniProtKB:B6YWB8 review: summary: >- Cas10 also degrades single-stranded DNA processively from a free end, so it carries the exonucleolytic mode in addition to the endonucleolytic one. action: NEW 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. supported_by: - reference_id: UniProtKB:A0A0A7HFE1 supporting_text: >- This subunit is a single-strand-specific deoxyribonuclease (ssDNase) which digests both linear and circular ssDNA; it has both exo- and endonuclease activity. reference_section_type: DATABASE_ENTRY - term: id: GO:0005524 label: ATP binding qualifier: enables evidence_type: IDA original_reference_id: PMID:28663439 review: summary: >- ATP is the substrate of the Palm-domain cyclase, which binds it and polymerises it into cyclic oligoadenylate. action: NEW 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. supported_by: - reference_id: PMID:28722012 supporting_text: >- its Cas10 subunit converts ATP into a cyclic oligoadenylate product full_text_unavailable: true - reference_id: UniProtKB:A0A0A7HFE1 supporting_text: >- 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. reference_section_type: DATABASE_ENTRY - term: id: GO:0046872 label: metal ion binding qualifier: enables evidence_type: IDA original_reference_id: PMID:27105119 review: summary: >- Both Cas10 activities are metal dependent, with different and partly non-overlapping sets of permissive divalent cations. action: NEW 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. supported_by: - reference_id: UniProtKB:A0A0A7HFE1 supporting_text: >- 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). reference_section_type: DATABASE_ENTRY - term: id: GO:0032991 label: protein-containing complex qualifier: part_of evidence_type: IDA original_reference_id: PMID:25458845 review: summary: >- Cas10 is a single-copy subunit of the Csm effector complex, which also contains Csm2, Csm3, Csm4, Csm5 and a mature crRNA. action: NEW 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. supported_by: - reference_id: PMID:25458845 supporting_text: >- When expressed in Escherichia coli, two complexes of different stoichiometry copurified with 40 and 72 nt crRNA species, respectively. full_text_unavailable: true - reference_id: UniProtKB:A0A0A7HFE1 supporting_text: >- Part of the Csm effector complex that includes at least Cas10(1), Csm2(3), Csm3(5), Csm4(1), Csm5(1) and mature crRNA reference_section_type: DATABASE_ENTRY - term: id: GO:0099048 label: CRISPR-cas system qualifier: involved_in evidence_type: IDA original_reference_id: PMID:27105119 review: 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. action: NEW 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. supported_by: - reference_id: PMID:27105119 supporting_text: >- 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 full_text_unavailable: true - term: id: GO:0051607 label: defense response to virus qualifier: involved_in evidence_type: IC original_reference_id: PMID:25458845 review: summary: >- The Csm system restricts invading phage, and the two Cas10 catalytic outputs are the DNA-destroying and signal-generating arms of that response. action: NEW 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. supported_by: - reference_id: PMID:25458845 supporting_text: >- In the heterologous E. coli host, StCsm restricts MS2 RNA phage in a Csm3 nuclease-dependent manner. full_text_unavailable: true - reference_id: PMID:28663439 supporting_text: >- This cyclic oligoadenylate-based signaling pathway coordinates different components of CRISPR-Cas to prevent phage infection and propagation. full_text_unavailable: true core_functions: - description: >- Metal-dependent, single-strand-specific deoxyribonuclease of the N-terminal HD domain, requiring Mn2+, Co2+ or Ni2+ and inactive with Mg2+. Base-pairing of the complex's crRNA to a nascent invader transcript activates the nuclease, which degrades the single-stranded DNA exposed in the transcription bubble, so that destruction is directed at invader loci that are actively transcribed and not at silent or host DNA. The D16A substitution abolishes this activity without affecting cyclic oligoadenylate synthesis. Activity is extinguished as Csm3 cleaves the bound target RNA and the fragments dissociate, and is suppressed on self transcripts when the crRNA 5' handle pairs with the target's 3' flanking sequence. molecular_function: id: GO:0000014 label: single-stranded DNA endonuclease activity directly_involved_in: - id: GO:0099048 label: CRISPR-cas system - id: GO:0051607 label: defense response to virus in_complex: id: GO:0032991 label: protein-containing complex supported_by: - reference_id: PMID:27105119 supporting_text: >- ssDNase activity is confined to the HD-domain of Cas10 full_text_unavailable: true - reference_id: PMID:27105119 supporting_text: >- base-pairing between crRNA and target RNA activates single-stranded DNA (ssDNA) degradation by StCsm full_text_unavailable: true - reference_id: UniProtKB:A0A0A7HFE1 supporting_text: >- MUTAGEN 16 /note="D->A: Dramatically decreased ssDNase activity. Wild-type synthesis of cOA." reference_section_type: DATABASE_ENTRY - description: >- Nucleotidyltransferase of the C-terminal Palm domain (GGDEF-like fold, residues 509-647) which, once the complex has bound a cognate target RNA, polymerises and cyclises ATP into cyclic oligoadenylates from cyclic triadenylate up to cyclic hexaadenylate with release of diphosphate. The reaction accepts ATP, 2'dATP or 3'dATP but no other nucleotide and requires a free 3'-OH ribose, and the enzyme can also cyclise linear pppA3 to pppA6. The product is a diffusible second messenger that leaves the complex and allosterically activates the standalone ribonuclease Csm6 by binding its CARF domain, turning one recognition event into an amplified, cell-wide RNA-degrading response. Substituting the Palm-domain aspartate pair at 575-576 abolishes this activity while leaving the HD nuclease intact, establishing the two centres as independent. GO has no term for this activity, so the proposed term is named here rather than forcing an ill-fitting id. proposed_molecular_function: cyclic oligoadenylate synthase activity directly_involved_in: - id: GO:0099048 label: CRISPR-cas system - id: GO:0051607 label: defense response to virus in_complex: id: GO:0032991 label: protein-containing complex supported_by: - reference_id: PMID:28663439 supporting_text: >- target RNA binding by the Csm effector complex of Streptococcus thermophilus triggers Cas10 to synthesize cyclic oligoadenylates full_text_unavailable: true - reference_id: PMID:28663439 supporting_text: >- Acting as signaling molecules, cyclic oligoadenylates bind Csm6 to activate its nonspecific RNA degradation. full_text_unavailable: true - reference_id: UniProtKB:A0A0A7HFE1 supporting_text: >- CATALYTIC ACTIVITY: Reaction=6 ATP = cyclic hexaadenylate + 6 diphosphate; Xref=Rhea:RHEA:58276 ... Evidence={ECO:0000269|PubMed:28663439}; reference_section_type: DATABASE_ENTRY proposed_new_terms: - proposed_name: cyclic oligoadenylate synthase activity proposed_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. proposed_parent: id: GO:0016779 label: nucleotidyltransferase activity proposed_mappings: - predicate: skos:closeMatch target_term: id: RHEA:58276 label: 6 ATP = cyclic hexaadenylate + 6 diphosphate - predicate: skos:closeMatch target_term: id: RHEA:58280 label: 4 ATP = cyclic tetraadenylate + 4 diphosphate supported_by: - reference_id: PMID:28663439 supporting_text: >- target RNA binding by the Csm effector complex of Streptococcus thermophilus triggers Cas10 to synthesize cyclic oligoadenylates full_text_unavailable: true - reference_id: PMID:28722012 supporting_text: >- Upon target RNA binding by the interference complex, its Cas10 subunit converts ATP into a cyclic oligoadenylate product, which allosterically activates Csm6 by binding to its CRISPR-associated Rossmann fold (CARF) domain. full_text_unavailable: true suggested_questions: - question: >- 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? - question: >- 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. - question: >- 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. - question: >- 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? suggested_experiments: - description: >- 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. - description: >- 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. - description: >- 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. - description: >- 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.