id: Q02062
gene_symbol: actI-ORF2
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:100226
  label: Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)
description: >-
  ActI-ORF2 (SCO5088) is the chain-length factor (CLF, KSbeta) of the actinorhodin
  "minimal" type II polyketide synthase in Streptomyces coelicolor. It is the
  non-catalytic partner of the ketosynthase ActI-ORF1 (KSalpha): together they form
  the heterodimeric KS-CLF that polymerizes the poly-beta-keto chain of the aromatic
  polyketide antibiotic actinorhodin. CLF is descended from a ketosynthase but lacks
  an active site; it regulates the final polyketide chain length, while the KS
  subunit carries out chain initiation and elongation. Chain elongation and the first
  cyclization occur within an amphipathic tunnel at the KS-CLF heterodimer interface
  (PMID:15286722; PDB 1TQY). This makes ActI-ORF2 a structural/specificity subunit
  that is only functional as part of the assembled KS-CLF complex, directly analogous
  to PqsB in the P. aeruginosa PqsBC condensing enzyme.
references:
- id: PMID:15286722
  title: An antibiotic factory caught in action.
  findings:
  - statement: >-
      CLF regulates polyketide chain length but has no active site; the KS subunit is
      the catalytic one.
    supporting_text: >-
      Although CLF regulates chain length, it does not have an active site; KS must
      catalyze both chain initiation and elongation.
  - statement: >-
      KS and CLF form a heterodimer; the polyketide is elongated in a tunnel at the
      heterodimer interface.
    supporting_text: >-
      the actinorhodin KS-CLF, which shows polyketides being elongated inside an
      amphipathic tunnel approximately 17 A in length at the heterodimer interface
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      PubMed-verified; PDB 1TQY structure paper. Cached entry is abstract-only, but
      the abstract explicitly states that CLF lacks an active site (non-catalytic).
- id: file:STRCO/actI-ORF2/actI-ORF2-notes.md
  title: actI-ORF2 review notes (BGC project) with predicted-complex evidence
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO terms
- id: GO_REF:0000117
  title: Gene Ontology annotation based on Ensembl/EnsemblGenomes orthology
existing_annotations:
- term:
    id: GO:0016746
    label: acyltransferase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    summary: >-
      InterPro-based (IEA) acyltransferase activity from the ketosynthase (thiolase-like)
      signature. ActI-ORF2 (CLF/KSbeta) descends from a ketosynthase but lacks an
      active site and is catalytically dead; the condensation activity belongs to the
      KS subunit within the KS-CLF complex.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Attributes a catalytic MF to a non-catalytic subunit. CLF contributes_to (is
      required for) the KS-CLF activity and sets chain length, but does not itself
      catalyze acyl transfer; the activity should be annotated to the type II PKS
      complex with a contributes_to qualifier.
    supported_by:
    - reference_id: PMID:15286722
      supporting_text: >-
        Although CLF regulates chain length, it does not have an active site; KS must
        catalyze both chain initiation and elongation.
- term:
    id: GO:0016747
    label: acyltransferase activity, transferring groups other than amino-acyl groups
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  qualifier: enables
  review:
    summary: >-
      Orthology-based (IEA) more-specific acyltransferase activity. Same issue as
      GO:0016746: it assigns catalysis to the non-catalytic CLF subunit.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      CLF has no active site; this catalytic MF over-annotates the subunit. Better
      represented as contributes_to / annotation to the KS-CLF complex.
    supported_by:
    - reference_id: PMID:15286722
      supporting_text: >-
        Although CLF regulates chain length, it does not have an active site; KS must
        catalyze both chain initiation and elongation.
core_functions:
- description: >-
    Chain-length-factor (CLF/KSbeta) subunit of the heterodimeric KS-CLF (type II PKS)
    complex with the ketosynthase ActI-ORF1; functions only as part of the assembled
    complex. Although non-catalytic, it is required for actinorhodin biosynthesis and
    determines the polyketide chain length (PMID:15286722; PDB 1TQY).
  contributes_to_molecular_function:
    id: GO:0016218
    label: polyketide synthase activity
  in_complex:
    id: GO:0034082
    label: type II polyketide synthase complex
  directly_involved_in:
    - id: GO:1901112
      label: actinorhodin biosynthetic process
  supported_by:
  - reference_id: PMID:15286722
    supporting_text: >-
      the actinorhodin KS-CLF, which shows polyketides being elongated inside an
      amphipathic tunnel approximately 17 A in length at the heterodimer interface
proposed_new_terms:
- proposed_name: polyketide chain length factor activity
  proposed_definition: >-
    The function of a catalytically inactive ketosynthase-like (KSbeta/CLF) subunit
    that, as part of a type II polyketide synthase (KS-CLF) complex, determines the
    number of chain-extension cycles and hence the final length of the nascent
    polyketide chain, without itself catalyzing condensation.
  justification: >-
    GO has no molecular function term capturing the chain-length-determining role of
    the type II PKS CLF/KSbeta subunit. The current IEA acyltransferase annotations
    mischaracterize this non-catalytic subunit as an enzyme; a dedicated term would
    let curators describe CLF accurately (cf. the non-catalytic PqsB partner of PqsBC).
suggested_questions:
- question: >-
    Should a contributes_to-qualified molecular function (or a dedicated
    "chain length factor" term) be the recommended annotation for type II PKS CLF
    subunits across the family, rather than enables acyltransferase activity?
suggested_experiments:
- description: >-
    Reconstitute KS-CLF with CLF variants of differing length specificity to confirm
    that CLF, though non-catalytic, dictates chain length within the assembled complex.