RvY_15948

id: A0A1D1VWP9
gene_symbol: RvY_15948
product_type: PROTEIN
status: IN_PROGRESS
taxon:
  id: NCBITaxon:947166
  label: Ramazzottius varieornatus
description: >-
  Copper chaperone for Cu/Zn superoxide dismutase (CCS homolog) from
  R. varieornatus, NOT a superoxide dismutase. UniProt classifies this protein
  as 'Superoxide dismutase copper/zinc binding domain-containing protein.'
  CCS proteins have a SOD-like fold but lack canonical Cu ligands because
  their function is to deliver copper to SOD enzymes rather than catalyze
  superoxide dismutation. Bioinformatic analysis
  (file:RAMVA/RvY_13070/RvY_13070-bioinformatics/RESULTS.md) confirms that
  the H46 → A and H48 → C substitutions at the canonical Cu site are
  consistent with chaperone function. The protein matches Pfam SODC
  (PF00080) but does NOT match either PROSITE Cu/Zn SOD signature, which is
  the expected pattern for a CCS chaperone vs a catalytic SOD. Notably, the
  GOA does NOT include GO:0004784 (SOD activity) for this protein - the
  automated pipelines correctly recognized it as a non-SOD protein and
  annotated only the Cu binding and superoxide metabolic process terms,
  which are appropriate for a chaperone that interacts with the Cu/Zn-SOD
  pathway.
existing_annotations:
- term:
    id: GO:0005507
    label: copper ion binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: >-
      Copper binding is the core function of CCS chaperones - they bind
      copper for delivery to SOD1. The annotation is correct, although the
      more specific GO:0016531 (superoxide dismutase copper chaperone
      activity) would better capture the molecular function.
    action: MODIFY
    reason: >-
      While the annotation is technically correct (CCS does bind copper),
      the more specific term GO:0016531 (superoxide dismutase copper
      chaperone activity) better captures the actual biological role of
      this protein. CCS binds copper specifically for the purpose of
      transferring it to SOD1.
    proposed_replacement_terms:
      - id: GO:0016531
        label: copper chaperone activity
- term:
    id: GO:0006801
    label: superoxide metabolic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: >-
      CCS contributes to superoxide metabolism indirectly by activating SOD1
      through copper delivery. The annotation is reasonable since the
      protein is part of the cellular machinery that handles superoxide,
      even though the chaperone itself does not catalyze the reaction.
      A more specific term like GO:0006878 (intracellular copper ion
      homeostasis) might be more accurate.
    action: KEEP_AS_NON_CORE
    reason: >-
      The protein contributes to superoxide metabolism only indirectly via
      its role in SOD1 activation. Kept as non-core but a more specific
      annotation focused on copper homeostasis would be preferable.
- term:
    id: GO:0046872
    label: metal ion binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: >-
      Parent term of GO:0005507 (copper ion binding). Redundant with the
      more specific Cu binding annotation.
    action: KEEP_AS_NON_CORE
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO
    terms
  findings: []
- id: file:RAMVA/RvY_13070/RvY_13070-bioinformatics/RESULTS.md
  title: Bioinformatics analysis of Cu/Zn SOD paralogs in R. varieornatus
  findings:
  - statement: "RvY_15948 is the copper chaperone (CCS homolog), not a SOD. H46->A and H48->C substitutions at the canonical Cu site are consistent with chaperone function. Matches Pfam SODC but neither PROSITE pattern."