RvY_00651

id: A0A1D1UKR0
gene_symbol: RvY_00651
product_type: PROTEIN
status: IN_PROGRESS
taxon:
  id: NCBITaxon:947166
  label: Ramazzottius varieornatus
description: >-
  Putative Cu/Zn superoxide dismutase from the tardigrade Ramazzottius varieornatus,
  one of approximately 16 CuZnSOD paralogs in the expanded antioxidant gene family
  of this extremotolerant organism. Sequence analysis shows 66% identity to human
  SOD1 (the highest among the paralogs analyzed) and preserves all four Cu-binding
  histidines (H46, H48, H63, H120), the four Zn-binding residues (H63, H71, H80,
  D83), and both intrachain disulfide cysteines (C57, C146). This is consistent
  with canonical SOD activity, though functional confirmation is lacking. No gene
  symbol "RvSOD" number has been assigned in the primary literature (only RvSOD15
  = RvY_13070 is explicitly mapped).
existing_annotations:
- term:
    id: GO:0004784
    label: superoxide dismutase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      Sequence conservation analysis (see file:RAMVA/RvY_13070/RvY_13070-bioinformatics/RESULTS.md)
      shows all four Cu-binding histidines, all four Zn-binding residues, and both
      disulfide cysteines are preserved. At 66% identity to human SOD1, this is the
      most conserved paralog analyzed. Canonical SOD activity is plausible but not
      experimentally verified. Note that Sim & Inoue (PMID:37358501) caution that
      some R. varieornatus SOD paralogs have subtle structural defects (electrostatic
      loop deletions, β3 sheet truncations) not detectable by primary sequence alone.
    action: ACCEPT
    reason: >-
      All catalytic residues are preserved at the sequence level. Without biochemical
      data to contradict the family-based annotation, ACCEPT is appropriate, though
      the confidence is limited to sequence-level inference.
    supported_by:
      - reference_id: file:RAMVA/RvY_13070/RvY_13070-bioinformatics/RESULTS.md
        supporting_text: >-
          RvY_00651 | A0A1D1UKR0 | 154 | 4/4 | 4/4 | 2/2 | 66.0% | Likely functional
- term:
    id: GO:0005507
    label: copper ion binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: >-
      All four canonical Cu-binding histidine residues are preserved in the
      sequence. Copper binding is very likely.
    action: ACCEPT
- term:
    id: GO:0006801
    label: superoxide metabolic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: >-
      Redundant parent term of GO:0019430 (removal of superoxide radicals), which
      is the more specific and preferred annotation. Both are currently present.
    action: KEEP_AS_NON_CORE
    reason: >-
      Technically correct but less informative than GO:0019430. Kept as non-core.
- term:
    id: GO:0019430
    label: removal of superoxide radicals
  evidence_type: IEA
  original_reference_id: GO_REF:0000108
  review:
    summary: >-
      This is the expected biological process for a canonical CuZnSOD and is
      inferred by logical reasoning from the enzymatic activity annotation.
    action: ACCEPT
- term:
    id: GO:0046872
    label: metal ion binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: >-
      Parent term of the more specific GO:0005507 (copper ion binding) already
      annotated. Both copper and zinc binding are expected for this protein, but
      this generic parent term is less informative.
    action: KEEP_AS_NON_CORE
    reason: >-
      Redundant with the more specific Cu/Zn binding annotations. Kept as non-core.
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO
    terms
  findings: []
- id: GO_REF:0000108
  title: Automatic assignment of GO terms using logical inference, based on on inter-ontology
    links
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: file:RAMVA/RvY_13070/RvY_13070-bioinformatics/RESULTS.md
  title: Bioinformatics analysis of Cu/Zn SOD paralogs in R. varieornatus
  findings:
  - statement: All 10 catalytic residues (Cu ligands, Zn ligands, disulfide cysteines) are preserved in RvY_00651 when aligned to human SOD1