RvY_01767

id: A0A1D1USM4
gene_symbol: RvY_01767
product_type: PROTEIN
status: IN_PROGRESS
taxon:
  id: NCBITaxon:947166
  label: Ramazzottius varieornatus
description: >-
  Mitochondrial manganese/iron superoxide dismutase (Mn/Fe-SOD) from the
  tardigrade Ramazzottius varieornatus. This is a member of the Mn/Fe-SOD
  family (InterPro IPR001189, IPR019831, IPR019832, IPR019833) - a completely
  different protein family from the Cu/Zn-SODs that constitute most of the
  R. varieornatus SOD repertoire. Mn/Fe-SODs are typically located in
  mitochondria (in eukaryotes) and use a single Mn or Fe ion for catalysis,
  unlike Cu/Zn-SODs which use a Cu+Zn binuclear center. The protein is
  predicted to be located in mitochondrion and may be part of a respiratory
  chain complex (UniRule annotations). 230 aa with an N-terminal extension
  consistent with a mitochondrial targeting peptide. NOTE: Earlier
  bioinformatic analysis incorrectly compared this protein to human SOD1
  (Cu/Zn-SOD) and found low sequence conservation - this was because they
  belong to different protein families, NOT because RvY_01767 is degraded.
existing_annotations:
- term:
    id: GO:0004784
    label: superoxide dismutase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      Standard automated annotation for the Mn/Fe-SOD family. The protein
      belongs to the Mn/Fe-SOD InterPro families (IPR001189, IPR019831,
      IPR019832, IPR019833), which is a distinct protein family from Cu/Zn-SOD.
      This annotation is appropriate for canonical Mn/Fe-SODs and we have no
      evidence to suggest this protein has lost catalytic function.
    action: ACCEPT
    reason: >-
      Family-based assignment is appropriate for an unreviewed Mn/Fe-SOD
      from a non-model organism with no experimental data.
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      Standard subcellular location for eukaryotic Mn-SOD (homologous to
      human SOD2). The protein has an N-terminal extension consistent with
      a mitochondrial targeting peptide.
    action: ACCEPT
- term:
    id: GO:0006801
    label: superoxide metabolic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: >-
      Standard biological process annotation for SOD enzymes.
    action: ACCEPT
- term:
    id: GO:0019430
    label: removal of superoxide radicals
  evidence_type: IEA
  original_reference_id: GO_REF:0000108
  review:
    summary: >-
      More specific child of GO:0006801, inferred from SOD activity.
    action: ACCEPT
- term:
    id: GO:0030145
    label: manganese ion binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000118
  review:
    summary: >-
      Mn-SOD requires manganese as catalytic cofactor. This annotation is
      consistent with the Mn/Fe-SOD family assignment.
    action: ACCEPT
- term:
    id: GO:0046872
    label: metal ion binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: >-
      Parent term of GO:0030145 (manganese ion binding). Redundant with the
      more specific annotation.
    action: KEEP_AS_NON_CORE
- term:
    id: GO:0098803
    label: respiratory chain complex
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: >-
      This annotation comes from an ARBA rule (ARBA00029130) and is unusual
      for a Mn-SOD. Mitochondrial Mn-SOD (SOD2) is typically located in the
      mitochondrial matrix as a soluble enzyme, NOT as part of the respiratory
      chain complex. The respiratory chain consists of complexes I-IV plus ATP
      synthase, none of which contain SOD as a constituent. This appears to
      be an over-annotation by the ARBA rule.
    action: REMOVE
    reason: >-
      Mitochondrial Mn-SOD is a soluble matrix protein, not part of the
      respiratory chain complex. The ARBA rule appears to be incorrect for
      this annotation.
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:0000117
  title: Automated transfer of annotation from UniProtKB ARBA records
  findings: []
- id: GO_REF:0000118
  title: TreeGrafter annotation based on PANTHER tree topology
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []