Cu/Zn superoxide dismutase family paralog from R. varieornatus with evidence of catalytic impairment. Bioinformatic analysis (file:RAMVA/RvY_13070/RvY_13070-bioinformatics/RESULTS.md) shows that while all four Cu-binding histidines are preserved at the residue level, the protein FAILS to match PROSITE PS00087 - the N-terminal H-x-H Cu coordination signature. PS00087 requires not just the catalytic histidines but also specific flanking residues that maintain the structural geometry of the Cu site loop. By analogy with the related paralog RvSOD15 (Sim & Inoue 2023, PMID:37358501), where restoring a missing histidine via V87H mutagenesis did NOT restore activity due to a flexible loop with non-canonical context, this paralog likely has impaired or absent canonical SOD activity despite retaining the catalytic residues. 292 aa with N-terminal extension; all 4 Cu His preserved by sequence but PROSITE PS00087 fails
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0004784
superoxide dismutase activity
|
IEA
GO_REF:0000120 |
MARK AS OVER ANNOTATED |
Summary: All four Cu-binding histidines are preserved at the residue level, but PROSITE PS00087 (the N-terminal Cu coordination signature) FAILS to match. PS00087 requires both the H-x-H motif AND specific flanking residues that maintain the structural context. This indicates divergence at the Cu site beyond just the catalytic residues themselves. By analogy with Sim & Inoue (PMID:37358501), where the V87H rescue mutant of RvSOD15 failed to restore activity due to a flexible loop with non-canonical context, this paralog likely has impaired catalytic function. The IEA annotation from Pfam family assignment is therefore probably incorrect.
Reason: PROSITE PS00087 failure indicates the canonical N-terminal Cu coordination structure is not intact, even though the catalytic histidines themselves are present. Without biochemical confirmation, the IEA SOD activity annotation should be marked as over-annotated.
Supporting Evidence:
file:RAMVA/RvY_13070/RvY_13070-bioinformatics/RESULTS.md
RvY_00650 | A0A1D1UDY8 | bioinformatic verdict: IMPAIRED
|
|
GO:0005507
copper ion binding
|
IEA
GO_REF:0000002 |
ACCEPT |
Summary: All four canonical Cu-binding histidines are preserved at the sequence level. Copper binding is likely.
|
|
GO:0006801
superoxide metabolic process
|
IEA
GO_REF:0000002 |
MARK AS OVER ANNOTATED |
Summary: Inferred from SOD activity. Same caveats as the MF annotation.
|
|
GO:0019430
removal of superoxide radicals
|
IEA
GO_REF:0000108 |
MARK AS OVER ANNOTATED |
Summary: Inferred from SOD activity. Same caveats as the MF annotation.
|
|
GO:0046872
metal ion binding
|
IEA
GO_REF:0000002 |
KEEP AS NON CORE |
Summary: Parent term of the more specific Cu/Zn binding annotations. Both Cu and Zn binding are likely.
|
id: A0A1D1UDY8
gene_symbol: RvY_00650
product_type: PROTEIN
status: IN_PROGRESS
taxon:
id: NCBITaxon:947166
label: Ramazzottius varieornatus
description: >-
Cu/Zn superoxide dismutase family paralog from R. varieornatus with evidence of catalytic impairment. Bioinformatic analysis (file:RAMVA/RvY_13070/RvY_13070-bioinformatics/RESULTS.md) shows that while all four Cu-binding histidines are preserved at the residue level, the protein FAILS to match PROSITE PS00087 - the N-terminal H-x-H Cu coordination signature. PS00087 requires not just the catalytic histidines but also specific flanking residues that maintain the structural geometry of the Cu site loop. By analogy with the related paralog RvSOD15 (Sim & Inoue 2023, PMID:37358501), where restoring a missing histidine via V87H mutagenesis did NOT restore activity due to a flexible loop with non-canonical context, this paralog likely has impaired or absent canonical SOD activity despite retaining the catalytic residues. 292 aa with N-terminal extension; all 4 Cu His preserved by sequence but PROSITE PS00087 fails
existing_annotations:
- term:
id: GO:0004784
label: superoxide dismutase activity
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
summary: >-
All four Cu-binding histidines are preserved at the residue level, but PROSITE PS00087 (the N-terminal Cu coordination signature) FAILS to match. PS00087 requires both the H-x-H motif AND specific flanking residues that maintain the structural context. This indicates divergence at the Cu site beyond just the catalytic residues themselves. By analogy with Sim & Inoue (PMID:37358501), where the V87H rescue mutant of RvSOD15 failed to restore activity due to a flexible loop with non-canonical context, this paralog likely has impaired catalytic function. The IEA annotation from Pfam family assignment is therefore probably incorrect.
action: MARK_AS_OVER_ANNOTATED
reason: >-
PROSITE PS00087 failure indicates the canonical N-terminal Cu coordination structure is not intact, even though the catalytic histidines themselves are present. Without biochemical confirmation, the IEA SOD activity annotation should be marked as over-annotated.
supported_by:
- reference_id: file:RAMVA/RvY_13070/RvY_13070-bioinformatics/RESULTS.md
supporting_text: >-
RvY_00650 | A0A1D1UDY8 | bioinformatic verdict: IMPAIRED
- term:
id: GO:0005507
label: copper ion binding
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
summary: >-
All four canonical Cu-binding histidines are preserved at the sequence level. Copper binding is likely.
action: ACCEPT
- term:
id: GO:0006801
label: superoxide metabolic process
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
summary: >-
Inferred from SOD activity. Same caveats as the MF annotation.
action: MARK_AS_OVER_ANNOTATED
- term:
id: GO:0019430
label: removal of superoxide radicals
evidence_type: IEA
original_reference_id: GO_REF:0000108
review:
summary: >-
Inferred from SOD activity. Same caveats as the MF annotation.
action: MARK_AS_OVER_ANNOTATED
- 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 Cu/Zn binding annotations. Both Cu and Zn binding are likely.
action: KEEP_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: "Bioinformatic verdict for RvY_00650: IMPAIRED. 292 aa with N-terminal extension; all 4 Cu His preserved by sequence but PROSITE PS00087 fails"