RvY_03757

Gene 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. 193 aa (172 mature); all 4 Cu His preserved by sequence but PROSITE PS00087 fails

Existing Annotations Review

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_03757 \| A0A1D1UP59 \| bioinformatic verdict: PROBABLY 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.

Gene Description

Existing Annotations Review

References

Deep Research

Falcon

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