RvY_17310

Gene Description

An unusually large (475 aa; ~455 mature, ~3x canonical CuZnSOD) Cu/Zn superoxide dismutase-family protein from R. varieornatus, with a C-terminal SOD domain preceded by a long disordered N-terminal extension. Its catalytic status is contested. Two independent analyses agree that all catalytic residues (four Cu-binding histidines, the Zn ligands, and the disulfide cysteines) are conserved at the sequence level; an AlphaFold model places the active-site geometry close to human SOD1. However, the protein fails to match PROSITE PS00087 (the N-terminal Cu-coordination signature), which depends on specific flanking residues, and one analysis reads this as probable impairment. R. varieornatus has an expanded Cu/Zn-SOD family containing both functional members and degenerate pseudoenzymes (e.g. RvSOD15 / RvY_13070, an experimentally characterized impaired paralog; Sim & Inoue 2023, PMID:37358501), so per-paralog assessment is required. Whether RvY_17310 retains canonical SOD activity is unresolved without a direct enzyme assay.

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0004784 superoxide dismutase activity	IEA GO_REF:0000003	UNDECIDED	Summary: EC2GO mapping from EC 1.15.1.1. Catalytic status is contested. All catalytic residues are preserved at the sequence level, but the protein fails PROSITE PS00087 (the N-terminal Cu-coordination signature), whose flanking-residue requirements are not met. A local bioinformatic analysis reads this as probable impairment by analogy to the experimentally confirmed impaired paralog RvSOD15; an independent OpenScientist run reads the AlphaFold active-site geometry as intact (close to human SOD1) and treats the PS00087 failure as a signature- stringency artifact. Neither has a direct enzyme assay on RvY_17310. Reason: The catalytic status is genuinely contested and cannot be resolved without a direct enzyme assay. Two independent analyses agree all catalytic residues are present at the sequence level. A local analysis marks the protein "probably impaired" on the basis of PROSITE PS00087 failure (reasoning by analogy to the experimentally confirmed impaired paralog RvSOD15). A separate OpenScientist run reaches the opposite reading: the AlphaFold active-site geometry matches human SOD1 with high-confidence pLDDT and ~53% SOD-domain identity, so it argues the PS00087 failure is a signature-stringency artifact rather than loss of function. The geometric evidence weakens the earlier over-annotation call but does not establish activity; marking UNDECIDED pending a recombinant SOD activity assay. Supporting Evidence: file:RAMVA/RvY_13070/RvY_13070-bioinformatics/RESULTS.md RvY_17310 \| A0A1D1W3Y1 \| bioinformatic verdict: PROBABLY IMPAIRED file:RAMVA/RvY_17310/RvY_17310-hypotheses/sod-activity-residue-geometry/openscientist.md 10/10 critical active-site residues conserved in register and correctly spaced relative to human SOD1. file:RAMVA/RvY_17310/RvY_17310-hypotheses/sod-activity-residue-geometry/openscientist.md The AlphaFold pLDDT values for all 10 active-site residues range from 94.4 to 98.7 (mean 97.3), indicating very high confidence in the predicted local structure of the catalytic core.
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	UNDECIDED	Summary: Inferred from SOD activity; same contested status as the MF annotation (GO:0004784) - unresolved pending a direct enzyme assay.
GO:0019430 removal of superoxide radicals	IEA GO_REF:0000108	UNDECIDED	Summary: Inferred from SOD activity; same contested status as the MF annotation (GO:0004784) - unresolved pending a direct enzyme assay.
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

OpenScientist

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