Copper chaperone for Cu/Zn superoxide dismutase (CCS homolog) from R. varieornatus, NOT a superoxide dismutase. UniProt classifies this protein as 'Superoxide dismutase copper/zinc binding domain-containing protein.' CCS proteins have a SOD-like fold but lack canonical Cu ligands because their function is to deliver copper to SOD enzymes rather than catalyze superoxide dismutation. Bioinformatic analysis (file:RAMVA/RvY_13070/RvY_13070-bioinformatics/RESULTS.md) confirms that the H46 → A and H48 → C substitutions at the canonical Cu site are consistent with chaperone function. The protein matches Pfam SODC (PF00080) but does NOT match either PROSITE Cu/Zn SOD signature, which is the expected pattern for a CCS chaperone vs a catalytic SOD. Notably, the GOA does NOT include GO:0004784 (SOD activity) for this protein - the automated pipelines correctly recognized it as a non-SOD protein and annotated only the Cu binding and superoxide metabolic process terms, which are appropriate for a chaperone that interacts with the Cu/Zn-SOD pathway.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005507 copper ion binding | IEA GO_REF:0000002 | MODIFY | Summary: Copper binding is the core function of CCS chaperones - they bind copper for delivery to SOD1. The annotation is correct, although the more specific GO:0016532 (superoxide dismutase copper chaperone activity) would better capture the molecular function. Reason: While the annotation is technically correct (CCS does bind copper), the more specific term GO:0016532 (superoxide dismutase copper chaperone activity) better captures the actual biological role of this protein. CCS binds copper specifically for the purpose of transferring it to SOD1. Proposed replacements: superoxide dismutase copper chaperone activity |
| GO:0006801 superoxide metabolic process | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: CCS contributes to superoxide metabolism indirectly by activating SOD1 through copper delivery. The annotation is reasonable since the protein is part of the cellular machinery that handles superoxide, even though the chaperone itself does not catalyze the reaction. A more specific term like GO:0006878 (intracellular copper ion homeostasis) might be more accurate. Reason: The protein contributes to superoxide metabolism only indirectly via its role in SOD1 activation. Kept as non-core but a more specific annotation focused on copper homeostasis would be preferable. |
| GO:0046872 metal ion binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: Parent term of GO:0005507 (copper ion binding). Redundant with the more specific Cu binding annotation. |
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