RvSOD15 is a Cu-Zn superoxide dismutase family member from the anhydrobiotic tardigrade Ramazzottius varieornatus. Crystal structures (PDB: 7YPP, 7YPR) confirm a standard CuZnSOD fold with homodimeric quaternary structure and binding of both copper and zinc ions. However, a critical catalytic histidine ligand (His87 in canonical CuZnSODs) is naturally replaced by valine (Val87), and structural analysis of the V87H mutant shows that even restoring histidine at this position does not restore stable copper coordination due to a nearby flexible loop. The authors conclude that RvSOD15 may have evolved to lose SOD catalytic function, challenging the assumption that expanded SOD gene families in tardigrades directly confer oxidative stress resistance. The protein has a signal peptide (residues 1-20), suggesting secretion.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004784 superoxide dismutase activity | IEA GO_REF:0000120 | MARK AS OVER ANNOTATED | Summary: This IEA annotation is based on automated mapping from the EC number (EC:1.15.1.1) and Rhea reaction. While RvSOD15 belongs to the Cu-Zn SOD family and retains the overall fold, the crystal structure study (PMID:37358501) reveals that one of the critical histidine ligands of the catalytic copper center is replaced by Val87. The authors explicitly state that RvSOD15 "may have evolved to lose the SOD function." Without experimental enzyme activity data, the catalytic activity annotation is questionable for this specific protein. Reason: The automated IEA annotation assigns superoxide dismutase activity based on family membership and EC number. However, PMID:37358501 demonstrates that a key catalytic residue (His87) is replaced by Val87, potentially abolishing enzymatic activity. No direct SOD activity assay has been reported for RvSOD15. The structural evidence suggests this protein may be a pseudoenzyme within the SOD family. A focused OpenScientist review independently judged this SOD-activity assignment over-annotated and emphasized that no alternative catalytic molecular-function term is currently supported. Supporting Evidence: PMID:37358501 In RvSOD15, one of the histidine ligands of the catalytic copper center is replaced by a valine (Val87). PMID:37358501 These studies show that RvSOD15 and some other RvSODs may have evolved to lose the SOD function, suggesting that gene duplications of antioxidant proteins do not solely explain the high stress tolerance of anhydrobiotic tardigrades. file:RAMVA/RvY_13070/RvY_13070-hypotheses/function-hypothesis-go-0004784/openscientist.md OpenScientist judged the GO:0004784 function-assignment hypothesis over-annotated, citing the Val87 copper-ligand substitution, the V87H reversion-mutant structure, and the absence of a direct RvSOD15 activity assay. |
| GO:0005507 copper ion binding | IEA GO_REF:0000002 | ACCEPT | Summary: IEA annotation from InterPro domain match (IPR024134). The crystal structure (PMID:37358501) confirms that copper is bound in the structure (PDB: 7YPP, 7YPR), though the coordination is unusual due to Val87 replacing a canonical His ligand. UniProt confirms copper binding with experimental evidence from the crystal structure. This annotation is supported by direct structural evidence. Reason: Copper binding is confirmed by the crystal structure at 2.1-2.2 A resolution. UniProt lists copper binding residues at positions 85, 104, and 162 with evidence from PMID:37358501 and PDB structures. Although the coordination is atypical (Val87 instead of His), copper is still present in the structure. Supporting Evidence: PMID:37358501 Here, crystal structures of a copper/zinc-containing SOD (RvSOD15) from an anhydrobiotic tardigrade, Ramazzottius varieornatus strain YOKOZUNA-1, are reported. |
| GO:0006801 superoxide metabolic process | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: IEA annotation from InterPro domain matches (IPR001424, IPR036423). This biological process annotation implies involvement in superoxide metabolism, but given that PMID:37358501 suggests RvSOD15 may have lost catalytic SOD function due to the Val87 substitution, the biological process annotation is even more questionable than the molecular function annotation. Reason: The structural evidence from PMID:37358501 indicates that RvSOD15 has a non-canonical active site (Val87 replacing a catalytic His ligand) and may have evolved to lose SOD function. Without direct evidence of superoxide metabolic activity, this biological process annotation based solely on domain membership is likely an over-annotation. Supporting Evidence: PMID:37358501 These studies show that RvSOD15 and some other RvSODs may have evolved to lose the SOD function. |
| GO:0046872 metal ion binding | IEA GO_REF:0000002 | ACCEPT | Summary: IEA annotation from InterPro domain matches (IPR001424, IPR036423). While technically correct (the protein does bind metal ions -- both Cu and Zn as confirmed by crystal structure), this is a very general term that is redundant with the more specific GO:0005507 (copper ion binding) and GO:0008270 (zinc ion binding) annotations that are already present with IDA evidence. Reason: The term is correct but redundant with more specific annotations. Since this is an IEA and the more specific terms (copper ion binding, zinc ion binding) are already annotated with IDA evidence, this general term adds little informational value but is not incorrect. Accepting as it is a valid broader annotation consistent with the IDA-supported specific terms. |
| GO:0004784 superoxide dismutase activity | ISS GO_REF:0000024 | MARK AS OVER ANNOTATED | Summary: ISS annotation transferred from UniProtKB:Q7JR71 (a Drosophila CuZnSOD) by curator judgment. While RvSOD15 has sequence similarity to functional CuZnSODs, the crystal structure (PMID:37358501) reveals that a key catalytic residue is mutated (Val87 instead of His), potentially abolishing enzymatic activity. The ISS transfer may not be appropriate for a protein where a critical active site residue is non-canonical. Reason: ISS transfer from a canonical CuZnSOD does not account for the Val87 substitution at a critical catalytic copper ligand position. PMID:37358501 explicitly raises doubt about SOD function in RvSOD15. Without direct enzymatic assay data, this annotation should be flagged as potentially over-annotated given the structural evidence for loss of function. The focused OpenScientist review reinforced that this ISS transfer does not account for paralog-specific active-site divergence. Supporting Evidence: PMID:37358501 In RvSOD15, one of the histidine ligands of the catalytic copper center is replaced by a valine (Val87). The crystal structures of the wild type and the V87H mutant show that even though a histidine is placed at position 87, a nearby flexible loop can destabilize the coordination of His87 to the Cu atom. file:RAMVA/RvY_13070/RvY_13070-hypotheses/function-hypothesis-go-0004784/openscientist.md OpenScientist concluded that domain-level Cu/Zn SOD classification conflicts with the function-level GO:0004784 assignment for RvSOD15, because the catalytic copper geometry has diverged from canonical enzymatic SODs. |
| GO:0008270 zinc ion binding | IDA PMID:37358501 Structure of a superoxide dismutase from a tardigrade: Ramaz... | ACCEPT | Summary: IDA annotation based on the crystal structure reported in PMID:37358501. Zinc binding is directly observed in the crystal structures (PDB: 7YPP, 7YPR). UniProt lists zinc binding residues at positions 104, 112, 121, and 124, all confirmed by the crystal structure with experimental evidence. The zinc site is structural (not catalytic) and all four zinc-coordinating residues are conserved. Reason: Zinc binding is directly demonstrated by the crystal structure at 2.1-2.2 A resolution. Unlike the catalytic copper site which has an atypical Val87 substitution, the structural zinc binding site appears to be fully canonical with four proper ligands confirmed in the electron density. Supporting Evidence: PMID:37358501 Here, crystal structures of a copper/zinc-containing SOD (RvSOD15) from an anhydrobiotic tardigrade, Ramazzottius varieornatus strain YOKOZUNA-1, are reported. |
| GO:0019430 removal of superoxide radicals | ISS GO_REF:0000024 | MARK AS OVER ANNOTATED | Summary: ISS annotation transferred from UniProtKB:Q7JR71 by curator judgment. This biological process term is closely related to superoxide dismutase activity and suffers from the same concern: RvSOD15 has a non-canonical active site (Val87 at a key catalytic position) and the authors of PMID:37358501 suggest it may have lost SOD function. Reason: Same concern as for the superoxide dismutase activity ISS annotation. The structural evidence from PMID:37358501 suggests this protein may not actually function in superoxide removal due to the Val87 substitution at a catalytic copper ligand position. ISS transfer from a canonical CuZnSOD does not account for this critical difference. The OpenScientist report flagged this BP annotation for coordinated review if the SOD catalytic activity term is removed or NOT-qualified. Supporting Evidence: PMID:37358501 These studies show that RvSOD15 and some other RvSODs may have evolved to lose the SOD function, suggesting that gene duplications of antioxidant proteins do not solely explain the high stress tolerance of anhydrobiotic tardigrades. file:RAMVA/RvY_13070/RvY_13070-hypotheses/function-hypothesis-go-0004784/openscientist.md OpenScientist recommended coordinated review of GO:0019430 because the process annotation depends on the same unverified SOD catalytic activity that is undermined by the RvSOD15 active-site structure. |
| GO:0042802 identical protein binding | IDA PMID:37358501 Structure of a superoxide dismutase from a tardigrade: Ramaz... | MODIFY | Summary: IDA annotation based on the crystal structure (PMID:37358501) which shows RvSOD15 as a homodimer. UniProt confirms homodimer status with experimental evidence. However, GO:0042802 (identical protein binding) is a generic term that is less informative than GO:0042803 (protein homodimerization activity) which is also annotated. The identical protein binding term is redundant when the more specific homodimerization term is present. Reason: GO:0042802 (identical protein binding) is a parent term of GO:0042803 (protein homodimerization activity). Since GO:0042803 is already annotated with the same evidence, this broader term is redundant and less informative. In general, 'protein binding' style annotations should be replaced with more specific terms when available. The homodimerization annotation captures the same information more precisely. Proposed replacements: protein homodimerization activity Supporting Evidence: PMID:37358501 Here, crystal structures of a copper/zinc-containing SOD (RvSOD15) from an anhydrobiotic tardigrade, Ramazzottius varieornatus strain YOKOZUNA-1, are reported. |
| GO:0042803 protein homodimerization activity | IDA PMID:37358501 Structure of a superoxide dismutase from a tardigrade: Ramaz... | ACCEPT | Summary: IDA annotation based on the crystal structure (PMID:37358501). The crystal structures (PDB: 7YPP at 2.2 A, 7YPR at 2.1 A) show RvSOD15 as a homodimer, consistent with the typical quaternary structure of CuZnSODs. UniProt explicitly states "Homodimer" with experimental evidence from PMID:37358501. This is a well-supported, specific, and informative annotation. Reason: Homodimerization is directly demonstrated by the crystal structure. CuZnSODs are well-known homodimers, and the structural data from PMID:37358501 confirms this for RvSOD15. The PDB structures contain multiple copies of the subunit in the asymmetric unit consistent with homodimeric arrangement. Supporting Evidence: PMID:37358501 Here, crystal structures of a copper/zinc-containing SOD (RvSOD15) from an anhydrobiotic tardigrade, Ramazzottius varieornatus strain YOKOZUNA-1, are reported. |
| GO:0005507 copper ion binding | IDA PMID:37358501 Structure of a superoxide dismutase from a tardigrade: Ramaz... | ACCEPT | Summary: IDA annotation based on the crystal structure (PMID:37358501). Copper binding is directly observed in the electron density maps of PDB: 7YPP and 7YPR. UniProt lists copper binding residues at positions 85, 104, and 162, all confirmed by the crystal structure. Although the copper coordination is atypical (Val87 instead of the canonical His ligand), copper is clearly bound in the structure. Reason: Copper binding is unambiguously demonstrated by the crystal structures at 2.1-2.2 A resolution. UniProt annotates specific copper-binding residues (His85, His104, His162) with evidence from PMID:37358501 and PDB structures. This is strong direct experimental evidence for copper ion binding, even though the coordination environment is atypical. Supporting Evidence: PMID:37358501 Here, crystal structures of a copper/zinc-containing SOD (RvSOD15) from an anhydrobiotic tardigrade, Ramazzottius varieornatus strain YOKOZUNA-1, are reported. |
| GO:0005576 extracellular region | IDA PMID:37358501 Structure of a superoxide dismutase from a tardigrade: Ramaz... | NEW | Summary: NEW annotation suggested based on the signal peptide (residues 1-20) identified in the UniProt record, indicating that RvSOD15 is a secreted protein targeted to the extracellular region. This is consistent with some CuZnSODs being extracellular (e.g., SOD3/EC-SOD in mammals). Reason: UniProt annotates a signal peptide at residues 1-20, and the protein is flagged as a Precursor. Signal peptides target proteins for secretion, suggesting localization to the extracellular region. This cellular component annotation is missing from the current GOA set and would provide important contextual information about where this protein functions. Note that the evidence code should likely be IEA (based on signal peptide prediction) rather than IDA unless the secretion has been experimentally confirmed. |
Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)