| Topic | Summary | Evidence type | Key sources |
|---|---|---|---|
| Functional annotation summary for RvY_00650-1 (A0A1D1UDY8): Gene/protein identifiers and organism | Target protein is UniProt A0A1D1UDY8, annotated as **superoxide dismutase [Cu-Zn]** (EC 1.15.1.1), gene **RvY_00650-1 / RvY_00650**, from **Ramazzottius varieornatus** (tardigrade). In the retrieved literature, this exact accession/gene ID was **not directly discussed**; published structural work instead focused on other R. varieornatus Cu/Zn SODs such as **RvSOD15 (GenBank GAV02514.1)** and additional RvSOD family members. | Direct for A0A1D1UDY8 (identifier from user/UniProt context) + Direct for R. varieornatus SOD | (pqac-00000001, pqac-00000003, pqac-00000007) |
| Protein family/domains | UniProt/domain context places A0A1D1UDY8 in the **Cu/Zn superoxide dismutase family** with **SOD-like_Cu/Zn_dom_sf, SOD_Cu/Zn_/chaperone, SOD_Cu/Zn_BS, SOD_Cu_Zn_dom, PF00080**. This matches the broader CuZnSOD fold described for tardigrade **RvSOD15**, which adopts a canonical CuZnSOD monomer architecture despite unusual active-site features. | Direct for A0A1D1UDY8 (family/domain assignment) + Direct for R. varieornatus SOD | (pqac-00000003, pqac-00000005) |
| Enzymatic reaction and substrate | Canonical Cu/Zn SODs catalyze **dismutation of superoxide radical**: **2 O2•− + 2 H+ -> H2O2 + O2**. Substrate specificity is principally **superoxide anion (O2•−)**. The spontaneous nonenzymatic rate is about **2 × 10^5 M−1 s−1** at physiological pH, and SOD catalysis accelerates this by about **10,000-fold**. For A0A1D1UDY8, this function is **inferred from family membership**, not directly demonstrated in the retrieved Ramazzottius paper set. | General CuZnSOD; inferred for A0A1D1UDY8 | (pqac-00000012, pqac-00000013) |
| Cofactors and active-site residues | Canonical CuZnSOD requires **catalytic Cu** for redox chemistry and **Zn** mainly for structural stabilization; Cu generally cannot be replaced, whereas Zn can sometimes be substituted experimentally. Superoxide is guided into the active site by a conserved **electrostatic loop** with positively charged residues. In R. varieornatus, several Cu/Zn SOD paralogs show **unusual substitutions/deletions**: e.g., **RvSOD15** carries **Val87** in place of a canonical Cu-ligating histidine, and some RvSODs show deletion of the electrostatic loop or β3 sheet and atypical metal-binding residues, suggesting reduced or lost canonical SOD activity in some paralogs. | Direct for R. varieornatus SOD + General CuZnSOD | (pqac-00000000, pqac-00000002, pqac-00000004, pqac-00000011, pqac-00000013) |
| Oligomeric state | Typical intracellular **SOD1/CuZnSOD** is a **~32 kDa homodimer**. Extracellular **SOD3** is typically a **~135 kDa homotetramer**. Structurally characterized tardigrade **RvSOD15** forms the **canonical CuZnSOD monomer fold** and assembled as typical **dimers** in the crystal. | Direct for R. varieornatus SOD + General CuZnSOD | (pqac-00000003, pqac-00000012) |
| Subcellular localization | In general, **SOD1** is mainly intracellular and distributed in the **cytoplasm, nucleus, and cell membrane**, whereas **SOD3/ecSOD** is **secreted/extracellular**, carrying a signal peptide and ECM/proteoglycan-binding features. For tardigrades, **RvSOD15** is specifically reported to have an **N-terminal signal peptide**, supporting a **secreted/extracellular localization**. For **A0A1D1UDY8/RvY_00650-1**, no direct localization evidence was found in the retrieved literature; localization remains an inference from family/domain annotation unless sequence-level targeting features are independently verified. | Direct for R. varieornatus SOD + General CuZnSOD | (pqac-00000001, pqac-00000003, pqac-00000011, pqac-00000012) |
| Evidence availability for the specific target | **Literature is limited for the specific protein A0A1D1UDY8 / RvY_00650-1.** The retrieved papers do **not mention RvY_00650 or UniProt A0A1D1UDY8** directly. There is, however, direct literature on **other R. varieornatus Cu/Zn SODs**, especially **RvSOD15**, plus review-level evidence that R. varieornatus has an expanded SOD repertoire (reported as **17 SOD genes**). Therefore, functional annotation of A0A1D1UDY8 must rely heavily on **family/domain inference** plus **organism-level paralog evidence**, while carefully avoiding overclaiming direct experimental support for this exact protein. | Direct for R. varieornatus SOD; limited direct evidence for A0A1D1UDY8 | (pqac-00000003, pqac-00000004, pqac-00000006, pqac-00000007) |
| Key quantitative data points | For tardigrade **RvSOD15**, crystal structures were solved at **2.20 Å** (wild type) and **2.10 Å** (V87H mutant), with **Rwork/Rfree ~19.3/23.2** and **~17.2/21.4**, respectively; AlphaFold/model comparisons included **pLDDT ~86.99** for RvSOD15, **77.15** for RvSOD12, **92.19** for RvSOD16 v1; Cu-associated water distances were **2.6–3.4 Å**; by analogy to a related mutant, activity may be around **10^-4 of canonical CuZnSODs** for RvSOD15-like active-site geometry. General CuZnSOD kinetics/applications reported: spontaneous superoxide disproportionation **~2 × 10^5 M−1 s−1**, enzyme acceleration **~10,000-fold**; food/biotech examples include **2476.21 ± 1.52 U g−1** SOD production by Lactobacillus plantarum, **19.827 ± 0.323 U mL−1** SOD in yogurt, and topical TAT-SOD causing **36.6 ± 18.4%** increase in minimum erythema dose and **47.6 ± 8.6%** reduction in sunburn cells. | Direct for R. varieornatus SOD + General CuZnSOD | (pqac-00000000, pqac-00000002, pqac-00000003, pqac-00000013, pqac-00000014, pqac-00000016) |


*Table: This table summarizes what can be stated directly versus inferred for Ramazzottius varieornatus gene RvY_00650-1 (UniProt A0A1D1UDY8), integrating direct tardigrade SOD evidence with general Cu/Zn SOD biology. It is useful for distinguishing target-specific support from paralog- and family-based annotation.*