RvY_10893

UniProt ID: A0A1D1VE88
Organism: Ramazzottius varieornatus
Review Status: IN PROGRESS
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Gene Description

Putative Cu/Zn superoxide dismutase paralog from R. varieornatus, one of approximately 10 CuZnSOD-family proteins encoded by this extremotolerant tardigrade. Bioinformatic analysis (file:RAMVA/RvY_13070/RvY_13070-bioinformatics/RESULTS.md) shows that all four canonical Cu-binding histidines, all four Zn-binding residues, and both intrachain disulfide cysteines are preserved at the sequence level. The protein matches both PROSITE Cu/Zn SOD signatures (PS00087 for the N-terminal Cu coordination loop and PS00332 for the C-terminal disulfide region), as well as the Pfam SODC family (PF00080). This is consistent with canonical Cu/Zn superoxide dismutase activity, although biochemical confirmation has not been published for this specific paralog. 185 aa (166 mature); all residues and PROSITE patterns match canonical CuZnSOD

Existing Annotations Review

GO Term Evidence Action Reason
GO:0004784 superoxide dismutase activity
IEA
GO_REF:0000120
ACCEPT
Summary: All catalytic residues (4 Cu His, 4 Zn ligands, 2 disulfide Cys) are preserved at the sequence level. PROSITE PS00087 (N-terminal Cu coordination signature) and PS00332 (C-terminal disulfide signature) both match. The protein is in Pfam family PF00080 (Sod_Cu). Canonical SOD activity is plausible based on sequence and motif analysis, though biochemical data are lacking for this specific paralog. ACCEPT with the caveat that confidence is limited to sequence-level inference.
Reason: All sequence-level criteria for canonical CuZnSOD are met.
Supporting Evidence:
file:RAMVA/RvY_13070/RvY_13070-bioinformatics/RESULTS.md
RvY_10893 | A0A1D1VE88 | bioinformatic verdict: FUNCTIONAL
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
ACCEPT
Summary: Inferred from SOD activity annotation.
GO:0019430 removal of superoxide radicals
IEA
GO_REF:0000108
ACCEPT
Summary: Inferred from SOD activity 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.

References

Gene Ontology annotation through association of InterPro records with GO terms
Automatic assignment of GO terms using logical inference, based on on inter-ontology links
Combined Automated Annotation using Multiple IEA Methods
file:RAMVA/RvY_13070/RvY_13070-bioinformatics/RESULTS.md
Bioinformatics analysis of Cu/Zn SOD paralogs in R. varieornatus
  • Bioinformatic verdict for RvY_10893: FUNCTIONAL. 185 aa (166 mature); all residues and PROSITE patterns match canonical CuZnSOD
Structure of a superoxide dismutase from a tardigrade: Ramazzottius varieornatus strain YOKOZUNA-1.
  • RvSOD15 structural work shows that even paralogs preserving the canonical Cu/Zn SOD signature residues may have subtle structural divergence that affects activity; sequence-level "FUNCTIONAL" predictions for tardigrade SOD paralogs remain provisional until biochemical assay.
file:RAMVA/RvY_10893/RvY_10893-deep-research-falcon.md
Deep research report on RvY_10893 (Falcon/Edison Scientific Literature)
  • No primary publication directly characterizes RvY_10893 / A0A1D1VE88; annotation as a canonical Cu/Zn SOD is supported by full Cu/Zn ligand and disulfide cysteine conservation plus both PROSITE Cu/Zn SOD signatures (PS00087, PS00332), consistent with the existing bioinformatic "FUNCTIONAL" verdict, but specific biochemical confirmation remains lacking.

Deep Research

Falcon

(RvY_10893-deep-research-falcon.md)
Research report: Functional annotation of **RvY_10893-1** (UniProt **A0A1D1VE88**) from *Ramazzottius varieornatus* (tardigrade) Falcon Edison Scientific Literature 26 citations 2 artifacts 2026-05-22T23:14:16.263846

The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.

You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.

We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.

We are interested in where in or outside the cell the gene product carries out its function.

We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.

Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.

Research report: Functional annotation of RvY_10893-1 (UniProt A0A1D1VE88) from Ramazzottius varieornatus (tardigrade)

Executive summary

UniProt accession A0A1D1VE88 (gene model RvY_10893-1 / RvY_10893) is annotated as a copper/zinc superoxide dismutase (Cu/Zn SOD; EC 1.15.1.1) belonging to the Cu/Zn SOD family with canonical Cu/Zn SOD domains (per user-provided UniProt context). Direct peer‑reviewed literature explicitly naming RvY_10893-1 or A0A1D1VE88 could not be retrieved in this run; therefore, gene-specific assertions beyond family-level inference are limited. However, recent structural and review literature in R. varieornatus shows that (i) R. varieornatus carries an expanded and diversified set of Cu/Zn SOD-like proteins, and (ii) at least one paralog (RvSOD15) is structurally Cu/Zn-SOD-like but has an unusual active site consistent with attenuated or lost canonical SOD activity—a key consideration when annotating any specific paralog in this species. (sim2023structureofa pages 3-4, sadowskabartosz2024antioxidantdefensein pages 15-16)

1. Identity verification (mandatory)

1.1 Target identity and ambiguity assessment

  • Target provided: UniProt A0A1D1VE88, organism Ramazzottius varieornatus, protein name “Superoxide dismutase [Cu-Zn]” (EC 1.15.1.1), Cu/Zn SOD family/domains (user-provided UniProt context).
  • Literature mapping: The best-matching R. varieornatus Cu/Zn-SOD primary study retrieved is a 2023 crystallography paper on RvSOD15 (PDB 7YPP/7YPR). This paper discusses multiple R. varieornatus SOD gene models (e.g., RvY_10892.1, RvY_10894.1) but does not explicitly link RvY_10893-1 or A0A1D1VE88 to RvSOD15 in the extracted sections; therefore RvSOD15 ≠ confirmed as A0A1D1VE88. (sim2023structureofa pages 3-4)

Conclusion: It is appropriate to annotate A0A1D1VE88 as a Cu/Zn SOD family member based on UniProt/domain context, but paralog-specific features (e.g., unusual metal-binding residues) cannot be assigned to A0A1D1VE88 without a definitive mapping. (sadowskabartosz2024antioxidantdefensein pages 15-16, sim2023structureofa pages 3-4)

2. Key concepts and definitions (current understanding)

2.1 Cu/Zn superoxide dismutase function (EC 1.15.1.1)

Cu/Zn SODs catalyze the dismutation of superoxide radicals to hydrogen peroxide and molecular oxygen:
[2O2^{\u2022-} + 2H^+ \rightarrow H_2O_2 + O_2] (sim2023structureofa pages 1-2, liu2025superoxidedismutasesin pages 2-4)

This reaction is central to redox homeostasis, reducing oxidative damage and shaping downstream signaling because the product H2O2 can act as a diffusible signaling molecule that is subsequently removed by catalase/peroxidases. (zheng2023theapplicationsand pages 1-2, liu2025superoxidedismutasesin pages 2-4)

2.2 Metal cofactors and active-site logic

Cu/Zn SODs use Cu for redox cycling during catalysis and Zn primarily for structural stabilization; the family is characterized by a conserved β‑barrel fold with functional loops (notably an “electrostatic loop” that guides substrate and a “metal-binding loop”). (liu2025superoxidedismutasesin pages 2-4, sim2023structureofa pages 3-4)

3. Tardigrade/R. varieornatus context: oxidative stress and SOD gene-family expansion

3.1 Biological rationale: oxidative stress during anhydrobiosis

During anhydrobiosis (extreme dehydration), tardigrade cells experience oxidative stress and must control reactive oxygen species (ROS), motivating interest in antioxidant enzymes including SODs. (sim2023structureofa pages 1-2)

3.2 Expanded SOD repertoires in R. varieornatus

A 2024 review synthesizing genomic data reports a major expansion of SOD genes in R. varieornatus, listing 17 SOD genes (compared with 3 in humans) and suggests distribution across subcellular compartments (mitochondria, cytosol, and peroxisomes) at the repertoire level (not per-gene mapping). (sadowskabartosz2024antioxidantdefensein pages 15-16, sadowskabartosz2024antioxidantdefensein pages 13-15)

A widely cited comparative genomics study reports that SOD gene families are duplicated in both H. dujardini and R. varieornatus and that, under slow desiccation, induced genes in R. varieornatus include antioxidant-related genes (SOD subtype not specified in the excerpt). (yoshida2017comparativegenomicsof pages 21-23)

4. Recent developments (prioritizing 2023–2024)

4.1 2023 crystal structures reveal atypical Cu/Zn SOD active sites in R. varieornatus

A 2023 Acta Crystallographica F paper reports X-ray structures of a R. varieornatus Cu/Zn SOD-like paralog (RvSOD15; PDB 7YPP) and a mutant (V87H; PDB 7YPR) (publication date: June 2023, URL: https://doi.org/10.1107/S2053230X2300523X). (sim2023structureofa pages 1-2)

Key mechanistic structural findings:
- Cu and Zn presence confirmed by anomalous scattering at their expected sites, supporting Cu/Zn-SOD family assignment even for a divergent paralog. (sim2023structureofa pages 3-4)
- RvSOD15 exhibits a non-canonical copper site: one histidine ligand is substituted by Val87, a position typically histidine in canonical Cu/Zn SODs. (sim2023structureofa pages 1-2, sim2023structureofa pages 3-4)
- Even after restoring histidine (V87H), His87 coordination to Cu is incomplete and geometrically unusual: only 3 of 6 molecules in the asymmetric unit show His87 coordination, with His87–Cu distances ~2.7–2.8 Å, longer than typical Cu–N distances (~2.03 Å cited for canonical coordination). (sim2023structureofa pages 4-7)
- The Cu site geometry is described as T-shaped with additional water ligands at 2.6–3.4 Å, consistent with weak/atypical coordination. (sim2023structureofa pages 4-7)
- The enzyme retains the Greek‑key β‑barrel fold and forms a typical eukaryotic-like dimer in the crystal. (sim2023structureofa pages 3-4, sim2023structureofa pages 4-7)

These data support the expert interpretation that at least some R. varieornatus Cu/Zn-SOD-like genes have diverged and may have low or absent canonical SOD enzymatic activity, complicating a “more copies = more antioxidant activity” narrative. (sim2023structureofa pages 1-2, sadowskabartosz2024antioxidantdefensein pages 15-16)

Figure evidence (cropped): Panels showing the RvSOD15 dimer/monomer with Val87 and the copper-site environment/His87 distances were extracted from the paper figures. (sim2023structureofa media ee91fdbf, sim2023structureofa media aef2495a)

4.2 2024 review synthesis: antioxidant defense in tardigrades

A 2024 review (publication date: August 2024, URL: https://doi.org/10.3390/ijms25158393) emphasizes that tardigrade resistance involves an “efficient antioxidant system,” including expanded antioxidant enzymes, and highlights the possibility that some expanded SOD paralogs may have lost canonical function (citing atypical residues and deletions in some modeled SODs). (sadowskabartosz2024antioxidantdefensein pages 15-16)

5. Functional annotation of A0A1D1VE88 (RvY_10893-1)

5.1 Primary molecular function (inference constrained by mapping limitations)

Given the UniProt-provided annotation and conserved Cu/Zn SOD family domains, the most defensible primary function for A0A1D1VE88 is:
- Enzymatic activity: superoxide dismutase (Cu/Zn), catalyzing 2O2•− + 2H+ → H2O2 + O2. (sim2023structureofa pages 1-2, liu2025superoxidedismutasesin pages 2-4)
- Substrate specificity: superoxide anion (O2•−); protons as cosubstrate; Cu and Zn as required cofactors for proper fold/activity. (liu2025superoxidedismutasesin pages 2-4, zheng2023theapplicationsand pages 2-4)

However, because R. varieornatus harbors multiple Cu/Zn SOD-like paralogs including atypical ones with disrupted metal-binding geometries, the degree of catalytic competence of any specific paralog should be treated as an empirical question unless sequence-to-paralog mapping is established. (sadowskabartosz2024antioxidantdefensein pages 15-16, sim2023structureofa pages 1-2)

5.2 Likely biological processes

At family level, Cu/Zn SODs participate in:
- Cellular response to oxidative stress via detoxification of superoxide, reducing oxidation of proteins, lipids, and nucleic acids. (sim2023structureofa pages 1-2, zheng2023theapplicationsand pages 1-2)
- Redox signaling modulation via controlling superoxide/H2O2 balance. (zheng2023theapplicationsand pages 1-2)

In tardigrades, antioxidant defenses are proposed to contribute to stress tolerance during desiccation and radiation exposure, and SOD gene family expansion has been repeatedly discussed in this context. (sim2023structureofa pages 1-2, sadowskabartosz2024antioxidantdefensein pages 15-16)

5.3 Subcellular localization (what can and cannot be concluded)

  • What is known for a specific R. varieornatus paralog (RvSOD15): RvSOD15 is predicted to possess an N-terminal signal peptide, indicating secretion (extracellular/pericellular space). (sim2023structureofa pages 3-4)
  • What is suggested at the repertoire level: a 2024 review suggests multiple SODs in R. varieornatus likely localize across mitochondria, cytosol, and peroxisomes, consistent with typical eukaryotic antioxidant compartmentalization. (sadowskabartosz2024antioxidantdefensein pages 13-15)

For A0A1D1VE88 specifically, localization cannot be asserted from the retrieved literature without sequence features (signal peptide vs targeting peptide) or experimental localization. The safest statement is: localization is expected to align with the targeting signals encoded by this paralog (cytosolic vs secreted vs organellar), but those signals were not extracted from primary literature in this run. (sadowskabartosz2024antioxidantdefensein pages 13-15, sim2023structureofa pages 3-4)

5.4 Pathways and network context

Cu/Zn SOD acts upstream of H2O2-removal systems (catalase, peroxidases, glutathione peroxidase/peroxiredoxins), making it part of an integrated antioxidant network controlling ROS during stress and recovery/rehydration. (zheng2023theapplicationsand pages 2-4, sadowskabartosz2024antioxidantdefensein pages 13-15)

6. Current applications and real-world implementations (2023–2024 emphasized)

Although applications are not specific to tardigrade SOD paralogs, the Cu/Zn SOD family is widely implemented in consumer and biomedical contexts.

6.1 Medicine/biomedicine and delivery technologies

A 2023 review in Antioxidants (publication date: Aug 2023, URL: https://doi.org/10.3390/antiox12091675) summarizes that SODs are used/considered in medicine with reported anti-tumor, anti-radiation, and anti-aging effects, but that practical deployment is limited by membrane permeability and persistence (short duration/stability), motivating development of conjugates and mimetics. (zheng2023theapplicationsand pages 1-2)

Representative implementation strategies and quantitative examples from this review include:
- Cell-penetrating peptide fusions (TAT‑SOD): topical administration before UVB increased minimum erythema dose by 36.6 ± 18.4% and reduced apoptotic “sunburn cells” by 47.6 ± 8.6% (mouse skin study summarized in the review). (zheng2023theapplicationsand pages 14-15)
- PEGylation: PEG of 41–72 kDa reported to retain ~90–100% activity in PEG–SOD conjugates (reviewed formulation example). (zheng2023theapplicationsand pages 14-15)
- Encapsulation and carriers: liposomes, niosomes (including hair follicle targeting), hydrogels, and polymer microcapsules are reviewed as routes to improve stability and delivery. (zheng2023theapplicationsand pages 14-15)

6.2 Food/agriculture and biotechnology

The same 2023 review summarizes transgenic and microbial SOD implementations, including a reported case where expression of a cassava CuZnSOD (mSOD1) in transgenic cucumber produced ~3× higher SOD-specific activity, illustrating the use of Cu/Zn SOD genes to modulate antioxidant capacity in plants. (zheng2023theapplicationsand pages 14-15)

7. Expert opinions and analysis (authoritative synthesis)

7.1 “Expansion does not imply function”: paralog diversification in tardigrades

  • The 2023 structural study concludes that RvSOD15 and some other R. varieornatus SOD-like proteins may have evolved to lose SOD function, suggesting that gene duplications alone do not explain high stress tolerance. (sim2023structureofa pages 1-2)
  • The 2024 tardigrade antioxidant-defense review echoes this interpretation by highlighting atypical structural features (e.g., deletions/metal-binding changes) among modeled SODs and again stating that some may have lost canonical function. (sadowskabartosz2024antioxidantdefensein pages 15-16)

This is a critical annotation caveat for A0A1D1VE88: family membership supports “SOD-like” function, but catalytic competence may vary among paralogs and should be validated by sequence inspection (metal-binding residues, conserved loops) and/or biochemical assay. (sadowskabartosz2024antioxidantdefensein pages 15-16, sim2023structureofa pages 1-2)

7.2 Desiccation transcriptomics: limited inducibility vs preparedness

Comparative genomics reports R. varieornatus exhibits relatively limited transcriptional regulation during anhydrobiosis compared with H. dujardini, with antioxidant-related genes among those induced during slow desiccation, consistent with a “preparedness/constitutive defense” perspective often discussed for this species. (yoshida2017comparativegenomicsof pages 21-23)

8. Key statistics and data points (recent studies)

  • SOD gene count in R. varieornatus: 17 SOD genes reported in a 2024 review synthesis (table-based). (sadowskabartosz2024antioxidantdefensein pages 15-16)
  • RvSOD15 structural metrics (2023):
  • Copper-site perturbation: His87–Cu distances ~2.7–2.8 Å in the V87H mutant where coordination occurs; only 3/6 molecules show coordination. (sim2023structureofa pages 4-7)
  • Water ligand distances to Cu: 2.6–3.4 Å (weak interactions). (sim2023structureofa pages 4-7)
  • Dimeric assembly observed in crystal (eukaryotic-like). (sim2023structureofa pages 3-4)
  • Topical UVB-protection example (SOD delivery; review of prior studies): TAT‑SOD increased minimum erythema dose by 36.6 ± 18.4% and reduced sunburn cells by 47.6 ± 8.6%. (zheng2023theapplicationsand pages 14-15)

9. Evidence summary table

The following table distinguishes direct experimental evidence in R. varieornatus (RvSOD15) from family-level inference and explicitly flags the mapping uncertainty to A0A1D1VE88.

Entity Evidence type Key finding Quantitative details Source (paper + year + URL) Citation context ID
RvSOD15 (Ramazzottius varieornatus strain YOKOZUNA-1) Crystal structure Cu/Zn-containing SOD-like enzyme; catalyzes the canonical Cu/Zn SOD reaction in the family context: dismutation of superoxide to O2 and H2O2; copper and zinc were confirmed at expected sites, supporting Cu/Zn-SOD family assignment Reaction given as 2O2•− + 2H+ -> O2 + H2O2; anomalous scattering confirmed Cu/Zn; structure solved at 2.2 A Sim & Inoue 2023, Acta Crystallogr F, https://doi.org/10.1107/S2053230X2300523X (sim2023structureofa pages 1-2, sim2023structureofa pages 3-4)
RvSOD15 Crystal structure Active site is highly unusual for a Cu/Zn SOD: one histidine ligand of the catalytic copper center is replaced by Val87, implying likely impairment of canonical SOD catalysis Val87 replaces the histidine found at the equivalent catalytic Cu-binding position in typical Cu/Zn SODs; 44% similarity to human SOD1 and 56% to H. exemplaris putative CuZnSOD Sim & Inoue 2023, Acta Crystallogr F, https://doi.org/10.1107/S2053230X2300523X (sim2023structureofa pages 1-2, sim2023structureofa pages 3-4)
RvSOD15 Crystal structure Overall fold remains Cu/Zn-SOD-like: Greek-key beta-barrel with electrostatic loop and metal-binding loop; forms a eukaryotic-like dimer Monomer has 8 antiparallel beta strands; 6 monomers in crystal, 4 forming dimers in asymmetric unit and others by symmetry; wild-type PDB 7ypp Sim & Inoue 2023, Acta Crystallogr F, https://doi.org/10.1107/S2053230X2300523X (sim2023structureofa pages 3-4, sim2023structureofa pages 4-7, sim2023structureofa media ee91fdbf)
RvSOD15 Crystal structure Zn site is close to canonical Cu/Zn SODs, but the catalytic Cu site is distorted; Cu is coordinated by only 3 histidines in T-shaped geometry with 2 weakly interacting waters, consistent with reduced activity WatA/WatB at 2.6-3.4 A from Cu; protein ligands comprise only 3 histidines; wild-type copper geometry T-shaped Sim & Inoue 2023, Acta Crystallogr F, https://doi.org/10.1107/S2053230X2300523X (sim2023structureofa pages 4-7, sim2023structureofa media ee91fdbf)
RvSOD15 V87H mutant Crystal structure / mutational inference Restoring His at position 87 does not fully rescue a catalytic copper site because a flexible loop destabilizes His87 coordination; supports very low or lost SOD activity Only 3 of 6 molecules show His87 coordination; His87-Cu distances are unusually long at 2.7-2.8 A versus typical approximately 2.03 A Sim & Inoue 2023, Acta Crystallogr F, https://doi.org/10.1107/S2053230X2300523X (sim2023structureofa pages 4-7, sim2023structureofa media ee91fdbf)
RvSOD15 Crystal structure / localization prediction Predicted to be secreted based on an N-terminal signal peptide, so likely functions outside the cytosol if expressed as annotated N-terminal signal peptide predicted; no direct localization experiment reported Sim & Inoue 2023, Acta Crystallogr F, https://doi.org/10.1107/S2053230X2300523X (sim2023structureofa pages 3-4, sim2023structureofa pages 2-3)
RvSOD15 Crystal structure / functional inference Electrostatic and metal-binding loops are altered relative to canonical Cu/Zn SODs, giving a less charged substrate-guiding surface and a more disordered metal-binding region; these features may depress activity Metal-binding loop has 2-residue insertion after Cys96; loop lacks helical structure seen in other CuZnSODs; Tyr97 adopts alternative conformations Sim & Inoue 2023, Acta Crystallogr F, https://doi.org/10.1107/S2053230X2300523X (sim2023structureofa pages 4-7)
R. varieornatus CuZn-SOD paralogs Genome/transcriptome + structural modeling The species has an expanded SOD repertoire, but several paralogs are atypical (truncated proteins, mutated ligand residues, deleted loops), suggesting diversification and possible neofunctionalization or loss of classical SOD activity Review summarizes 17 SOD genes in R. varieornatus (vs 3 in humans); structural classes include alpha, beta, gamma, delta, epsilon; beta/gamma include mutated metal sites or missing electrostatic loop/beta3 sheet Sadowska-Bartosz & Bartosz 2024, Int J Mol Sci, https://doi.org/10.3390/ijms25158393; Sim & Inoue 2023, https://doi.org/10.1107/S2053230X2300523X (sadowskabartosz2024antioxidantdefensein pages 15-16, sadowskabartosz2024antioxidantdefensein pages 13-15, sim2023structureofa pages 7-9)
R. varieornatus CuZn-SOD paralogs Genome/transcriptome Antioxidant genes, including SOD family members, are constitutively abundant and/or induced under slow desiccation; R. varieornatus shows more limited transcriptional change than H. dujardini, implying preparedness rather than strong inducibility SOD duplicated in both tardigrade species compared; genes induced by slow desiccation included antioxidant-related genes; no gene-specific fold change for RvY_10893-1 reported Yoshida et al. 2017, PLOS Biology, https://doi.org/10.1371/journal.pbio.2002266 (yoshida2017comparativegenomicsof pages 21-23)
R. varieornatus SOD family Genome/review High constitutive antioxidant capacity is part of tardigrade stress biology; CuZn-SODs are described as highly expressed in R. varieornatus, though paralog-specific values are not given 16-17 SODs reported for R. varieornatus depending on source/table interpretation; probable localization across mitochondria, cytosol, and peroxisomes Sadowska-Bartosz & Bartosz 2024, Int J Mol Sci, https://doi.org/10.3390/ijms25158393 (sadowskabartosz2024antioxidantdefensein pages 13-15)
General Cu/Zn SOD1 Review / canonical family framework Canonical Cu/Zn SODs are homodimeric beta-barrel metalloenzymes that bind Cu and Zn and dismutate superoxide radicals; this is the baseline for annotating R. varieornatus homologs Reaction: 2O2•− + 2H+ -> H2O2 + O2; typical Cu/Zn SOD1 forms homodimer; each monomer is a beta-barrel plus loops Liu et al. 2025, Antioxidants, https://doi.org/10.3390/antiox14070809 (liu2025superoxidedismutasesin pages 2-4)
General Cu/Zn SOD1 vs A0A1D1VE88 mapping Annotation inference UniProt A0A1D1VE88 (gene RvY_10893-1) is annotated as a Cu/Zn superoxide dismutase, but the retrieved literature directly characterizes RvSOD15 and broader paralog sets rather than explicitly mapping A0A1D1VE88 to RvSOD15; therefore, functional annotation for A0A1D1VE88 should rely primarily on UniProt family/domain assignment plus indirect species-level evidence UniProt-provided domains match Cu/Zn SOD family; literature directly names nearby paralogs such as RvSOD12 (RvY_10892.1), RvSOD14 (RvY_10894.1), and RvSOD15, but no explicit paper-based mapping of A0A1D1VE88/RvY_10893-1 to RvSOD15 was found Sim & Inoue 2023, Acta Crystallogr F, https://doi.org/10.1107/S2053230X2300523X; Sadowska-Bartosz & Bartosz 2024, https://doi.org/10.3390/ijms25158393 (sim2023structureofa pages 3-4, sadowskabartosz2024antioxidantdefensein pages 15-16)

Table: This table summarizes the strongest evidence relevant to functional annotation of Ramazzottius varieornatus Cu/Zn superoxide dismutases, emphasizing the structurally characterized RvSOD15 and how far current literature can be mapped to UniProt A0A1D1VE88 (RvY_10893-1). It is useful for distinguishing direct experimental findings from family-level inference and for flagging the current mapping uncertainty for the specific target accession.

10. Practical annotation recommendations for A0A1D1VE88 (next-step evidence needed)

Given the mapping uncertainty, the most actionable, evidence-aligned annotation strategy is:
1. Assign core molecular function: Cu/Zn superoxide dismutase (EC 1.15.1.1) with the canonical dismutation reaction (family-consistent). (sim2023structureofa pages 1-2, liu2025superoxidedismutasesin pages 2-4)
2. Flag potential paralog divergence: In R. varieornatus, some Cu/Zn SOD-like paralogs have disrupted Cu-site ligation and altered loops consistent with reduced activity; therefore A0A1D1VE88 should be annotated with a cautionary note pending residue-level verification. (sadowskabartosz2024antioxidantdefensein pages 15-16, sim2023structureofa pages 1-2)
3. Determine localization from sequence features: evaluate whether A0A1D1VE88 encodes a signal peptide (secreted like RvSOD15) or other targeting motifs; secretion prediction is paralog-specific. (sim2023structureofa pages 3-4)
4. Empirical validation priority: biochemical activity assay (superoxide dismutation), metal-binding validation, and stress-condition expression profiling for this specific gene model.

References (URLs and publication dates)

  • Sim KS, Inoue T. Structure of a superoxide dismutase from a tardigrade: Ramazzottius varieornatus strain YOKOZUNA-1. Acta Crystallographica Section F (June 2023). https://doi.org/10.1107/S2053230X2300523X (sim2023structureofa pages 1-2)
  • Sadowska-Bartosz I, Bartosz G. Antioxidant Defense in the Toughest Animals on the Earth: Its Contribution to the Extreme Resistance of Tardigrades. International Journal of Molecular Sciences (Aug 2024). https://doi.org/10.3390/ijms25158393 (sadowskabartosz2024antioxidantdefensein pages 15-16)
  • Zheng M et al. The Applications and Mechanisms of Superoxide Dismutase in Medicine, Food, and Cosmetics. Antioxidants (Aug 2023). https://doi.org/10.3390/antiox12091675 (zheng2023theapplicationsand pages 1-2)
  • Yoshida Y et al. Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus. PLOS Biology (Jul 2017). https://doi.org/10.1371/journal.pbio.2002266 (yoshida2017comparativegenomicsof pages 21-23)

References

  1. (sim2023structureofa pages 3-4): Kee-Shin Sim and Tsuyoshi Inoue. Structure of a superoxide dismutase from a tardigrade: ramazzottius varieornatus strain yokozuna-1. Acta crystallographica. Section F, Structural biology communications, 79:169-179, Jun 2023. URL: https://doi.org/10.1107/s2053230x2300523x, doi:10.1107/s2053230x2300523x. This article has 5 citations.

  2. (sadowskabartosz2024antioxidantdefensein pages 15-16): Izabela Sadowska-Bartosz and Grzegorz Bartosz. Antioxidant defense in the toughest animals on the earth: its contribution to the extreme resistance of tardigrades. International Journal of Molecular Sciences, 25:8393, Aug 2024. URL: https://doi.org/10.3390/ijms25158393, doi:10.3390/ijms25158393. This article has 14 citations.

  3. (sim2023structureofa pages 1-2): Kee-Shin Sim and Tsuyoshi Inoue. Structure of a superoxide dismutase from a tardigrade: ramazzottius varieornatus strain yokozuna-1. Acta crystallographica. Section F, Structural biology communications, 79:169-179, Jun 2023. URL: https://doi.org/10.1107/s2053230x2300523x, doi:10.1107/s2053230x2300523x. This article has 5 citations.

  4. (liu2025superoxidedismutasesin pages 2-4): Tong Liu, Jiajin Shang, and Qijun Chen. Superoxide dismutases in immune regulation and infectious diseases. Antioxidants, 14:809, Jun 2025. URL: https://doi.org/10.3390/antiox14070809, doi:10.3390/antiox14070809. This article has 12 citations.

  5. (zheng2023theapplicationsand pages 1-2): Mengli Zheng, Yating Liu, Guanfeng Zhang, Zhikang Yang, Weiwei Xu, and Qinghua Chen. The applications and mechanisms of superoxide dismutase in medicine, food, and cosmetics. Antioxidants, 12:1675, Aug 2023. URL: https://doi.org/10.3390/antiox12091675, doi:10.3390/antiox12091675. This article has 373 citations.

  6. (sadowskabartosz2024antioxidantdefensein pages 13-15): Izabela Sadowska-Bartosz and Grzegorz Bartosz. Antioxidant defense in the toughest animals on the earth: its contribution to the extreme resistance of tardigrades. International Journal of Molecular Sciences, 25:8393, Aug 2024. URL: https://doi.org/10.3390/ijms25158393, doi:10.3390/ijms25158393. This article has 14 citations.

  7. (yoshida2017comparativegenomicsof pages 21-23): Yuki Yoshida, Georgios Koutsovoulos, Dominik R. Laetsch, Lewis Stevens, Sujai Kumar, Daiki D. Horikawa, Kyoko Ishino, Shiori Komine, Takekazu Kunieda, Masaru Tomita, Mark Blaxter, and Kazuharu Arakawa. Comparative genomics of the tardigrades hypsibius dujardini and ramazzottius varieornatus. PLOS Biology, 15:e2002266, Jul 2017. URL: https://doi.org/10.1371/journal.pbio.2002266, doi:10.1371/journal.pbio.2002266. This article has 250 citations and is from a highest quality peer-reviewed journal.

  8. (sim2023structureofa pages 4-7): Kee-Shin Sim and Tsuyoshi Inoue. Structure of a superoxide dismutase from a tardigrade: ramazzottius varieornatus strain yokozuna-1. Acta crystallographica. Section F, Structural biology communications, 79:169-179, Jun 2023. URL: https://doi.org/10.1107/s2053230x2300523x, doi:10.1107/s2053230x2300523x. This article has 5 citations.

  9. (sim2023structureofa media ee91fdbf): Kee-Shin Sim and Tsuyoshi Inoue. Structure of a superoxide dismutase from a tardigrade: ramazzottius varieornatus strain yokozuna-1. Acta crystallographica. Section F, Structural biology communications, 79:169-179, Jun 2023. URL: https://doi.org/10.1107/s2053230x2300523x, doi:10.1107/s2053230x2300523x. This article has 5 citations.

  10. (sim2023structureofa media aef2495a): Kee-Shin Sim and Tsuyoshi Inoue. Structure of a superoxide dismutase from a tardigrade: ramazzottius varieornatus strain yokozuna-1. Acta crystallographica. Section F, Structural biology communications, 79:169-179, Jun 2023. URL: https://doi.org/10.1107/s2053230x2300523x, doi:10.1107/s2053230x2300523x. This article has 5 citations.

  11. (zheng2023theapplicationsand pages 2-4): Mengli Zheng, Yating Liu, Guanfeng Zhang, Zhikang Yang, Weiwei Xu, and Qinghua Chen. The applications and mechanisms of superoxide dismutase in medicine, food, and cosmetics. Antioxidants, 12:1675, Aug 2023. URL: https://doi.org/10.3390/antiox12091675, doi:10.3390/antiox12091675. This article has 373 citations.

  12. (zheng2023theapplicationsand pages 14-15): Mengli Zheng, Yating Liu, Guanfeng Zhang, Zhikang Yang, Weiwei Xu, and Qinghua Chen. The applications and mechanisms of superoxide dismutase in medicine, food, and cosmetics. Antioxidants, 12:1675, Aug 2023. URL: https://doi.org/10.3390/antiox12091675, doi:10.3390/antiox12091675. This article has 373 citations.

  13. (sim2023structureofa pages 2-3): Kee-Shin Sim and Tsuyoshi Inoue. Structure of a superoxide dismutase from a tardigrade: ramazzottius varieornatus strain yokozuna-1. Acta crystallographica. Section F, Structural biology communications, 79:169-179, Jun 2023. URL: https://doi.org/10.1107/s2053230x2300523x, doi:10.1107/s2053230x2300523x. This article has 5 citations.

  14. (sim2023structureofa pages 7-9): Kee-Shin Sim and Tsuyoshi Inoue. Structure of a superoxide dismutase from a tardigrade: ramazzottius varieornatus strain yokozuna-1. Acta crystallographica. Section F, Structural biology communications, 79:169-179, Jun 2023. URL: https://doi.org/10.1107/s2053230x2300523x, doi:10.1107/s2053230x2300523x. This article has 5 citations.

Artifacts

Citations

  1. sim2023structureofa pages 3-4
  2. sim2023structureofa pages 1-2
  3. yoshida2017comparativegenomicsof pages 21-23
  4. sim2023structureofa pages 4-7
  5. sadowskabartosz2024antioxidantdefensein pages 15-16
  6. zheng2023theapplicationsand pages 1-2
  7. sadowskabartosz2024antioxidantdefensein pages 13-15
  8. zheng2023theapplicationsand pages 14-15
  9. liu2025superoxidedismutasesin pages 2-4
  10. zheng2023theapplicationsand pages 2-4
  11. sim2023structureofa pages 2-3
  12. sim2023structureofa pages 7-9
  13. Cu-Zn
  14. 2O2^{\u2022-} + 2H^+ \rightarrow H_2O_2 + O_2\
  15. https://doi.org/10.1107/S2053230X2300523X
  16. https://doi.org/10.3390/ijms25158393
  17. https://doi.org/10.3390/antiox12091675
  18. https://doi.org/10.3390/ijms25158393;
  19. https://doi.org/10.1371/journal.pbio.2002266
  20. https://doi.org/10.3390/antiox14070809
  21. https://doi.org/10.1107/S2053230X2300523X;
  22. https://doi.org/10.1107/s2053230x2300523x,
  23. https://doi.org/10.3390/ijms25158393,
  24. https://doi.org/10.3390/antiox14070809,
  25. https://doi.org/10.3390/antiox12091675,
  26. https://doi.org/10.1371/journal.pbio.2002266,

📄 View Raw YAML

id: A0A1D1VE88
gene_symbol: RvY_10893
product_type: PROTEIN
status: IN_PROGRESS
taxon:
  id: NCBITaxon:947166
  label: Ramazzottius varieornatus
description: >-
  Putative Cu/Zn superoxide dismutase paralog from R. varieornatus, one of approximately 10 CuZnSOD-family proteins encoded by this extremotolerant tardigrade. Bioinformatic analysis (file:RAMVA/RvY_13070/RvY_13070-bioinformatics/RESULTS.md) shows that all four canonical Cu-binding histidines, all four Zn-binding residues, and both intrachain disulfide cysteines are preserved at the sequence level. The protein matches both PROSITE Cu/Zn SOD signatures (PS00087 for the N-terminal Cu coordination loop and PS00332 for the C-terminal disulfide region), as well as the Pfam SODC family (PF00080). This is consistent with canonical Cu/Zn superoxide dismutase activity, although biochemical confirmation has not been published for this specific paralog. 185 aa (166 mature); all residues and PROSITE patterns match canonical CuZnSOD
existing_annotations:
- term:
    id: GO:0004784
    label: superoxide dismutase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      All catalytic residues (4 Cu His, 4 Zn ligands, 2 disulfide Cys) are preserved at the sequence level. PROSITE PS00087 (N-terminal Cu coordination signature) and PS00332 (C-terminal disulfide signature) both match. The protein is in Pfam family PF00080 (Sod_Cu). Canonical SOD activity is plausible based on sequence and motif analysis, though biochemical data are lacking for this specific paralog. ACCEPT with the caveat that confidence is limited to sequence-level inference.
    action: ACCEPT
    reason: >-
      All sequence-level criteria for canonical CuZnSOD are met.
    supported_by:
      - reference_id: file:RAMVA/RvY_13070/RvY_13070-bioinformatics/RESULTS.md
        supporting_text: >-
          RvY_10893 | A0A1D1VE88 | bioinformatic verdict: FUNCTIONAL
- term:
    id: GO:0005507
    label: copper ion binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: >-
      All four canonical Cu-binding histidines are preserved at the sequence level. Copper binding is likely.
    action: ACCEPT
- term:
    id: GO:0006801
    label: superoxide metabolic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: >-
      Inferred from SOD activity annotation.
    action: ACCEPT
- term:
    id: GO:0019430
    label: removal of superoxide radicals
  evidence_type: IEA
  original_reference_id: GO_REF:0000108
  review:
    summary: >-
      Inferred from SOD activity annotation.
    action: ACCEPT
- term:
    id: GO:0046872
    label: metal ion binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: >-
      Parent term of the more specific Cu/Zn binding annotations. Both Cu and Zn binding are likely.
    action: KEEP_AS_NON_CORE
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO
    terms
  findings: []
- id: GO_REF:0000108
  title: Automatic assignment of GO terms using logical inference, based on on inter-ontology
    links
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: file:RAMVA/RvY_13070/RvY_13070-bioinformatics/RESULTS.md
  title: Bioinformatics analysis of Cu/Zn SOD paralogs in R. varieornatus
  findings:
  - statement: "Bioinformatic verdict for RvY_10893: FUNCTIONAL. 185 aa (166 mature); all residues and PROSITE patterns match canonical CuZnSOD"
- id: PMID:37358501
  title: "Structure of a superoxide dismutase from a tardigrade: Ramazzottius varieornatus strain YOKOZUNA-1."
  findings:
  - statement: RvSOD15 structural work shows that even paralogs preserving the
      canonical Cu/Zn SOD signature residues may have subtle structural divergence
      that affects activity; sequence-level "FUNCTIONAL" predictions for tardigrade
      SOD paralogs remain provisional until biochemical assay.
- id: file:RAMVA/RvY_10893/RvY_10893-deep-research-falcon.md
  title: Deep research report on RvY_10893 (Falcon/Edison Scientific Literature)
  findings:
  - statement: No primary publication directly characterizes RvY_10893 / A0A1D1VE88;
      annotation as a canonical Cu/Zn SOD is supported by full Cu/Zn ligand and
      disulfide cysteine conservation plus both PROSITE Cu/Zn SOD signatures
      (PS00087, PS00332), consistent with the existing bioinformatic "FUNCTIONAL"
      verdict, but specific biochemical confirmation remains lacking.