Gene Ontology annotation through association of InterPro records with GO terms
Annotation inferences using phylogenetic trees
Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt
UniProtKB reviewed entry for S. pombe Pmp20 (O14313)
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The reviewed record describes the target-specific catalytic-site divergence.
"Pmp20 lacks the resolving cysteine residue."
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The reviewed record reports a cytoplasmic pool.
"SUBCELLULAR LOCATION: Cytoplasm"
UniProtKB reviewed entry for human mitochondrial PRDX5 (P30044)
Reproducible bioinformatics assessment of pmp20 thioredoxin-dependent peroxidase activity
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pmp20 lacks sequence-level resolving cysteine support
"- `pmp20`: 156 aa, **1 cysteine** total (`C43`), act-site annotated at 43, **no candidate resolving cysteine**."
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Active-control resolving cysteine sites do not map to cysteine in pmp20
"Active-control resolving positions do **not** map to cysteine in `pmp20`:"
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AlphaFold model includes only one cysteine for pmp20
"`pmp20`: model has only one cysteine SG atom (C43), so no Cys-Cys pair geometry is possible in the monomer."
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Most Prx5-like homologs retain resolving-cysteine architecture, unlike pmp20
"- Panel size: 27 reviewed eukaryotic Prx5-like proteins (`prx5_panel.tsv`).
- Catalytic-state counts (`prx5_phylogeny_report.json`):
- `peroxidatic_plus_resolving`: 23
- `peroxidatic_only`: 4
- `pmp20` class: `peroxidatic_only` (`prx5_catalytic_state.tsv`)."
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Prx5 dimer template mapping does not support a template-like C(P)-C(R) pair in pmp20
"target_supports_template_like_cp_cr_pair = no"
ORFeome cloning and global analysis of protein localization in the fission yeast Schizosaccharomyces pombe.
Distinct functional roles of peroxiredoxin isozymes and glutathione peroxidase from fission yeast, Schizosaccharomyces pombe.
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Pmp20 has no thioredoxin-dependent peroxidase activity.
"However, peroxidase activity was not observed for PMP20 (peroxisomal membrane protein 20)."
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Pmp20 has weak chaperone activity (inhibits thermal aggregation).
"TPx, PMP20, and GPx inhibited thermal aggregation of citrate synthase at 43(o)C, but BCP failed to inhibit the aggregation. The chaperone activities of PMP20 and GPx were weaker than that of TPx."
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Pmp20 may act as a molecular chaperone rather than a peroxidase.
"The fission yeast PMP20 without thioredoxin-dependent peroxidase activity may act as a molecular chaperone."
A genetic approach to study H2O2 scavenging in fission yeast--distinct roles of peroxiredoxin and catalase.
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Tpx1 is the main enzyme controlling low peroxide levels during aerobic growth in S. pombe.
"Tpx1 is the only enzyme with sufficient sensitivity for peroxides and cellular abundance as to control the low levels produced during aerobic growth"
Antioxidant system within yeast peroxisome. Biochemical and physiological characterization of CbPmp20 in the methylotrophic yeast Candida boidinii.
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C. boidinii CbPmp20 (ortholog) has glutathione peroxidase activity and is essential for growth on methanol, more important than catalase.
"The His(6)-tagged CbPmp20 fusion protein was found to have glutathione peroxidase activity in vitro toward alkyl hydroperoxides and H(2)O(2)."
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CbPmp20 pmp20-deletion strain has more severe growth defect than catalase deletion and does not accumulate H2O2.
"the pmp20Delta strain had a more severe growth defect than the cta1Delta strain, which lacks catalase, another antioxidant enzyme within the peroxisome."
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CbPmp20 likely decomposes lipid hydroperoxides at peroxisomal membranes rather than bulk H2O2.
"it is speculated to be the main function of CbPmp20 is to decompose reactive oxygen species generated at peroxisomal membrane surface, e.g. lipid hydroperoxides, rather than to decompose H(2)O(2)."
Absence of the peroxiredoxin Pmp20 causes peroxisomal protein leakage and necrotic cell death.
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H. polymorpha Pmp20 (ortholog) deletion causes peroxisomal protein leakage and necrotic cell death on methanol.
"This growth defect was paralleled by leakage of peroxisomal matrix proteins into the cytosol."
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Absence of Pmp20 leads to loss of peroxisome membrane integrity and necrotic cell death.
"We conclude that the absence of the peroxisomal peroxiredoxin leads to loss of peroxisome membrane integrity and necrotic cell death."
Peroxiredoxin 5: structure, mechanism, and function of the mammalian atypical 2-Cys peroxiredoxin.
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Mammalian PRDX5 (Pmp20 ortholog) reduces alkyl hydroperoxides and peroxynitrite efficiently, but H2O2 more modestly.
"PRDX5 is a peroxidase that can use cytosolic or mitochondrial thioredoxins to reduce alkyl hydroperoxides or peroxynitrite with high rate constants in the 10(6) to 10(7) M(-1)s(-1) range, whereas its reaction with hydrogen peroxide is more modest, in the 10(5) M(-1)s(-1) range."
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PRDX5 is viewed as a cytoprotective antioxidant rather than a redox sensor.
"PRDX5 has been viewed mainly as a cytoprotective antioxidant enzyme acting against endogenous or exogenous peroxide attacks rather than as a redox sensor."
Falcon (Edison) deep research report on S. pombe pmp20 (O14313) function, localization, and peroxiredoxin-family context
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Falcon synthesis confirms pmp20 identity as a Prx5-subfamily peroxiredoxin-family protein
whose best-supported direct S. pombe role is chaperone-like (holdase) anti-aggregation
activity, with peroxidase chemistry only inferred at the family level.
"The *S. pombe* gene **pmp20** (UniProt **O14313**; ORF **SPCC330.06c**) encodes a **Prx5-subfamily peroxiredoxin (peroxiredoxin family; redoxin/thioredoxin-fold protein)** that is discussed in the yeast literature as a **peroxisomal reactive oxygen species (ROS) detoxification factor** and as a protein with **additional chaperone-like (“holdase”) activity** under heat stress"
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The most direct S. pombe experimental claim identified by falcon is in vitro inhibition
of citrate synthase thermal aggregation at 43C, supporting a chaperone-like protein
quality-control role.
"the most direct *S. pombe* experimental claim is **in vitro inhibition of citrate synthase thermal aggregation at 43°C**, supporting a chaperone-like role in protein quality control"
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Falcon places S. pombe Pmp20p in the peroxisome based on multiple yeast-focused reviews,
consistent with the IBA peroxisome annotation.
"In the accessible literature, *S. pombe* Pmp20p is treated as **peroxisomal** in multiple yeast-focused reviews and models"
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Falcon found no direct S. pombe substrate-specificity data; organic hydroperoxides are
only a family-level inference (via Ahp1/PRDX5 orthologs) and remain unconfirmed for pmp20.
"Direct substrate specificity for *S. pombe* Pmp20 was not found in accessible primary data"
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Falcon notes that organic-peroxide substrate preference for pmp20 is an inference from
family members and requires S. pombe-specific enzymology to confirm.
"For *S. pombe* Pmp20 (Prx5-like), organic hydroperoxides are a plausible physiological substrate class (inference from family), but this remains to be confirmed by *S. pombe*-specific enzymology"
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Falcon's expert synthesis proposes a dual function for S. pombe Pmp20p: antioxidant
defense plus molecular chaperone-like activity.
"Pmp20p may have a **dual function**: antioxidant defense plus **molecular chaperone-like activity**"
OpenScientist focused review of pmp20 thioredoxin peroxidase activity
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The focused hypothesis review judged GO:0008379 thioredoxin peroxidase activity over-annotated for pmp20 and recommended removing or suppressing the computational annotation.
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The direct PMID:20356456 assay refutes thioredoxin-dependent peroxidase activity and supports holdase activity.
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The report emphasizes that the thermal aggregation protection assay supports holdase-type anti-aggregation activity rather than peroxidase activity.
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PMID:24521463 provides organism-level context that peroxide scavenging in S. pombe is primarily attributed to Tpx1, catalase, and Gpx1, not pmp20.
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The report states that a non-thioredoxin reductant was not tested.
"Glutathione peroxidase activity not explicitly tested"
PANTHER family PTHR10430 (PEROXIREDOXIN) functional diversity analysis
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Peroxiredoxin family has extensive mechanistic diversity across six classes; GO annotations should not be naively propagated without active-site profiling.
"Active-site profiling approaches (DASP/PREX; MISST) were developed specifically because no single BLAST-like threshold can resolve these subgroups."
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Hyperoxidized peroxiredoxins can switch to chaperone/holdase activity, representing a functional divergence from simple detoxification.
"hyperoxidized forms can produce high-molecular-weight species associated with **chaperone-like (holdase) activity**"
Automatic assignment of GO terms using logical inference, based on on inter-ontology links
Kim et al. 2010 primary full text (PMID:20356456), unedited PDF extraction
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GSH-dependent peroxidase activity was tested and was negative, contrary to both provider reports.
"None of the fission yeast Prxs
and GPx showed GSH-dependent peroxidase activity (data not
shown)."
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The oxidative protein-protection assay was negative for Pmp20.
"PMP20 did not show any
protective effect against the thiol MCO system."
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Pmp20 physiological holdase function still requires investigation.
"Further
studies will be required to determine whether the fission yeast
PMP20 functions as a molecular chaperone in vivo."
OpenScientist focused review of pmp20 broader peroxiredoxin prediction
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The report states that a non-thioredoxin reductant was not tested.
"The only direct *S. pombe* assay used thioredoxin and was negative"
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The provider acknowledges direct catalytic activity is not proven by its structural analysis.
"direct catalytic activity in *S. pombe* remains unproven."
openai research on S. pombe Pmp20
pmp20 superseded propagation evidence and judgments
PTHR10430 PAINT ancestral assertions