id: A9PCL4 gene_symbol: PRX2 product_type: PROTEIN status: DRAFT taxon: id: NCBITaxon:3694 label: Populus trichocarpa description: Type II (1-Cys, glutaredoxin/thioredoxin-dependent) peroxiredoxin of the Prx5 subfamily. It is a thiol-based peroxidase that uses a conserved redox-active peroxidatic cysteine to reduce hydrogen peroxide and organic, fatty acid, and phospholipid hydroperoxides to water and the corresponding alcohols, receiving reducing equivalents preferentially from glutaredoxin or from thioredoxin. Through peroxide detoxification it contributes to cell protection against oxidative stress and to cellular redox homeostasis. alternative_records: - id: B9ILP9 relationship: REFERENCE_PROTEOME_EQUIVALENT reference_proteome: UP000006729 reviewed_on: '2026-10-19' reason: 'Retain A9PCL4 as the primary Swiss-Prot accession. B9ILP9 at POPTR_018G083500 is the manually assessed reference-proteome counterpart: 161/162 identical residues, full ungapped coverage, and only N117D. The competing POPTR_001G423500 paralog (A0A2K2CCD0) differs at seven residues. The original EF146010 cDNA is explicitly from Nisqually-1, so a different cultivar cannot explain this pair. This is a sequence-supported locus assignment, not a shared primary-record locus cross-reference; the one-residue discrepancy remains unexplained.' evidence: - type: SEQUENCE_COMPARISON description: MMseqs2 searched all 77,340 sequences in UP000006729 (release 2026_03); global BLOSUM62 alignments were computed for every returned hit. B9ILP9 ranks first by global alignment score, with 99.3827% identity including gap columns, 100.0% query coverage and 100.0% target coverage. The saved candidate table and alignments retain competing matches and residue-level differences. The search is heuristic, and sequence similarity alone is not definitive genomic mapping. Identity over paired residues is 99.3827% (161/162); gap columns are excluded from this denominator. supported_by: - reference_id: file:POPTR/PRX2/PRX2-record-evidence.yaml supporting_text: |- query_length: 162 target_length: 162 alignment_columns: 162 identities: 161 mismatches: 1 gap_columns: 0 identity_percent: 99.3827 query_coverage_percent: 100.0 target_coverage_percent: 100.0 - type: PROTEOME_MEMBERSHIP description: Current UniProtKB and proteome records place B9ILP9, but not A9PCL4, in reference proteome UP000006729. Both UniProt records use NCBITaxon:3694; source-organism qualifications are recorded separately. supported_by: - reference_id: file:POPTR/PRX2/PRX2-record-evidence.yaml supporting_text: |- reference_proteome: UP000006729 proteome_is_reference: true proteome_taxon_matches: true primary_in_reference_proteome: false alternative_in_reference_proteome: true - type: RECORD_HISTORY description: UniSave versions 37 (2015), 62 (2020), and 77 (2024) lack Proteomes cross-references. These dated samples support longstanding absence at those dates; they do not establish uninterrupted absence, a removal event, or UniProt's motivation. supported_by: - reference_id: file:POPTR/PRX2/PRX2-record-evidence.yaml supporting_text: |- sampled_history_versions: - 37 - 62 - 77 sampled_versions_with_proteome_links: [] - type: CURATION_CONTEXT description: ENA source EF146010 identifies cultivar 383-2499 (Nisqually-1), matching the reference cultivar. The sequence discrepancy could reflect allele or sequence/model differences; the records do not establish which explanation applies. supported_by: - reference_id: file:POPTR/PRX2/PRX2-record-evidence.yaml supporting_text: /cultivar="383-2499 (Nisqually-1)" existing_annotations: - term: id: GO:0008379 label: thioredoxin peroxidase activity evidence_type: IEA original_reference_id: GO_REF:0000002 qualifier: enables review: summary: Thioredoxin peroxidase activity is supported because the enzyme can use thioredoxin as a reductant, but the protein preferentially uses glutaredoxin, so this term captures only part of the demonstrated activity. action: KEEP_AS_NON_CORE reason: UniProt and the biochemical literature show this peroxiredoxin uses either glutaredoxin or thioredoxin as a proton donor and preferentially uses glutaredoxin; the more general peroxiredoxin activity term better represents the core function, while thioredoxin peroxidase activity remains a correct supporting molecular function. supported_by: - reference_id: file:POPTR/PRX2/PRX2-uniprot.txt record_section: ["CC:FUNCTION"] supporting_text: Thiol-specific peroxidase that catalyzes the reduction of hydrogen peroxide and organic hydroperoxides to water and alcohols - reference_id: file:POPTR/PRX2/PRX2-deep-research-openai.md supporting_text: Peroxiredoxin activity reducing peroxides with electron donation via thioredoxin and/or glutaredoxin systems. - term: id: GO:0016491 label: oxidoreductase activity evidence_type: IEA original_reference_id: GO_REF:0000002 qualifier: enables review: summary: Oxidoreductase activity is correct but is a high-level parent term that is less informative than the specific peroxiredoxin activity for this characterized enzyme. action: KEEP_AS_NON_CORE reason: The specific peroxiredoxin activity and thioredoxin peroxidase activity terms already capture the redox catalysis; the generic oxidoreductase parent is true but redundant, so it is retained as a non-core annotation rather than the principal function. supported_by: - reference_id: file:POPTR/PRX2/PRX2-uniprot.txt record_section: ["CC:FUNCTION"] supporting_text: Thiol-specific peroxidase that catalyzes the reduction of hydrogen peroxide and organic hydroperoxides to water and alcohols - term: id: GO:0034599 label: cellular response to oxidative stress evidence_type: IEA original_reference_id: GO_REF:0000002 qualifier: involved_in review: summary: Cellular response to oxidative stress is the direct biological process for this peroxide-detoxifying antioxidant enzyme. action: ACCEPT reason: UniProt states the protein plays a role in cell protection against oxidative stress by detoxifying peroxides, which is exactly a cellular response to oxidative stress. supported_by: - reference_id: file:POPTR/PRX2/PRX2-uniprot.txt record_section: ["CC:FUNCTION"] supporting_text: Plays a role in cell protection against oxidative stress by detoxifying peroxides. - reference_id: file:POPTR/PRX2/PRX2-deep-research-openai.md supporting_text: Redox buffering and peroxide detoxification functions are consistent with stress-responsive antioxidant networks in plant tissues. - term: id: GO:0051920 label: peroxiredoxin activity evidence_type: IEA original_reference_id: GO_REF:0000116 qualifier: enables review: summary: Peroxiredoxin activity is the precise core molecular function, matching the glutaredoxin-dependent hydroperoxide reduction reaction and EC 1.11.1.25. action: ACCEPT reason: UniProt records the glutaredoxin-dependent reduction of hydroperoxides under EC 1.11.1.25, which is exactly peroxiredoxin activity, and the enzyme belongs to the peroxiredoxin family. supported_by: - reference_id: file:POPTR/PRX2/PRX2-uniprot.txt record_section: ["CC:CATALYTIC ACTIVITY"] supporting_text: Reaction=[glutaredoxin]-dithiol + a hydroperoxide = [glutaredoxin]- - reference_id: file:POPTR/PRX2/PRX2-deep-research-openai.md supporting_text: Peroxiredoxin activity reducing peroxides with electron donation via thioredoxin and/or glutaredoxin systems. - term: id: GO:0098869 label: cellular oxidant detoxification evidence_type: IEA original_reference_id: GO_REF:0000120 qualifier: involved_in review: summary: Cellular oxidant detoxification fits the role of this peroxiredoxin in detoxifying peroxides to protect the cell. action: ACCEPT reason: The enzyme detoxifies hydrogen peroxide and organic hydroperoxides, which is a cellular oxidant detoxification process underlying its protective antioxidant role. supported_by: - reference_id: file:POPTR/PRX2/PRX2-uniprot.txt record_section: ["CC:FUNCTION"] supporting_text: Plays a role in cell protection against oxidative stress by detoxifying peroxides. - reference_id: file:POPTR/PRX2/PRX2-deep-research-openai.md supporting_text: Redox buffering and peroxide detoxification functions are consistent with stress-responsive antioxidant networks in plant tissues. references: - id: file:POPTR/PRX2/PRX2-record-evidence.yaml title: Compact archived record and sequence evidence for A9PCL4 - id: GO_REF:0000002 title: Gene Ontology annotation through association of InterPro records with GO terms findings: - statement: GO_REF:0000002 supplied one or more source GOA annotations reviewed in this file. - id: GO_REF:0000116 title: Automatic Gene Ontology annotation based on Rhea mapping findings: - statement: GO_REF:0000116 supplied the Rhea-based peroxiredoxin activity annotation reviewed in this file. - id: GO_REF:0000120 title: Combined Automated Annotation using Multiple IEA Methods findings: - statement: GO_REF:0000120 supplied the cellular oxidant detoxification annotation reviewed in this file. - id: file:POPTR/PRX2/PRX2-uniprot.txt title: UniProtKB reviewed entry for PRX2 findings: - statement: UniProt describes PRX2 as a 1-Cys glutaredoxin/thioredoxin-dependent peroxiredoxin (Prx5 subfamily) that reduces hydrogen peroxide and organic, fatty acid, and phospholipid hydroperoxides and protects cells against oxidative stress. - id: file:POPTR/PRX2/PRX2-deep-research-openai.md title: Deep research synthesis for PRX2 findings: - statement: Deep research supports peroxiredoxin/peroxidase activity as the core function and a redox buffering / peroxide detoxification role for PRX2. - id: file:POPTR/PRX2/PRX2-goa.tsv title: QuickGO GOA annotations for PRX2 findings: - statement: GOA rows supplied the existing_annotations reviewed in this file. core_functions: - description: Reduces hydrogen peroxide and organic, fatty acid, and phospholipid hydroperoxides to water and alcohols using a peroxidatic cysteine and glutaredoxin/thioredoxin as electron donors, thereby detoxifying peroxides and protecting the cell against oxidative stress. molecular_function: id: GO:0051920 label: peroxiredoxin activity directly_involved_in: - id: GO:0098869 label: cellular oxidant detoxification - id: GO:0034599 label: cellular response to oxidative stress locations: [] supported_by: - reference_id: file:POPTR/PRX2/PRX2-uniprot.txt record_section: ["CC:FUNCTION"] supporting_text: Thiol-specific peroxidase that catalyzes the reduction of hydrogen peroxide and organic hydroperoxides to water and alcohols - reference_id: file:POPTR/PRX2/PRX2-uniprot.txt record_section: ["CC:FUNCTION"] supporting_text: Plays a role in cell protection against oxidative stress by detoxifying peroxides. proposed_new_terms: [] suggested_questions: - question: Which subcellular compartments and physiological or stress conditions most depend on PRX2-mediated peroxide detoxification in poplar? suggested_experiments: - description: Assay recombinant PRX2 peroxidase activity against hydrogen peroxide and phospholipid hydroperoxides with glutaredoxin versus thioredoxin reducing systems, and characterize the catalytic cysteine via site-directed mutagenesis. experiment_type: targeted enzymatic and mechanistic assay