id: A0A3B6GK97 gene_symbol: A0A3B6GK97 product_type: PROTEIN status: COMPLETE taxon: id: NCBITaxon:4565 label: Triticum aestivum description: Patatin-like (PNPLA domain) protein of bread wheat (Triticum aestivum), encoded by the chromosome 3D locus TraesCS3D02G033600 in a tandem cluster of patatin genes. It belongs to PANTHER subfamily PTHR32176:SF103, a grass-specific clade of soluble patatin-type proteins whose nearest characterised relatives are the Arabidopsis pPLAII lipid acyl hydrolases (PLP1, PLP2, PLP4, PLP5), from which it is separated by a gene duplication that predates the monocot-dicot split. The deposited 302-residue protein contains only the C-terminal two-thirds of the patatin fold. Genomic sequence upstream of the annotated start encodes a further N-terminal region that matches the full-length 444-residue chromosome 3B homoeolog (TraesCS3B02G036500), so the 302-residue model is probably incomplete. Neither the reconstructed N-terminal region nor the 3B homoeolog carries the catalytic serine nucleophile (G-T-S-T-G) or the canonical oxyanion glycines (DGGG) of patatin enzymes; only the catalytic aspartate of the Ser-Asp dyad is retained. The product is therefore predicted to be a non-catalytic patatin-like protein. Its biological role, expression and any non-enzymatic activity are unknown, and no experimental data exist for this protein. gene_model_issues: - issue_type: TRUNCATED_GENE_MODEL status: SUSPECTED description: >- The 302-residue model probably lacks about 140 N-terminal residues: genomic sequence about 1.5 kb upstream of the annotated start aligns to residues 1-150 of the full-length 444-residue chromosome 3B homoeolog (A0A3B6FIU7). The reconstructed N-terminal region does not restore the catalytic serine or the oxyanion glycines, so the truncation does not explain the missing active site. evidence_types: - ORTHOLOG_COMPARISON - GENOMIC_SEQUENCE supported_by: - reference_id: file:WHEAT/A0A3B6GK97/A0A3B6GK97-bioinformatics/RESULTS-rereview.md supporting_text: '**incomplete gene model**: its true product probably resembles the 444-aa 3B homoeolog' - reference_id: file:WHEAT/A0A3B6GK97/A0A3B6GK97-bioinformatics/RESULTS-rereview.md supporting_text: The reconstructed N-terminal region, however, does **not** restore the active site existing_annotations: - term: id: GO:0006629 label: lipid metabolic process evidence_type: IEA original_reference_id: GO_REF:0000002 qualifier: involved_in review: summary: InterPro2GO transfer from the PNPLA domain (IPR002641) to lipid metabolic process. The mapping assumes a catalytically competent patatin lipid acyl hydrolase, which this product is predicted not to be. action: MARK_AS_OVER_ANNOTATED reason: The patatin/PNPLA domain places patatin enzymes in lipid metabolism because they hydrolyse glycerolipid acyl esters with a Ser-Asp dyad [PMID:12779324]. This product lacks the serine nucleophile. The re-review analysis shows that the 302-aa model is an incomplete gene model, but the genomic sequence upstream of the 3D locus and the full-length 3B homoeolog (A0A3B6FIU7, 93% identical) both lack the G-T-S-T-G elbow and carry a corrupted oxyanion block, so the catalytic serine is absent from the locus itself and not just from the model. A non-catalytic patatin-like protein could still have some lipid-related role (for example lipid binding), so the term is not shown to be false, but no evidence places this protein in lipid metabolism and the domain-based inference rests on an activity it cannot perform. The previous review accepted this row before the gene-model analysis was done; it is changed here to MARK_AS_OVER_ANNOTATED. supported_by: - reference_id: PMID:12779324 supporting_text: patatin has a Ser-Asp catalytic dyad - reference_id: file:WHEAT/A0A3B6GK97/A0A3B6GK97-bioinformatics/RESULTS-rereview.md supporting_text: Even the reconstructed full-length product, and the full-length 3B homoeolog, lack the catalytic serine nucleophile and the canonical oxyanion glycines. - reference_id: file:WHEAT/A0A3B6GK97/A0A3B6GK97-bioinformatics/RESULTS.md supporting_text: the modeled 302-aa sequence lacks the entire N-terminal half of the patatin - reference_id: file:WHEAT/A0A3B6GK97/A0A3B6GK97-uniprot.txt record_section: [PE] supporting_text: 'PE 3: Inferred from homology;' - term: id: GO:0016787 label: hydrolase activity evidence_type: IEA original_reference_id: GO_REF:0000117 qualifier: enables review: summary: ARBA rule assigning hydrolase activity on the basis of patatin family membership. The product lacks the catalytic serine nucleophile that patatin-type ester hydrolysis requires, in the deposited model, in the upstream genomic sequence that probably encodes its true N-terminus, and in its full-length 3B homoeolog. action: REMOVE reason: Patatin-family hydrolysis uses a Ser-Asp dyad, and mutation of the serine abolishes esterase activity [PMID:12779324]. The serine sits in the G-T-S-T-G nucleophile elbow, which every active pPLA reference and every intact chromosome-3 SF103 paralog carries (3A TraesCS3A02G046500, 3B TraesCS3B02G036800 and 3D TraesCS3D02G033200/033500). The query has no G-x-S-x-G motif, and the re-review analysis shows that this is not just a gene-model truncation. The 8 kb upstream of the annotated start encodes an N-terminal region matching the 3B homoeolog A0A3B6FIU7 at 87% identity, and both have an unrelated segment where the nucleophile elbow should be and SIDGGD/SIDGGS where intact paralogs have SIDGGG. A protein without the nucleophile cannot carry out patatin-type acyl-ester hydrolysis. No other hydrolase domain is present. This is a pseudoenzyme over-annotation by an electronic rule, so the annotation is removed. The previous review's MODIFY to carboxylic ester hydrolase activity (GO:0052689) is withdrawn for the same reason. The UniProt FUNCTION text describing lipolytic acyl hydrolase activity is itself an ARBA prediction and is not independent support. supported_by: - reference_id: PMID:12779324 supporting_text: "Ser77 and Asp215 were \ncritical for both esterase and bioactivity" - reference_id: file:WHEAT/A0A3B6GK97/A0A3B6GK97-bioinformatics/RESULTS-rereview.md supporting_text: The 3B/3D homoeolog pair is therefore predicted to encode a **non-catalytic patatin-like protein** - reference_id: file:WHEAT/A0A3B6GK97/A0A3B6GK97-bioinformatics/RESULTS.md supporting_text: Without the nucleophilic Ser, acyl-ester hydrolysis is mechanistically impossible references: - id: GO_REF:0000002 title: Gene Ontology annotation through association of InterPro records with GO terms findings: [] reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: InterPro2GO mapping reference. IPR002641 (Patatin-like phospholipase domain) maps to GO:0006629 lipid metabolic process, matching the GOA annotation. The mapping is sound for catalytically intact patatin proteins but over-reaches for this non-catalytic member. - id: GO_REF:0000117 title: Electronic Gene Ontology annotations created by ARBA machine learning models findings: [] reference_review: relevance: LOW correctness: VERIFIED review_notes: ARBA electronic-annotation reference. The rule assigns hydrolase activity from family membership and does not check for the catalytic serine, which this product lacks; the annotation is removed in this review. - id: GO_REF:0000033 title: Annotation inferences using phylogenetic trees findings: - statement: 'GO_Central assigns this protein two IBA (phylogenetic) molecular-function annotations confirming lipase activity: GO:0004620 glycerophospholipase activity and GO:0047372 monoacylglycerol lipase activity (both ECO:0000318, GO_REF:0000033, assigned 2017-02-28). These are present in AmiGO/GOlr but were NOT returned by the QuickGO GOA pull used to seed this review, so they are recorded here as out-of-band evidence rather than as existing_annotations entries.' supporting_text: Annotation inferences using phylogenetic trees reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: 'GO_Central phylogenetic (PAINT/IBA) annotation reference. The UniProt record lists IBA GO:0004620 glycerophospholipase activity and GO:0047372 monoacylglycerol lipase activity, propagated from the eukaryote-level PAINT node PTN001282408 (seeded by Arabidopsis AT4G37050, AT4G37060 and AT4G37070; interpro/panther/PTHR32176/PTHR32176-paint.tsv). 2026-10-20 re-review: the node placement is sound for the family, but this descendant has lost the catalytic serine, so the propagated lipase activities are not expected to hold for this product. This is a target-specific loss that PAINT propagation does not detect. These IBA rows are not in the GOA seed and are therefore not reviewed as existing annotations; the reference is no longer used as support for any function.' - id: PMID:12779324 title: 'The crystal structure, mutagenesis, and activity studies reveal that patatin is a lipid acyl hydrolase with a Ser-Asp catalytic dyad' findings: - statement: Patatin is a lipid acyl hydrolase that uses a non-classical Ser-Asp catalytic dyad rather than the canonical Ser-His-Asp triad; this defines the catalytic mechanism of the patatin/PNPLA domain family to which this wheat protein belongs. supporting_text: patatin has a Ser-Asp catalytic dyad - statement: Mutation of the catalytic serine or aspartate abolishes patatin esterase activity, so a patatin-family protein lacking the serine is not expected to be an active hydrolase. supporting_text: "Ser77 and Asp215 were \ncritical for both esterase and bioactivity" reference_review: relevance: HIGH correctness: VERIFIED review_notes: PubMed-verified (PMID:12779324). Defines the Ser-Asp dyad of the patatin family. Used in the re-review to argue that loss of the serine in this product precludes patatin-type hydrolase activity. - id: PMID:16297072 title: A pathogen-inducible patatin-like lipid acyl hydrolase facilitates fungal and bacterial host colonization in Arabidopsis findings: - statement: Plant patatin-like proteins (e.g. Arabidopsis PLP2) are pathogen-inducible cytoplasmic lipid acyl hydrolases with broad substrate specificity that contribute to lipid-based signaling in plant-pathogen interactions; this is the basis for the family-level "plant defense" association but has not been shown for this wheat protein. supporting_text: PLP2 encodes a cytoplasmic lipid acyl hydrolase with wide substrate specificity reference_review: relevance: LOW correctness: VERIFIED review_notes: PubMed-verified (PMID:16297072). Characterises Arabidopsis PLP2/pPLAIIalpha (O48723), which by the PANTHER tree is an out-paralog of this protein (separated at duplication node PTN009133995), not an ortholog. Background only; not used as support for any annotation in the re-review. - id: file:WHEAT/A0A3B6GK97/A0A3B6GK97-deep-research-falcon.md title: 'Deep research report: PNPLA domain-containing protein A0A3B6GK97 in wheat (Triticum aestivum) - family-level functional annotation from scientific literature' findings: - statement: Plant PNPLA/patatin proteins function as calcium-independent phospholipases with lipase/phospholipase A-type activities. Their primary roles include lipid mobilization during seed germination, membrane phospholipid turnover, and stress adaptation. Substrate specificity includes phosphatidylcholine, phosphatidylserine, triacylglycerols, and lysophospholipids. supporting_text: The best-supported plant functions are lipid mobilization during seed germination, initiation of storage-oil breakdown, membrane phospholipid turnover, and remodeling of LD surfaces to allow access of TAG lipases - statement: No direct literature exists for A0A3B6GK97; all functional inferences are family-level, drawn from rice OsPLB, Arabidopsis PLP/pPLA, rapeseed patatin-like lipase, and potato patatin studies. supporting_text: Direct literature on the wheat protein A0A3B6GK97 is not available in the current scientific literature reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: Edison/falcon deep research report. Family-level review of plant PNPLA/patatin proteins; confirms that no gene-specific literature exists. Its family-level functions assume catalytic competence and so do not transfer to this non-catalytic member; no longer used as support in the re-review. - id: file:WHEAT/A0A3B6GK97/A0A3B6GK97-bioinformatics/RESULTS.md title: 'Bioinformatics analysis: pPLA subfamily placement and catalytic-site integrity of A0A3B6GK97' findings: - statement: By sequence identity (42-50% to pPLAII / rice pPLAs vs ~23% to pPLAIII and ~16% to pPLAI) and neighbour-joining placement, A0A3B6GK97 belongs to the pPLAII subfamily of plant patatin-related phospholipase A - the soluble lipid-acyl-hydrolase (defense/wounding/stress) clade - not pPLAIII (galactolipase/growth) or pPLAI (iPLA2-like). The single-domain architecture and this placement make a membrane trafficking role very unlikely. supporting_text: A0A3B6GK97 belongs to the pPLAII subfamily - statement: The modeled 302-aa sequence LACKS the N-terminal half of the patatin catalytic domain - both the oxyanion glycine-rich block (DGGG) and the catalytic-serine nucleophile elbow (G-T-S-T-G) are absent (zero G-x-S-x-G motifs in 302 aa), while the catalytic Asp is retained. As modeled the protein is predicted catalytically inactive; most parsimoniously an incomplete/incorrect gene model, though a genuine degenerate pseudo-enzyme cannot be excluded from sequence alone. supporting_text: the modeled 302-aa sequence lacks the entire N-terminal half of the patatin reference_review: relevance: HIGH correctness: VERIFIED review_notes: Reproducible in-repo analysis (MSA of 13 characterized plant pPLAs + query). Its catalytic-site result stands. Its "pPLAII subfamily" placement holds only in the broad sense of the pPLAII-type clade; the PANTHER tree (RESULTS-rereview.md) shows the protein is not an ortholog of any Arabidopsis pPLAII gene. Its open question (gene-model artifact vs genuine loss) is answered by RESULTS-rereview.md - the model is incomplete, and the locus still lacks the catalytic serine. The second finding's quote was corrected in the re-review to a verbatim substring of RESULTS.md. - id: file:WHEAT/A0A3B6GK97/A0A3B6GK97-bioinformatics/RESULTS-rereview.md title: 'Re-review analysis (2026-10-20): gene model, homoeologs and phylogenetic placement of A0A3B6GK97' findings: - statement: The 302-aa TraesCS3D02G033600 model is incomplete; genomic sequence about 1.5 kb upstream encodes an N-terminal region matching the 444-aa 3B homoeolog A0A3B6FIU7. supporting_text: The 302-aa model is an incomplete gene model - statement: Neither the reconstructed 3D N-terminus nor the 3B homoeolog carries the catalytic serine elbow or the canonical oxyanion glycines, so the product is predicted to be a non-catalytic patatin-like protein. supporting_text: Even the reconstructed full-length product, and the full-length 3B homoeolog, lack the catalytic serine nucleophile and the canonical oxyanion glycines. - statement: In the PANTHER 19 tree the protein sits in grass-specific subfamily SF103, sister to rice PLP2, and is separated from the Arabidopsis pPLAII proteins by duplication node PTN009133995. supporting_text: A0A3B6GK97 is therefore not an ortholog of any Arabidopsis pPLAII protein. reference_review: relevance: HIGH correctness: VERIFIED review_notes: Reproducible re-review analysis (UniProt and Ensembl REST, PANTHER tree API). Exon structure is inferred from protein-to-genome similarity, not spliced alignment, and expression was not examined. - id: file:WHEAT/A0A3B6GK97/A0A3B6GK97-uniprot.txt title: UniProtKB entry A0A3B6GK97 reference_review: relevance: LOW correctness: VERIFIED review_notes: Cited only for the protein existence level (PE 3), to show that the annotations rest on homology inference. core_functions: [] proposed_new_terms: [] suggested_questions: - question: Is TraesCS3D02G033600 expressed, and does its transcript include the upstream N-terminal exons that match the 3B homoeolog TraesCS3B02G036500? - question: Do the 3B/3D homoeologs (TraesCS3B02G036500, TraesCS3D02G033600) encode a stable non-catalytic patatin-like protein with a function of its own (for example lipid binding, or regulation of active paralogs in the same cluster), or are they degenerating copies? - question: Should the IBA lipase annotations (GO:0004620, GO:0047372) propagated from PAINT node PTN001282408 be blocked for SF103 members that have lost the catalytic serine, such as A0A3B6GK97 and A0A3B6FIU7? suggested_experiments: - description: Map RNA-seq reads and full-length transcripts to the TraesCS3D02G033600 and TraesCS3B02G036500 loci to establish expression and the true exon structure, and check whether the reconstructed N-terminus is translated. experiment_type: transcriptomics / gene model curation - description: Express the full-length homoeolog product and an intact paralog (for example TraesCS3A02G046500) and compare acyl hydrolase activity against phospholipids, galactolipids and acylglycerols, to test the prediction that the serine-less protein is inactive. Restoring the G-T-S-T-G elbow would test whether the serine alone accounts for any difference. experiment_type: in vitro enzyme assay