A0A3B6GK97

UniProt ID: A0A3B6GK97
Organism: Triticum aestivum
Review Status: COMPLETE
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Gene 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

The protein sequence of this entry may not correspond to a single real gene product (for example, two neighbouring genes joined into one model, or a truncated model). Read the name, features and annotations of the entry with this in mind.

TRUNCATED GENE MODEL SUSPECTED ORTHOLOG COMPARISONGENOMIC SEQUENCE

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.

Supported by:

Existing Annotations Review

GO Term Evidence Action Reason
GO:0006629 lipid metabolic process
IEA
GO_REF:0000002
MARK AS OVER ANNOTATED
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.
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.
Supporting Evidence:
PMID:12779324
patatin has a Ser-Asp catalytic dyad
file:WHEAT/A0A3B6GK97/A0A3B6GK97-bioinformatics/RESULTS-rereview.md
Even the reconstructed full-length product, and the full-length 3B homoeolog, lack the catalytic serine nucleophile and the canonical oxyanion glycines.
file:WHEAT/A0A3B6GK97/A0A3B6GK97-bioinformatics/RESULTS.md
the modeled 302-aa sequence lacks the entire N-terminal half of the patatin
file:WHEAT/A0A3B6GK97/A0A3B6GK97-uniprot.txt
PE 3: Inferred from homology;
GO:0016787 hydrolase activity
IEA
GO_REF:0000117
REMOVE
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.
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.
Supporting Evidence:
PMID:12779324
Ser77 and Asp215 were critical for both esterase and bioactivity
file:WHEAT/A0A3B6GK97/A0A3B6GK97-bioinformatics/RESULTS-rereview.md
The 3B/3D homoeolog pair is therefore predicted to encode a **non-catalytic patatin-like protein**
file:WHEAT/A0A3B6GK97/A0A3B6GK97-bioinformatics/RESULTS.md
Without the nucleophilic Ser, acyl-ester hydrolysis is mechanistically impossible

References

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Suggested Questions for Experts

Q: Is TraesCS3D02G033600 expressed, and does its transcript include the upstream N-terminal exons that match the 3B homoeolog TraesCS3B02G036500?

Q: 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?

Q: 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

Experiment: 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.

Type: transcriptomics / gene model curation

Experiment: 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.

Type: in vitro enzyme assay

External Prediction Reviews

These computational predictions are reviewed separately from the GOA annotation set used for this review. The assessments below are from this project and do not constitute official GO annotations or endorsement by GO/UniProt. They are not included in the existing annotation review above.

ProtNLM2 External predictions

View prediction review YAML Β· A0A3B6GK97-protnlm-predictions-review.yaml Β· Review status: COMPLETE

Patatin-like (PNPLA) protein of the grass-specific PANTHER subfamily PTHR32176:SF103. The deposited 302-residue model is incomplete, but neither the upstream genomic sequence that probably encodes its N-terminus nor the full-length 3B homoeolog carries the catalytic serine nucleophile or the canonical oxyanion glycines, so the product is predicted to be a non-catalytic patatin-like protein. Lipase activity is contradicted, and participation in lipid catabolism is unresolved.

Source documents: genes/WHEAT/A0A3B6GK97/A0A3B6GK97-uniprot.txt Β· genes/WHEAT/A0A3B6GK97/A0A3B6GK97-goa.tsv Β· publications/PMID_12779324.md Β· genes/WHEAT/A0A3B6GK97/A0A3B6GK97-bioinformatics/RESULTS.md Β· genes/WHEAT/A0A3B6GK97/A0A3B6GK97-bioinformatics/RESULTS-rereview.md Β· genes/WHEAT/A0A3B6GK97/A0A3B6GK97-ai-review.yaml

Review score: 2 = concordant with evidence; 1 = uncertain; 0 = discordant with evidence. This is an assessment score, not a model probability.

GO:0016298 lipase activity GO_MF
NPI β€” Nonparalog incorrect Review score: 0/2
Prediction method: ProtNLM2 Β· Version: UniProt 2024_06 pilot
PSEUDOENZYME OVERANNOTATION
Review rationale: Patatin-family acyl-ester hydrolysis depends on a Ser-Asp catalytic dyad, and mutation of the serine abolishes esterase activity (PMID:12779324). The deposited 302-residue model lacks the N-terminal catalytic region, and the gene-model analysis shows that this is not only a truncation artifact: the upstream genomic sequence that probably encodes the true N-terminus and the full-length 3B homoeolog both lack the G-T-S-T-G nucleophile elbow and the canonical DGGG oxyanion block, while intact paralogs in the same chromosome-3 cluster retain them. The protein is therefore predicted to be a non-catalytic patatin-like protein, and lipase activity is refuted. The gene review removes the electronic hydrolase activity annotation on these grounds. The lipase IBAs in the UniProt record propagate from a family-level PAINT node and do not detect this target-specific loss of the catalytic serine. No experimental data exist for this protein.
Supporting Evidence:
GO:0016042 lipid catabolic process GO_BP
UNC β€” Uncertain Review score: 1/2
Prediction method: ProtNLM2 Β· Version: UniProt 2024_06 pilot
Review rationale: Lipid catabolic process is not carried by this gene in GOA; the gene has only the broader InterPro2GO lipid metabolic process annotation, which the gene review marks as over-annotated. Patatin-family membership would place the protein in lipid catabolism through acyl-ester hydrolysis, but the locus lacks the catalytic serine nucleophile and canonical oxyanion glycines, so hydrolysis by this protein cannot be assumed. A non-catalytic participant (for example a lipid-binding or regulatory role alongside the active paralogs in the same cluster) could still be involved in the process, so the absence of catalysis does not refute the term. No expression, interaction or phenotype data exist for this protein, and no literature on it was found, so the prediction can be neither validated nor refuted.
Supporting Evidence:

Deep Research

Falcon

(A0A3B6GK97-deep-research-falcon.md)

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πŸ“š Additional Documentation

Notes

(A0A3B6GK97-notes.md)

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Bioinformatics Results

(RESULTS.md)

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πŸ“„ View Raw YAML

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