pqqD2 (PP_2681) encodes PqqA binding protein 2, a second PqqD-family peptide chaperone associated with pyrroloquinoline quinone (PQQ) biosynthesis in Pseudomonas putida KT2440. Like PqqD1, it is annotated as a PqqA-binding protein that presents PqqA to PqqE, supporting early precursor-peptide modification during PQQ cofactor production.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0018189 pyrroloquinoline quinone biosynthetic process | IEA GO_REF:0000120 | ACCEPT | Summary: This biological-process annotation is correct. UniProt identifies pqqD2 as PqqA binding protein 2 and states that it presents PqqA to PqqE in the PQQ biosynthetic pathway. GOA places the annotation through UniRule/UniPathway UPA00539. Asta confirms the KT2440 identity as a PqqD-family protein with PQQD/PqqD_bac domains. Reason: PqqD2 is a PqqD-family PQQ-biosynthesis accessory protein; the biological-process term captures its pathway role while leaving the precise division of labor between the two KT2440 PqqD paralogs open. Supporting Evidence: file:PSEPK/pqqD2/pqqD2-uniprot.txt FUNCTION: Functions as a PqqA binding protein and presents PqqA to file:PSEPK/pqqD2/pqqD2-uniprot.txt PATHWAY: Cofactor biosynthesis; pyrroloquinoline quinone biosynthesis. file:PSEPK/pqqD2/pqqD2-goa.tsv GO:0018189 pyrroloquinoline quinone biosynthetic process file:PSEPK/pqqD2/pqqD2-deep-research-asta.md Protein Description:** RecName: Full=PqqA binding protein 2 PMID:26961875 These results indicate that PqqE, in conjunction with PqqD, carries out the first step in PQQ biosynthesis |
| GO:0048038 quinone binding | IEA GO_REF:0000002 | REMOVE | Summary: This InterPro-derived molecular-function annotation is unsupported and likely incorrect at the gene level. The KT2440 UniProt record describes PqqD2 as a PqqA-binding protein that presents the precursor peptide to PqqE; the available evidence supports peptide binding and presentation, not binding of a mature quinone. Reason: The InterPro mapping appears to conflate PqqD family association with the PQQ pathway and direct binding of the pathway's mature quinone product. Remove the annotation unless direct quinone-binding evidence emerges; a specific PqqA peptide-chaperone or peptide-presentation term would better represent the supported molecular role. Supporting Evidence: file:PSEPK/pqqD2/pqqD2-goa.tsv GO:0048038 quinone binding file:PSEPK/pqqD2/pqqD2-uniprot.txt DR GO; GO:0048038; F:quinone binding; IEA:InterPro. file:PSEPK/pqqD2/pqqD2-uniprot.txt FUNCTION: Functions as a PqqA binding protein and presents PqqA to |
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Download this section (compressed HTML)Q: Does pqqD2 compensate for pqqD1 in KT2440 PQQ biosynthesis, or is it active in a distinct regulatory or ecological context?
Experiment: Compare PQQ production, quinoprotein activity, and PqqA modified-peptide intermediates in pqqD1, pqqD2, and double deletion strains complemented with each individual allele.
Hypothesis: pqqD2 can support PqqE-dependent PqqA cross-linking during KT2440 PQQ biosynthesis.
Type: targeted genetics and metabolite/peptide mass spectrometry
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