pqqD1 (PP_0377) encodes PqqA binding protein 1, a PqqD-family peptide chaperone in pyrroloquinoline quinone (PQQ) biosynthesis. It binds the PqqA precursor peptide and presents it to the radical-SAM enzyme PqqE, supporting formation of the early Glu-Tyr cross-linked PqqA intermediate 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 pqqD1 as a PqqA binding protein in PQQ biosynthesis and states that it presents PqqA to PqqE. GOA places the annotation through UniRule/UniPathway UPA00539. Asta confirms the KT2440 identity as PqqA binding protein 1 with PqqD-family domains. Reason: PqqD1 is a core PQQ-biosynthesis accessory protein that links the PqqA precursor peptide to PqqE-dependent radical-SAM chemistry; the process annotation captures its pathway role even though it is not itself the catalytic enzyme. Supporting Evidence: file:PSEPK/pqqD1/pqqD1-uniprot.txt FUNCTION: Functions as a PqqA binding protein and presents PqqA to file:PSEPK/pqqD1/pqqD1-uniprot.txt PATHWAY: Cofactor biosynthesis; pyrroloquinoline quinone biosynthesis. file:PSEPK/pqqD1/pqqD1-goa.tsv GO:0018189 pyrroloquinoline quinone biosynthetic process file:PSEPK/pqqD1/pqqD1-deep-research-asta.md Protein Description:** RecName: Full=PqqA binding protein 1 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 PqqD1 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/pqqD1/pqqD1-goa.tsv GO:0048038 quinone binding file:PSEPK/pqqD1/pqqD1-uniprot.txt DR GO; GO:0048038; F:quinone binding; IEA:InterPro. file:PSEPK/pqqD1/pqqD1-uniprot.txt FUNCTION: Functions as a PqqA binding protein and presents PqqA to |
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Download this section (compressed HTML)Q: Are pqqD1 and pqqD2 functionally redundant in KT2440 PQQ biosynthesis, or do they support different PqqA/PqqE complexes or growth conditions?
Experiment: Construct pqqD1, pqqD2, and double deletion mutants, complement each allele, and quantify PQQ production plus PqqA cross-linked peptide intermediates by LC-MS under PQQ-inducing conditions.
Hypothesis: pqqD1 supports PqqE-dependent PqqA cross-linking during KT2440 PQQ biosynthesis.
Type: targeted genetics and metabolite/peptide mass spectrometry
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Download this section (compressed HTML)The OpenScientist report supports the conserved interpretation of PqqD1 as a
PqqA-binding peptide chaperone that presents the precursor to PqqE. It should
not be used as the source for KT2440 locus order: the report assigns PqqE to
PP_0378, but the local reviewed UniProt records identify pqqC as PP_0378 and
pqqE as PP_0376.
The report also gives a precise pairwise identity and alignment-derived motifs
for PqqD1 and PqqD2 without retaining a reproducible alignment artifact. Those
quantitative claims were not added to the review. The curated function remains
anchored to the reviewed UniProt record and experimental PqqD/PqqA/PqqE
literature already cited in the review.
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