pqqF (PP_0381, Q88QV3) encodes a 766-residue, zinc-dependent peptidase M16-family metalloendopeptidase associated with pyrroloquinoline quinone (PQQ) biosynthesis in P. putida KT2440. It lies in the chromosomal PQQ biosynthesis locus organized pqqFABCDEG, where pqqF is transcribed independently of the core pqqCDEG module. Q88QV3 has the single-chain M16A-like PqqF architecture; the characterized Methylorubrum extorquens two-component M16B PqqF/PqqG protease is an alternative realization and does not establish a heterodimeric partner for Q88QV3. In particular, the adjacent KT2440 PP_0375 protein called a putative pqqG is an S9-family peptidase, not the homologous M16B PqqG subunit. PqqF is inferred from its family, locus, and characterized orthologs to process a PqqA-derived peptide during PQQ maturation. No KT2440-specific knockout or biochemical assay of Q88QV3 has been reported, and its exact substrate state remains unresolved.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004222 metalloendopeptidase activity | IEA GO_REF:0000120 | ACCEPT | Summary: This is the best current molecular-function annotation for PqqF. UniProt assigns PqqF to the peptidase M16 family with a bound zinc ion, and the GOA record maps it to metalloendopeptidase activity. Deep research confirms that characterized PqqF orthologs are zinc-dependent M16-family metallopeptidases that act on the PQQ precursor peptide PqqA (Serratia FS14 crystal structure; Methylorubrum two-component PqqF/PqqG protease). Reason: The peptidase M16 family assignment, the conserved Zn-binding/active-site residues, and direct biochemical/structural evidence from PqqF orthologs all support a zinc metalloendopeptidase function in PQQ maturation. Supporting Evidence: file:PSEPK/pqqF/pqqF-uniprot.txt Belongs to the peptidase M16 family. file:PSEPK/pqqF/pqqF-goa.tsv GO:0004222 metalloendopeptidase activity file:PSEPK/pqqF/pqqF-deep-research-falcon.md PqqF/PqqG are **M16-family zinc metallopeptidases** acting on the PQQ precursor peptide PqqA PMID:31427437 can rapidly catalyze cleavage of PqqA into smaller peptides |
| GO:0006508 proteolysis | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: Proteolysis is directionally correct for an M16 metalloendopeptidase that cleaves the PqqA precursor peptide, but it is too broad to represent the core biological role of this pathway enzyme. The informative biological process is pyrroloquinoline quinone biosynthesis, within which the proteolytic step liberates the PQQ precursor. Reason: The more informative biological process is pyrroloquinoline quinone biosynthesis; generic proteolysis captures only the chemistry, not the pathway context in which PqqF processes PqqA. Supporting Evidence: file:PSEPK/pqqF/pqqF-uniprot.txt Belongs to the peptidase M16 family. file:PSEPK/pqqF/pqqF-goa.tsv GO:0006508 proteolysis file:PSEPK/pqqF/pqqF-deep-research-falcon.md zinc-dependent M16-family endopeptidase that participates in **processing the PqqA precursor peptide** |
| GO:0008270 zinc ion binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: Zinc ion binding is consistent with the metalloendopeptidase assignment and should be retained as a non-core cofactor-binding annotation. UniProt records one zinc ion bound per subunit with conserved Zn-coordinating residues, and characterized PqqF orthologs are zinc-dependent M16 metallopeptidases. Reason: The core function is the pathway metalloendopeptidase activity, with zinc binding as a supporting cofactor feature required for catalysis. Supporting Evidence: file:PSEPK/pqqF/pqqF-uniprot.txt COFACTOR: file:PSEPK/pqqF/pqqF-goa.tsv GO:0008270 zinc ion binding file:PSEPK/pqqF/pqqF-deep-research-falcon.md PqqF/PqqG are **M16-family zinc metallopeptidases** acting on the PQQ precursor peptide PqqA |
| GO:0018189 pyrroloquinoline quinone biosynthetic process | IEA GO_REF:0000120 | ACCEPT | Summary: This is the appropriate pathway-process annotation for the KT2440 PqqF-family protein. Q88QV3 is assigned to the UniPathway PQQ pathway and lies within the KT2440 pqqFABCDEG locus, while characterized PqqF systems support a precursor-proteolysis role. No direct KT2440 knockout or substrate assay was retrieved. Reason: The pathway-specific term captures the strong locus- and orthology-supported biological context of the peptidase activity without treating the characterized Methylorubrum PqqF/PqqG complex as a direct assay of Q88QV3. Supporting Evidence: file:PSEPK/pqqF/pqqF-uniprot.txt Required for coenzyme pyrroloquinoline quinone (PQQ) file:PSEPK/pqqF/pqqF-uniprot.txt PATHWAY: Cofactor biosynthesis; pyrroloquinoline quinone biosynthesis. file:PSEPK/pqqF/pqqF-goa.tsv GO:0018189 pyrroloquinoline quinone biosynthetic process file:PSEPK/pqqF/pqqF-deep-research-falcon.md pqqFABCDEG PMID:31427437 a protease/peptidase required for the excision of an early, cross-linked di-amino acid precursor to pyrroloquinoline quinone |
| GO:0046872 metal ion binding | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: Metal ion binding is overly broad once zinc ion binding and metalloendopeptidase activity are present. The specific cofactor is a single zinc ion per subunit. Reason: Prefer the more specific zinc ion binding term for the cofactor feature; generic metal ion binding adds no information beyond GO:0008270. Supporting Evidence: file:PSEPK/pqqF/pqqF-goa.tsv GO:0046872 metal ion binding file:PSEPK/pqqF/pqqF-goa.tsv GO:0008270 zinc ion binding |
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Download this section (compressed HTML)Q: What is the direct PqqF substrate in KT2440 PQQ biosynthesis, and does PP_0375 or another cellular protease contribute independently to precursor processing?
Experiment: Compare PqqA-derived peptide fragments and PQQ accumulation in wild-type, pqqF deletion, and catalytic-site (Zn-binding) mutant strains using targeted LC-MS/MS, paralleling the in vitro PqqA cleavage assays established for the Methylorubrum extorquens PqqF/PqqG protease.
Hypothesis: PqqF is the zinc metalloendopeptidase that processes PqqA-derived intermediates during KT2440 PQQ maturation.
Type: genetics plus peptidomics
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