PvdQ is a periplasmic N-terminal nucleophile (Ntn) hydrolase of the peptidase S45 family (penicillin amidase fold) that acts as an acyl-homoserine lactone (AHL) acylase (EC 3.5.1.97). It is synthesized as an inactive precursor with a cleavable signal peptide and exported to the periplasm, where it undergoes autoproteolytic maturation into an alpha and a beta subunit; the N-terminal serine of the beta subunit is the catalytic nucleophile. The enzyme hydrolyzes the amide bond linking the acyl chain to the homoserine lactone moiety of N-acyl-L-homoserine lactones, releasing L-homoserine lactone and the corresponding free fatty acid, with a preference for long acyl chains (roughly 11-14 carbons). Through this activity PvdQ has two related physiological roles documented in Pseudomonas. In the pyoverdine biosynthetic pathway it acts as a maturation enzyme, removing a fatty-acyl (e.g. myristoyl/myristoleoyl) group from an acylated ferribactin/pyoverdine precursor in the periplasm, a step required to produce mature fluorescent pyoverdine siderophore. By cleaving long-chain AHL quorum-sensing signals it also confers quorum-quenching activity, degrading the diffusible signals that coordinate population-density-dependent gene expression in many Gram-negative bacteria.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0016787 hydrolase activity | IEA GO_REF:0000002 | MODIFY | Summary: General hydrolase activity is correct but uninformatively broad for an enzyme whose activity is well defined as an amide hydrolase (AHL acylase). Reason: PvdQ is an Ntn-hydrolase that cleaves the amide bond of N-acyl-homoserine lactones (EC 3.5.1.97). The more specific child term GO:0016811 captures this and is also annotated, so the bare grandparent should be replaced by the specific term. Proposed replacements: hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides |
| GO:0016811 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides | IEA GO_REF:0000002 | ACCEPT | Summary: Accurate molecular function. The AHL acylase reaction (EC 3.5.1.97) hydrolyzes the linear amide bond between the acyl chain and the homoserine lactone, which is precisely an amidohydrolase acting on a carbon-nitrogen bond in a linear amide. Reason: This is the most specific molecular-function term available in GO for AHL acylase activity (there is no dedicated 'acyl-homoserine lactone acylase activity' term; note GO:0102007 is a lactonohydrolase, a different reaction). Consistent with UniProt EC 3.5.1.97 and the Ntn-hydrolase mechanism of the PvdQ family. |
| GO:0017000 antibiotic biosynthetic process | IEA GO_REF:0000002 | MODIFY | Summary: Over-broad and mischaracterized BP inferred electronically from InterPro. PvdQ participates in biosynthesis of the siderophore pyoverdine, not of an antibiotic; its other documented role is quorum quenching via AHL degradation. Reason: The IEA InterPro mapping applies a generic 'antibiotic biosynthetic process' to S45 peptidases (the family includes penicillin/beta-lactam acylases), but pyoverdine is an iron-chelating siderophore, not an antibiotic. The supported biological role of PvdQ is periplasmic maturation of the pyoverdine precursor. Replace with the specific pyoverdine biosynthesis term. Proposed replacements: pyoverdine biosynthetic process |
| GO:0042597 periplasmic space | IEA GO_REF:0000044 | ACCEPT | Summary: Correct subcellular localization. PvdQ carries a Sec signal peptide and is exported to the periplasm, where it matures (autoproteolysis to alpha/beta subunits) and acts on its periplasmic substrates (acylated pyoverdine precursor; AHLs). Reason: Supported by the UniProt signal-peptide annotation and the well-established periplasmic localization of PvdQ-family enzymes. The mapped term matches the UniProt subcellular location (SL-0200). |
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