PvdA is the likely KT2440 ortholog of the pyoverdine biosynthetic ornithine N5-monooxygenase. By homology to experimentally characterized PvdA proteins, it is an FAD- and NADPH-dependent enzyme that hydroxylates L-ornithine early in pyoverdine assembly, generating a precursor required for hydroxamate formation. In Pseudomonas putida KT2440, pyoverdine is the characterized siderophore produced under iron limitation, so PvdA is best interpreted as a dedicated pyoverdine-biosynthetic enzyme rather than as a general iron homeostasis factor.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0006879 intracellular iron ion homeostasis | IEA GO_REF:0000118 | MODIFY | Summary: This TreeGrafter annotation points to the downstream physiological role of pyoverdine in iron acquisition, but it does not capture PvdA's direct function. PvdA is the dedicated ornithine N5-monooxygenase of the pyoverdine pathway, and KT2440 pyoverdine production under iron limitation is experimentally established at the strain level. Reason: GO:0006879 is too broad and indirect for a pathway enzyme. The more precise direct process term is GO:0002049 pyoverdine biosynthetic process. Proposed replacements: pyoverdine biosynthetic process Supporting Evidence: PMID:8106324 The enzyme L-ornithine N5-oxygenase catalyzes the hydroxylation of L-ornithine (L-Orn), which represents an early step in the biosynthesis of the peptidic moiety of the fluorescent siderophore pyoverdin in Pseudomonas aeruginosa. PMID:19459056 Structural analysis of the pyoverdine produced by the closely related P. putida KT2440 showed that this strain produces an already characterised pyoverdine, but different from P. entomophila, and no evidence was found for the production of a second siderophore. PMID:30346656 Fluorescent pseudomonads produce and secrete a siderophore termed pyoverdine to capture iron when it becomes scarce. file:PSEPK/pvdA/pvdA-deep-research-manual.md The current seeded annotation, `GO:0006879 intracellular iron ion homeostasis`, is biologically related but too broad for PvdA. file:PSEPK/pvdA/pvdA-deep-research-falcon.md PvdA functions in the **cytoplasmic phase** of **pyoverdine siderophore biosynthesis**, supplying a modified amino acid building block needed by the **NRPS assembly line**. |
| GO:0002049 pyoverdine biosynthetic process | ISS PMID:8106324 Cloning and nucleotide sequence of the pvdA gene encoding th... | NEW | Summary: Proposed new BP annotation. PvdA catalyzes an early committed reaction in pyoverdine assembly, and loss of pvdA in homologous systems abolishes pyoverdine production unless the hydroxylated precursor is supplied. Reason: This is the direct biological-process annotation for the enzyme and is more informative than the broad iron-homeostasis term. Falcon deep research confirms PvdA supplies a committed tailoring building block for the pyoverdine NRPS assembly line. Supporting Evidence: PMID:8106324 the pvdA mutant obtained by gene disruption also disclosed no pyoverdin synthesis, lacked L-Orn N5-oxygenase activity, was complemented by the cloned pvdA gene, and produced pyoverdin at wild-type levels when fed with the biosynthetic precursor L-N5-OH-Orn. PMID:19459056 Structural analysis of the pyoverdine produced by the closely related P. putida KT2440 showed that this strain produces an already characterised pyoverdine, but different from P. entomophila, and no evidence was found for the production of a second siderophore. file:PSEPK/pvdA/pvdA-deep-research-falcon.md **pvdA encodes the enzyme catalyzing the N5-hydroxylation of L-ornithine** to produce **N5-hydroxyornithine**, which is subsequently **formylated by PvdF** to yield **N5-formyl-N5-hydroxyornithine (L-fOHOrn)**. |
| GO:0031172 ornithine N5-monooxygenase activity | ISS PMID:17015659 Heterologous expression, purification, and characterization ... | NEW | Summary: Proposed new MF annotation. PvdA is the dedicated flavin-dependent ornithine N5-monooxygenase that initiates hydroxamate formation during pyoverdine synthesis. Reason: This is the core catalytic activity of PvdA and the most informative molecular-function term for the KT2440 ortholog. The GO definition of GO:0031172 (L-ornithine + O2 + H+ = N5-hydroxy-L-ornithine + H2O) matches the reaction PvdA catalyzes, and falcon deep research places it in the Class B flavoprotein (FAD + O2 + NADPH) N-hydroxylating monooxygenase family. The UniProtKB-KW IEA term GO:0016491 oxidoreductase activity is a true but uninformative parent of this activity. Supporting Evidence: PMID:17015659 Formation of the iron-chelating hydroxamate functional group in pyoverdine requires the enzyme PvdA, a flavin-dependent monooxygenase that catalyzes the N(5) hydroxylation of l-ornithine. PMID:21757711 The ornithine hydroxylase from Pseudomonas aeruginosa (PvdA) catalyzes the FAD-dependent hydroxylation of the side chain amine of ornithine, which is subsequently formylated to generate the iron-chelating hydroxamates of the siderophore pyoverdin. file:PSEPK/pvdA/pvdA-deep-research-manual.md The key missing molecular-function term is `GO:0031172 ornithine N5-monooxygenase activity`, supported by the biochemical and structural literature on characterized PvdA homologs. file:PSEPK/pvdA/pvdA-deep-research-falcon.md dependence on **FAD** as a flavin cofactor and **molecular oxygen** as the oxygen donor, proceeding through **C4a-peroxy/hydroperoxyflavin** intermediates that effect oxygen transfer to the substrate amine |
| GO:0005737 cytoplasm | ISS PMID:22498339 High cellular organization of pyoverdine biosynthesis in Pse... | NEW | Summary: Proposed new CC annotation. Homolog studies place PvdA among the cytoplasmic enzymes of the pyoverdine pathway, although some membrane association and polar clustering have also been observed. Falcon deep research reinforces that pyoverdine biosynthesis initiates in the cytoplasm and that PvdA physically interacts with all four pyoverdine NRPSs in a membrane-associated multienzyme "siderosome" context. Reason: Cytoplasm is the conservative and best-supported location to annotate the KT2440 ortholog. A plasma membrane term would overstate the current evidence for this strain, even though PAO1 homolog studies report partial membrane association via an N-terminal inner-membrane-anchoring region. Supporting Evidence: PMID:22498339 generate P.aeruginosa strains producing fluorescent fusions with PvdA, one of the initial enzymes in the biosynthetic pathway of PVDI in the cytoplasm PMID:18757814 The inferred topological model resembled a eukaryotic reverse signal-anchor (type III) protein, with a single N-terminal domain anchored to the inner membrane, and the bulk of the protein spanning the cytosol. file:PSEPK/pvdA/pvdA-deep-research-falcon.md Pyoverdine biosynthesis initiates in the **cytoplasm** |
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Download this section (compressed HTML)Q: Is KT2440 PvdA predominantly soluble-cytoplasmic or does it become membrane-associated and old-pole clustered during active pyoverdine synthesis, as described for the PAO1 homolog?
Suggested experts: Ignacio J. Schalk, Holger Jung
Q: Does KT2440 PvdA show the same strict ornithine specificity and NADPH/FAD coupling behavior reported for the PAO1 enzyme, or are there strain-specific kinetic differences?
Suggested experts: Sharon Y. N. Seah, Anne L. Lamb
Experiment: Construct a clean pvdA deletion or catalytic-site mutant in KT2440, measure pyoverdine fluorescence and LC-MS profiles under iron limitation, and test rescue with plasmid-borne pvdA or exogenous N5-hydroxyornithine.
Hypothesis: PP_3796 is the dedicated ornithine N5-monooxygenase required for KT2440 pyoverdine biosynthesis.
Type: genetics and metabolite rescue
Experiment: Build a chromosomal fluorescent or epitope-tagged PvdA allele, then compare localization and fractionation patterns in iron-replete versus iron-limited growth while quantifying pyoverdine output.
Hypothesis: KT2440 PvdA undergoes regulated membrane association during active pyoverdine production.
Type: localization and cell biology
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