pvdA Gene Review Notes

Identity and Orthology

• pvdA (PP_3796, UniProt Q88GC8) is annotated in UniProt as L-ornithine 5-monooxygenase and belongs to the lysine N(6)-hydroxylase/L-ornithine N(5)-oxygenase family [file:PSEPK/pvdA/pvdA-uniprot.txt "DE SubName: Full=L-ornithine 5-monooxygenase"; file:PSEPK/pvdA/pvdA-uniprot.txt "CC -!- SIMILARITY: Belongs to the lysine N(6)-hydroxylase/L-ornithine N(5)-oxygenase family."].
• The matched PANTHER subfamily (PTHR42802:SF1) contains reviewed bacterial pvdA proteins from Pseudomonas aeruginosa (Q51548) and Burkholderia cepacia (O51940), supporting conservative transfer of the core enzyme function to KT2440 [file:interpro/panther/PTHR42802/PTHR42802-entries.csv "Q51548,L-ornithine N(5)-monooxygenase"; file:interpro/panther/PTHR42802/PTHR42802-entries.csv "O51940,L-ornithine N(5)-monooxygenase"].

Enzymatic Function

• PvdA catalyzes L-ornithine N5 hydroxylation, an early committed step in pyoverdine biosynthesis PMID:8106324.
• Loss of pvdA abolishes pyoverdine synthesis in the homologous P. aeruginosa system and can be rescued by the hydroxylated precursor, directly tying the enzyme to pyoverdine biosynthesis rather than general iron physiology PMID:8106324.
• Purified PvdA is a flavin-dependent monooxygenase that specifically uses NADPH and FAD [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:17015659 "The enzyme is specific for NADPH and flavin adenine dinucleotide (FAD(+)) as cofactors, as it cannot utilize NADH and flavin mononucleotide."; 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."].

Localization and Cell Biology

• The conservative localization call is cytoplasm: PvdA is described as one of the initial enzymes in the biosynthetic pathway of PVDI in the cytoplasm PMID:22498339.
• There is also evidence for membrane association and spatial organization, so plasma membrane is plausible biology but not the safest core term to transfer directly to KT2440 without gene-specific localization data [PMID:18757814 "Cell fractionation and proteinase K accessibility experiments in P. aeruginosa confirmed the membrane-bound nature of PvdA, but excluded the transmembrane topology of its N-terminal hydrophobic region."; PMID:22498339 "Cellular fractionation indicated that a substantial amount of PvdA-YFP was located in the membrane fraction."].

KT2440 Context

• P. putida KT2440 produces a characterized pyoverdine and no second siderophore was detected in the cited structural study PMID:19459056.
• Pyoverdine secretion in KT2440 is iron responsive and contributes to growth under iron limitation [PMID:30346656 "Expression from the respective promoters is stimulated by iron limitation albeit to varying degrees."; PMID:30346656 "Deletion of pvdRT-opmQ leads to reduced amounts of pyoverdine in the medium and decreased growth under iron limitation."].
• Pyoverdine turnover is physiologically important in KT2440 and linked to oxidative-stress adaptation PMID:31451546.

Curation Takeaways

• The seeded TreeGrafter term GO:0006879 intracellular iron ion homeostasis is too broad for a dedicated pathway enzyme. The direct process term should be GO:0002049 pyoverdine biosynthetic process [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."].
• The core missing MF term is GO:0031172 ornithine N5-monooxygenase activity [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."].
• Conservative CC addition is GO:0005737 cytoplasm; I would not make plasma membrane a core KT2440 annotation without direct localization data in this strain [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."].