NmoA (PA4202) is a 351-residue FMN-dependent class I nitronate monooxygenase with a TIM-barrel fold. It uses molecular oxygen to oxidise anionic alkyl nitronates, with propionate 3-nitronate (P3N) as its best substrate (kcat about 1300 s-1, Km 110 uM), yielding malonate semialdehyde plus nitrite and nitrate. One FMN is bound tightly but non-covalently per subunit, and a flavin semiquinone forms as a catalytic intermediate; neutral nitroalkanes are at best very poor substrates. The gene is repressed by the divergently encoded LysR-family regulator NmoR, and a deletion mutant is less tolerant of 3-nitropropionate, consistent with a role in nitronate detoxification and in the catabolic route by which pseudomonads use 3-nitropropionate as a nitrogen and carbon source.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0018580 nitronate monooxygenase activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN001284536 (PTHR42747), whose only seed is NmoA itself. For NmoA the claim is established by kinetics on purified protein, so the row is correct for this gene. Reason: NmoA appearing in its own With/From is the expected marker of experimental grounding on the target, not circularity. The node placement is a separate matter: another leaf of the same node, P. aeruginosa PA0660 (Q9I5R1), was purified and found to lack this activity, so the IBD sits above at least one member that does not have it. That is recorded as a GO_CENTRAL source defect on the node and does not affect the IBA on NmoA. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN001284536 Β· PTN001284536 (PTHR42747) SUPPORTS TRANSFER 23 leaf IBAs in 19 taxa in the PAINT leaf file (bacteria, fungi, amoebae, choanoflagellates). Correct for NmoA; the node also covers PA0660, for which the activity was experimentally excluded. UniProtKB:Q9HWH9 Β· nmoA (self; sole IBD seed) SUPPORTS TRANSFER The PseudoCAP IDA to PMID:25002579 is a direct assay on purified NmoA, which is proper descendant evidence for the node. Supporting Evidence: PMID:25002579 The enzyme is active on P3N and other alkyl nitronates, but cannot oxidize nitroalkanes. |
| GO:0018580 nitronate monooxygenase activity | IDA PMID:25002579 The combined structural and kinetic characterization of a ba... | ACCEPT | Summary: PseudoCAP IDA and the sole seed of the IBD at PTN001284536. PA4202 was cloned, expressed, purified and kinetically characterised on P3N and other alkyl nitronates. Reason: A direct activity assay on the purified gene product, not a mutant phenotype: the enzyme turns over P3N with kcat 1300 s-1 and Km 110 uM, carries tightly bound FMN, and forms a flavosemiquinone intermediate; the 1.44 A structure resolves the FMN site. The seed is therefore sound and the IBD is justified for a node of class I NMOs. Supporting Evidence: PMID:25002579 Here, we have cloned and expressed the gene pa4202 of Pseudomonas aeruginosa PAO1, purified the resulting protein, and characterized it. PMID:25002579 Thus, PA4202 is the first NMO identified and characterized in bacteria. |
| GO:0018580 nitronate monooxygenase activity | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO mapping of the NMO family signature IPR004136, which NmoA matches. Reason: The family assignment is correct and the mapped term is exactly the experimentally demonstrated activity, so this row reinforces the IDA. The signature is shared by proteins that lack the activity (PA0660), so it is weak support in general, but for this gene the claim is right. Supporting Evidence: file:PSEAE/nmoA/nmoA-uniprot.txt DR InterPro; IPR004136; NMO. |
| GO:0010181 FMN binding | IDA PMID:25002579 The combined structural and kinetic characterization of a ba... | NEW | Summary: One FMN is bound tightly and non-covalently per subunit, shown by absorption spectroscopy, mass spectrometry and the 1.44 A structure, with the contacting residues recorded as UniProt binding sites. Reason: Directly demonstrated cofactor binding, and a supporting, non-catalytic aspect of the characterised flavoenzyme activity; GOA has no FMN binding row for this gene. Supporting Evidence: PMID:25002579 Absorption spectroscopy, mass spectrometry, and x-ray crystallography demonstrate a tightly, non-covalently bound FMN in the active site of the enzyme. file:PSEAE/nmoA/nmoA-uniprot.txt Note=Binds 1 FMN per subunit. |
| GO:0070458 cellular detoxification of nitrogen compound | IMP PMID:25384477 Pseudomonas aeruginosa LysR PA4203 regulator NmoR acts as a ... | NEW | Summary: A chromosomal nmoA deletion is more sensitive to 3-nitropropionate and no longer releases nitrite in proportion to the 3-NPA supplied, so NmoA itself performs the step that removes the nitronate from the cell. Reason: The gene product does the work of the process: it is the enzyme that destroys the nitronate, and the nitrite released in vivo is the product of its own reaction, so this is participation rather than mere necessity. The process term is absent from GOA for this gene, although UniProt carries the Detoxification keyword and the FUNCTION statement. Supporting Evidence: PMID:25384477 Finally, deletion of the nmoA gene resulted in an increased sensitivity of the cells to 3-nitropropionic acid (3-NPA), confirming the role of the nitronate monooxygenase protein in the detoxification of nitronate. PMID:25384477 The Ξ nmoA mutant was clearly less able to grow in the presence of high concentrations of P3N. |
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Download this section (compressed HTML)Q: Does NmoA use free FMNH2 as a co-substrate (GO:0036434) or only its own tightly bound FMN, and should the two nitronate monooxygenase terms be distinguished on this gene?
Q: Can P. aeruginosa PAO1 itself grow on 3-nitropropionate as a nitrogen or carbon source, or is NmoA's role confined to keeping the intracellular nitronate level low?
Experiment: Growth and metabolite tests of wild type and delta-nmoA PAO1 on 3-nitropropionate as sole nitrogen source, with quantification of malonate semialdehyde, nitrite and nitrate, to distinguish a catabolic from a purely protective role.
Experiment: Side-by-side assay of NmoA and the other PTHR42747 members from the same PAINT node (for example yrpB, SO_0471, Rv2781c) on alkyl nitronates and on NAD(P)H plus quinones, to establish how far across the clade class I NMO activity extends and so where the IBD belongs.
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