PA1024 is a soluble, monomeric FMN-dependent flavoenzyme with a TIM-barrel fold, a member of the Pfam NMO (nitronate monooxygenase) family that was long annotated as 2-nitropropane dioxygenase. Kinetic characterisation of the purified enzyme showed that it has no nitronate monooxygenase activity. It is an NADH:quinone reductase that prefers NADH to NADPH and reduces a broad range of benzo- and naphthoquinones to hydroquinones by a Ping Pong Bi Bi mechanism. It also has a minor NADH oxidase activity, and it does not reduce azo dyes. It is the founding member of a class of NADH:quinone reductases within the NMO family. Its physiological role is unknown; it may help keep the NAD+/NADH balance.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0016491 oxidoreductase activity | IBA GO_REF:0000033 | MODIFY | Summary: PAINT IBA from node PTN002844975, whose sole seed is PA1024 itself (PseudoCAP IDA and UniProt EXP, PMID:27502282). The oxidoreductase claim is correct for PA1024, but GO:0050136 already describes the activity more precisely. Reason: The IBD rests on direct enzymology of the purified protein, and the generic node term is a cautious, defensible choice for a clade of about 120 leaves spanning bacteria, fungi and plants, where only PA1024 has been characterised. The PAO1 true NMO, PA4202, sits under a different node. For this gene the generic term is true but less specific than the evidence supports. It is refined to NADH dehydrogenase (quinone) (non-electrogenic) activity, which the gene already carries by EXP. The node annotation is not disputed. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN002844975 · PTN002844975 SUPPORTS TRANSFER A cross-kingdom clade (bacteria, fungi, plants; QuickGO lists 111 GO:0016491 IBA leaves on 2026-10-28). PA1024 is the only seed and the only PAO1 leaf. The generic node term suits the clade's breadth. UniProtKB:Q9I4V0 · PA1024 SUPPORTS TRANSFER The target's own direct enzymology (PMID:27502282) is the IBD seed. This is expected, not circular. Proposed replacements: NADH dehydrogenase (quinone) (non-electrogenic) activity Supporting Evidence: PMID:27502282 Purified PA1024 did not exhibit nitronate monooxygenase activity; however, it displayed NADH:quinone reductase and a small NADH:oxidase activity. |
| GO:0016491 oxidoreductase activity | IDA PMID:27502282 Functional Annotation of a Presumed Nitronate Monoxygenase R... | MODIFY | Summary: PseudoCAP IDA from the kinetic characterisation of purified PA1024. Correct, but generic. This row is the sole seed of the PAINT IBD at PTN002844975. Reason: The paper assays the purified enzyme directly and shows NADH:quinone reductase activity, so the seed is direct biochemical evidence, not a phenotype. The term is too general for what the paper shows. It is refined to GO:0050136, the term UniProt assigned by EXP from the same paper. Proposed replacements: NADH dehydrogenase (quinone) (non-electrogenic) activity Supporting Evidence: PMID:27502282 PA1024 could reduce a broad spectrum of quinone substrates via a Ping Pong Bi Bi steady-state kinetic mechanism, generating the corresponding hydroquinones. |
| GO:0018580 nitronate monooxygenase activity | IEA GO_REF:0000002 | REMOVE | Summary: InterPro2GO transfer from the NMO family signature IPR004136. Enzyme assays directly contradict it for PA1024. Reason: The purified enzyme was tested against nitronates and nitroalkanes and showed no nitronate monooxygenase activity. UniProt records this lack of activity, and attributes the earlier NMO report to a non-enzymatic reaction. IPR004136 covers both true NMOs and the PA1024-type NADH:quinone reductase class. Mapping the whole entry to GO:0018580 is therefore too broad, and this is a demonstrably wrong electronic transfer for this protein. Supporting Evidence: PMID:27502282 Purified PA1024 did not exhibit nitronate monooxygenase activity file:PSEAE/PA1024/PA1024-uniprot.txt Does not exhibit nitronate monooxygenase activity; is inactive against propionate 3-nitronate, 3-nitropropionate, nitroethane, 1-nitropropane, 2-nitropropane, and the anionic forms ethylnitronate, propyl-1-nitronate, and propyl-2-nitronate. |
| GO:0050136 NADH dehydrogenase (quinone) (non-electrogenic) activity | EXP PMID:27502282 Functional Annotation of a Presumed Nitronate Monoxygenase R... | ACCEPT | Summary: UniProt EXP from steady-state kinetics of purified PA1024 with NADH and a broad panel of quinones. Reason: This is the core catalytic activity (EC 1.6.5.9, RHEA:46160). The enzyme is NADH-preferring, which makes the NAD(P)H term GO:0003955 less accurate. It reduces benzo- and naphthoquinones broadly, so the ubiquinone- and menaquinone-specific children do not fit. Supporting Evidence: PMID:27502282 The enzyme preferred NADH to NADPH as a reducing substrate. file:PSEAE/PA1024/PA1024-uniprot.txt Catalyzes the NADH-dependent reduction of a broad spectrum of quinone substrates, generating the corresponding hydroquinones. |
| GO:0050136 NADH dehydrogenase (quinone) (non-electrogenic) activity | IEA GO_REF:0000120 | ACCEPT | Summary: Electronic mapping from the curated EC 1.6.5.9 / RHEA:46160 reaction in UniProt. It agrees with the EXP row. Reason: The reaction mapping rests on curated experimental catalytic-activity data (ECO:0000269) and matches the EXP annotation. Supporting Evidence: file:PSEAE/PA1024/PA1024-uniprot.txt Reaction=a quinone + NADH + H(+) = a quinol + NAD(+); |
| GO:0010181 FMN binding | IDA PMID:16682407 Crystal structure of 2-nitropropane dioxygenase complexed wi... | NEW | Summary: FMN is bound in the crystal structures and is the cofactor of the characterised enzyme. Reason: Both papers establish FMN as the bound cofactor (1 per subunit), and the binding residues are defined in the crystal structures (PDB 2GJL, 2GJN). It is a supporting, non-catalytic aspect of the core flavoenzyme function. Supporting Evidence: PMID:16682407 a binary complex with FMN and a ternary complex with both FMN and 2-nitropropane file:PSEAE/PA1024/PA1024-uniprot.txt Binds 1 FMN per subunit. |
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Download this section (compressed HTML)Q: What is the physiological quinone substrate of PA1024, and in what process does it act? Possible roles include NAD+/NADH balance during fatty acid catabolism and defence against quinone toxicity.
Q: Should the PAINT node PTN002844975 stay at generic oxidoreductase activity, or are the cross-kingdom members (plants, fungi, mycobacteria) close enough to PA1024 in the conserved NQR motifs to justify propagating NADH:quinone reductase activity?
Experiment: Construct a PA1024 deletion mutant and profile its growth on fatty acids and its quinone tolerance, and measure intracellular NAD+/NADH ratios, to define the physiological role.
Type: genetic knockout with metabolic phenotyping
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