nmoA (PA4202, Q9HWH9) — curation notes

Gene identity

UniProt Q9HWH9, NMO_PSEAE, 351 aa, reviewed; PseudoCAP PA4202; matches the
worklist accession. Named nmoA in PMID:25384477; UniProt RecName "Nitronate
monooxygenase", EC 1.13.12.- with ECO:0000269|PubMed:25002579. PDB 4Q4K
(1.44 A, with FMN); PANTHER PTHR42747:SF3.

What is established

Purified, kinetically characterised enzyme. PA4202 was cloned, expressed and
purified, and is active on propionate 3-nitronate (P3N) and other alkyl
nitronates but not on nitroalkanes PMID:25002579. P3N is
the best substrate (kcat app 1300 s-1, Km app 110 uM); UniProt also records
Km 5 mM for ethylnitronate and 6 mM for propyl-1-nitronate.
Cofactor and fold. "Absorption spectroscopy, mass spectrometry, and x-ray
crystallography demonstrate a tightly, non-covalently bound FMN in the active
site of the enzyme" PMID:25002579; UniProt CC:COFACTOR "Binds 1 FMN per
subunit", with binding sites at 21, 69, 176, 181, 218 and 237-240 from
PDB 4Q4K. TIM-barrel fold. A flavosemiquinone forms within 7.5 ms on
anaerobic reduction with P3N, consistent with a catalytic intermediate.
Class definition. Four motifs shared with the fungal NMO of
Cyberlindnera saturnus define class I NMO (bacterial, fungal, two animal);
Neurospora crassa NMO lacks them and defines class II PMID:25002579.
In vivo role. A chromosomal deletion is less tolerant of 3-NPA
PMID:25384477,
and "The Δ nmoA mutant was clearly less able to grow in the presence of high
concentrations of P3N."; the mutant also fails to show the dose-dependent
nitrite release seen in wild type and in the ΔnmoR mutant.
Regulation. "Here we show that PA4203 ( nmoR ) represses its own transcription
and the expression of nmoA." PMID:25384477; nmoA is cotranscribed with ddlA
but ddlA has an internal promoter.
Pathway context. 3-NPA/P3N can serve pseudomonads as sole carbon, nitrogen and
energy source, via P3N denitration to malonic semialdehyde and then acetyl-CoA
PMID:20382807. That enzyme was purified from 3NPA-degrading isolates, not
from PAO1, so for PAO1 the catabolic role is plausible but not shown.

Relevance of other PAO1 NMO-family members

PA0660 (Q9I5R1) is a leaf of the same PAINT node and was purified: "Despite
its annotation, PA0660 did not exhibit nitronate monooxygenase activity."
PMID:31075192; it is an NAD(P)H:quinone reductase and the proposed paradigm
of a new class defined by six conserved motifs.
PA1024 (Q9I4V0, already reviewed in this repository) is likewise an
NADH:quinone reductase with no NMO activity, in a different PANTHER family
(PTHR32332).
PMID:29885842 reports a PA4202 ternary complex with neutral nitroethane and
low-efficiency nitroalkane turnover via H183. This is a minor in vitro
activity, not a reason to annotate nitroalkane oxidase activity (GO:0052664);
UniProt's FUNCTION explicitly says PA4202 cannot oxidise nitroalkanes.

PseudoCAP IBA-seed assessment

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale
PTN001284536	GO:0018580 nitronate monooxygenase activity	1 (sole seed)	23 (19 taxa, PAINT leaf GAF)	GO:0018580, IDA, PMID:25002579 (PseudoCAP)	SOUND (seed); node over-broad	The seed is a direct enzyme assay on purified NmoA, not a mutant phenotype: steady-state kinetics on P3N and other alkyl nitronates, tightly bound FMN, a semiquinone intermediate and a 1.44 A structure. A sole seed is not weak support here. The node term is however carried to at least one leaf where it is experimentally false: P. aeruginosa PA0660 (Q9I5R1) has no NMO activity and is an NAD(P)H:quinone reductase (PMID:31075192). Recorded as a GO_CENTRAL `WRONG_TERM`/CHECK defect asking for a NOT at the PA0660 branch or for the IBD to move down to the class I (four-motif) group. The PseudoCAP row itself needs no defect.

PseudoCAP has only this one annotation for PA4202, so no other seed needs
assessment.

Decisions summary

ACCEPT: GO:0018580 IDA (the seed), IEA (InterPro IPR004136), IBA.
NEW: GO:0010181 FMN binding (IDA, PMID:25002579); GO:0070458 cellular
detoxification of nitrogen compound (IMP, PMID:25384477) — NmoA is itself the
enzyme that removes the nitronate, so this is participation, not necessity.
No REMOVE. One GO_CENTRAL source defect at PTN001284536; no PseudoCAP defect.