Hsero_1012 (fdeJ) encodes an NAD(P)-binding Rossmann-fold protein of the NAD-dependent epimerase/dehydratase (extended short-chain dehydrogenase/reductase) family in the naringenin degradation (fde) locus of Herbaspirillum seropedicae SmR1. KEGG assigns FdeJ to the reaction that releases oxaloacetate from the A-ring cleavage product, a step KEGG marks as unclear. The fold does not by itself establish that chemistry, and no FdeJ protein has been characterized, so its molecular function is unresolved.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003978 UDP-glucose 4-epimerase activity | IEA GO_REF:0000003 | MARK AS OVER ANNOTATED | Summary: The UDP-glucose-specific EC assertion is more precise than the available evidence supports. Reason: GO:0003978 specifically describes UDP-glucose/UDP-galactose interconversion. Its EC2GO relation is correct, but the source EC 5.1.3.2 on D8J0X4 is an unvetted EMBL submitter assertion (ECO:0000313, ADJ62529.1). PF01370/IPR001509 supports an NAD-dependent epimerase/dehydratase fold with multiple substrate specificities, not this UDP-sugar reaction. The alternative FdeJ assignment and separate K01784 genes strengthen the need to withdraw the unsupported specific mapping; they are not a negative enzyme assay. MARK_AS_OVER_ANNOTATED records over-specificity while leaving possible activity unresolved, rather than making absence the burden of proof. Supporting Evidence: file:HERSS/Hsero_1007/Hsero_1007-bioinformatics/RESULTS.md Hsero_1012 submitter name/EC 'UDP-glucose 4-epimerase': SmR1 genes in the dedicated KO K01784: Hsero_2010, Hsero_4409; Hsero_1012 in K01784: False file:HERSS/Hsero_1007/Hsero_1007-bioinformatics/RESULTS.md KEGG mapping: `hse:Hsero_1012 -> ko:K26183` (fdeJ; naringenin degradation protein FdeJ) |
| GO:0046275 flavonoid catabolic process | IC PMID:27059806 Genetic and functional characterization of a novel meta-path... | REMOVE | Summary: Withdraw the inherited FdeJ process proposal; an individual flavonoid-catabolic step has not been established. Reason: The conserved locus and orthology identify a candidate FdeJ protein, but the epimerase/dehydratase fold does not establish the proposed oxaloacetate-releasing R13076 reaction. The available whole-operon phenotype, including the probably polar fdeA insertion, does not show which step this individual protein performs. There is no independently assayed donor for this particular role; the corresponding BRADU comparator bll6421 likewise carries no process assertion. Retain the original source payload and row position while withdrawing the active proposal. The retired flag records this curator decision, not disappearance of an upstream GOA row or proof of biological absence. Native participation remains an open question. REMOVE records withdrawal of this earlier curator-authored NEW proposal, not removal of a current GOA assertion. It does not claim that the protein is biologically incapable of participating in flavonoid catabolism. Supporting Evidence: PMID:23125118 We show that this operon is involved in naringenin degradation and that its expression is induced by naringenin and chrysin, two closely related flavonoids. PMID:27059806 After meta-cleavage of the A-ring, the subsequent metabolic steps generate oxaloacetic acid that is metabolized via the tricarboxylic acid cycle. file:HERSS/Hsero_1007/Hsero_1007-bioinformatics/RESULTS.md KEGG mapping: `hse:Hsero_1012 -> ko:K26183` (fdeJ; naringenin degradation protein FdeJ) |
Loading supporting content…
Download this section (compressed HTML)Q: Does purified Hsero_1012 epimerize UDP-glucose, act on a flavonoid-derived substrate, or support both activities? The broad fold and other GalE genes do not discriminate these alternatives.
Experiment: Couple purified FdeC and FdeJ with 5,7,8-trihydroxyflavanone and NAD(P)+/NAD(P)H, detecting oxaloacetate enzymatically and the lactone by LC-MS/MS.
Type: coupled enzyme assay
What is not known — curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: The reaction catalysed by FdeJ, and whether an epimerase/dehydratase-fold protein can release oxaloacetate from the A-ring cleavage product as KEGG proposes, is unknown.
OPEN BIOLOGY
What is known: FdeJ membership and pathway placement nominate a candidate; they do not establish which native flavonoid-catabolic step the target performs. The inherited process proposal is retired pending participation evidence.
Significance: The R13076 step is the least constrained reaction in the pathway.
What would resolve it: Assay purified FdeJ with the FdeC cleavage product and NAD(P)(H), and test an fdeJ deletion for intermediate accumulation.
Provenance (the field's own admissions):
Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)