Hsero_1011

UniProt ID: D8J0X3
Organism: Herbaspirillum seropedicae SmR1
Review Status: COMPLETE
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Gene Description

Hsero_1011 (fdeI) encodes a fumarylacetoacetate hydrolase (FAH)-family protein with an N-terminal FAA_hydro_N domain and the C-terminal FAH catalytic domain, in the naringenin degradation (fde) locus of Herbaspirillum seropedicae SmR1. The FAH superfamily includes hydrolases, decarboxylases, isomerases and hydratases. KEGG assigns FdeI to the two late pathway reactions, decarboxylation of a flavonoid-derived beta-keto acid and dehydration of the resulting hydroxyketone; neither reaction has been tested, and KEGG marks both as unclear, so its molecular function is unresolved.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0003824 catalytic activity
IEA
GO_REF:0000002
ACCEPT
Summary: Catalytic activity is as specific as the evidence allows: FAH-fold membership establishes an enzyme, but not which reaction class.
Reason: FAH-family catalytic-domain membership supports enzymatic activity. A more specific term is not supported: the FAH fold includes hydrolases, decarboxylases, isomerases and hydratases, and KEGG marks both reactions assigned to FdeI, the R13078 decarboxylation and the R13079 dehydration, as unclear, so catalytic activity is as specific as the evidence supports. The predicted decarboxylase role is carried in the knowledge gap, matching the FdeH (Hsero_1010) and FdeJ (Hsero_1012) reviews, which assert no specific molecular function either.
Supporting Evidence:
file:HERSS/Hsero_1011/Hsero_1011-uniprot.txt
InterPro; IPR011234; Fumarylacetoacetase-like_C.
file:HERSS/Hsero_1007/Hsero_1007-bioinformatics/RESULTS.md
R13078: 5-Hydroxy-5-(4-hydroxyphenyl)-3-oxopentanoate <=> 4-Hydroxy-4-(4-hydroxyphenyl)-butan-2-one + CO2; KEGG comment: decarboxylation unclear reaction; orthology: K26185 naringenin degradation protein FdeI
GO:0046275 flavonoid catabolic process
IC
PMID:27059806
Genetic and functional characterization of a novel meta-path...
REMOVE
Summary: Withdraw the inherited FdeI process proposal; an individual flavonoid-catabolic step has not been established.
Reason: The conserved locus and orthology identify a candidate FdeI protein, but the FAH fold supports multiple reaction classes, while the proposed R13078/R13079 transformations are untested. 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 bll6422 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_1011 -> ko:K26185` (fdeI; naringenin degradation protein FdeI)

References

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Suggested Experiments

Experiment: Purify FdeI and assay CO2 release and dehydration with the R13078 and R13079 substrates; construct an fdeI deletion and profile intermediates.

Type: enzyme assay and genetics

Knowledge Gaps

What is not known β€” curated, literature-grounded statements of the open unknowns (the inverse of core functions).

Gap: Whether FdeI catalyses the R13078 decarboxylation, the R13079 dehydration, both, or neither is unknown.

OPEN BIOLOGY

What is known: FdeI 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: Both late reactions are KEGG predictions marked unclear.

What would resolve it: Assay purified FdeI with the R13078 beta-keto acid and R13079 hydroxyketone and identify products; test an fdeI deletion for intermediate accumulation.

Provenance (the field's own admissions):

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Notes

(Hsero_1011-notes.md)

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