NicD is an alpha/beta-hydrolase-fold N-formylmaleamate deformylase in the aerobic nicotinate degradation pathway of Pseudomonas putida KT2440. It hydrolyzes the ring-cleavage product of NicX to maleamate and formate, supplying substrate to the maleamate amidase NicF. Mutagenesis supports Ser101, Asp125 and His245 as essential catalytic residues.
Definition: Catalysis of the reaction N-formylmaleamate + H2O = maleamate + formate + H(+).
Justification: The substrate-specific reaction is experimentally established, whereas the existing GO parent groups many unrelated linear-amide hydrolases. QuickGO exact-substrate searches did not recover a matching molecular function.
Parent term: hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0016020 membrane | IEA GO_REF:0000118 | MARK AS OVER ANNOTATED | Summary: Membrane location is a family-level TreeGrafter propagation without target support. Reason: This IEA is a TreeGrafter transfer from the broad PTHR43798 alpha/beta-hydrolase family, whose name and experimental members are dominated by monoacylglycerol-lipase-like enzymes that act at lipid interfaces. The membrane IBD sits at PTN001661081, which has a single mouse seed (the ABHD6 clade, which is membrane-anchored) but spans the bacterial SF31 and SF33 subfamilies. That placement is assessed as too deep in interpro/panther/PTHR43798/PTHR43798-review.yaml. Nothing specific to NicD supports a membrane location. The record carries no transmembrane or signal-peptide feature and no curated subcellular location. Activity was recovered from soluble crude extracts (PMID:18678916), and the substrate and product are small soluble intracellular catabolites. Peripheral association cannot be strictly excluded without fractionation, so the row is marked as an over-annotation rather than removed. No replacement cytosol term is proposed because no localization experiment exists. Supporting Evidence: file:interpro/panther/PTHR43798/PTHR43798-paint.tsv PTHR43798 PTN001661081 GO:0016020 C IBD false MGI:MGI:1913332 file:PSEPK/nicD/nicD-deep-research-falcon.md NicD was assayed in **soluble crude extracts** after heterologous expression; no membrane segment, signal peptide, or export evidence is reported in the cited sources. |
| GO:1901848 nicotinate catabolic process | IDA PMID:18678916 Deciphering the genetic determinants for aerobic nicotinic a... | ACCEPT | Summary: nicD directly performs a lower-pathway chemical step in nicotinate catabolism. Reason: Recombinant NicD-dependent conversion of N-formylmaleamate to maleamate/formate and nicD disruption/complementation place this catalyst in the native KT2440 pathway. The primary full text was inspected externally; the local cache is abstract-only. Supporting Evidence: file:PSEPK/nicD/nicD-uniprot.txt Reaction=N-formylmaleamate + H2O = maleamate + formate + H(+); PMID:18678916 Further conversion of N-formylmaleamic acid to formic and maleamic acid is catalyzed by the NicD protein |
| GO:0016811 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides | IDA PMID:18678916 Deciphering the genetic determinants for aerobic nicotinic a... | MODIFY | Summary: Refine the broad linear-amide hydrolase activity to the characterized substrate-specific reaction. Reason: The linear-amide hydrolase parent is correct but less specific than the demonstrated N-formylmaleamate deformylase activity. No exact current GO term was recovered; the replacement corresponds to the supported proposed term. The full paper supports S101/D125/H245 by loss-of-activity substitutions; E221A retains approximately 70% activity, so the current predicted E221 active-site feature is not used to override experiment. Proposed replacements: N-formylmaleamate deformylase activity Supporting Evidence: file:PSEPK/nicD/nicD-uniprot.txt Reaction=N-formylmaleamate + H2O = maleamate + formate + H(+); PMID:18678916 Further conversion of N-formylmaleamic acid to formic and maleamic acid is catalyzed by the NicD protein |
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Download this section (compressed HTML)Q: Can an exact GO molecular-function term be added for N-formylmaleamate deformylase activity?
Experiment: Determine cellular localization by fractionation with soluble and membrane markers, rather than inferring it from whole-cell extract activity.
Type: subcellular fractionation
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