LpdG (PP_4187) is a class-I pyridine nucleotide-disulfide oxidoreductase with dihydrolipoyl dehydrogenase activity. It uses FAD and NAD+ to reoxidize protein-bound dihydrolipoyllysine, allowing it to serve as a shared E3 enzyme for lipoyl-dependent multienzyme systems. Orthology and operon context support its assignment as the KT2440 counterpart of characterized P. putida LPD-glc, which serves pyruvate and 2-oxoglutarate dehydrogenases and the glycine oxidation system in the characterized strains. The glycine-cleavage role has not been tested directly in KT2440.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004148 dihydrolipoyl dehydrogenase (NADH) activity | IEA GO_REF:0000120 | ACCEPT | Summary: dihydrolipoyl dehydrogenase (NADH) activity is consistent with the curated UniProt name, EC/family evidence, and the gene product role summarized here. Reason: The P. putida lpdG product LPD-glc is the biochemically characterized E3 and glycine-oxidation L-factor; Q88FB1 is the KT2440 lpdG locus and matches the NCBIfam lipoamide dehydrogenase model. The UniProt EC line is ARBA/RuleBase-derived and is not cited. Supporting Evidence: file:PSEPK/lpdG/lpdG-deep-research-openscientist.md The enzyme catalyzes the **NAD⁺-dependent oxidation of protein-bound dihydrolipoyl cofactors**. PMID:1902462 LPD-glc, which is the E3 component of the pyruvate and 2-ketoglutarate dehydrogenase complexes and the L-factor for the glycine oxidation system file:PSEPK/lpdG/lpdG-uniprot.txt DR NCBIfam; TIGR01350; lipoamide_DH; 1. |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: A cytoplasmic location is plausible for this soluble bacterial enzyme but is not a core function. Reason: LPD-glc is the E3 of the soluble pyruvate and 2-oxoglutarate dehydrogenase complexes and the L-factor of the glycine oxidation system, and the record has no signal peptide or transmembrane feature, so the cytoplasmic location holds. The UniProt subcellular-location line behind this mapping is an ARBA prediction and is not cited. Location is context rather than core function. Supporting Evidence: file:PSEPK/lpdG/lpdG-deep-research-openscientist.md The protein functions as a **homodimer in the cytoplasm**, binding one FAD per subunit. PMID:1902462 LPD-glc, which is the E3 component of the pyruvate and 2-ketoglutarate dehydrogenase complexes and the L-factor for the glycine oxidation system |
| GO:0006103 2-oxoglutarate metabolic process | IEA GO_REF:0000118 | MODIFY | Summary: True but broad; the E3 acts in OGDH-catalysed 2-oxoglutarate decarboxylation. Reason: Correct but general: the E3 takes part in 2-oxoglutarate metabolism by reoxidizing the lipoyl arm of the 2-oxoglutarate dehydrogenase E2 during oxidative decarboxylation of 2-oxoglutarate to succinyl-CoA. MODIFY to GO:0120551, as in the DLD and E. coli lpd reviews. Proposed replacements: 2-oxoglutarate decarboxylation to succinyl-CoA Supporting Evidence: PMID:1902462 LPD-glc, which is the E3 component of the pyruvate and 2-ketoglutarate dehydrogenase complexes and the L-factor for the glycine oxidation system |
| GO:0016491 oxidoreductase activity | IEA GO_REF:0000002 | MODIFY | Summary: Oxidoreductase activity is true but is a broad InterPro2GO parent of the specific E3 activity. Reason: Correct but general. The specific child GO:0004148 dihydrolipoyl dehydrogenase (NADH) activity, already accepted on this gene, is the supported refinement. Treated the same way in the DLD and E. coli lpd reviews. Proposed replacements: dihydrolipoyl dehydrogenase (NADH) activity Supporting Evidence: file:PSEPK/lpdG/lpdG-uniprot.txt DR NCBIfam; TIGR01350; lipoamide_DH; 1. |
| GO:0016668 oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor | IEA GO_REF:0000002 | MODIFY | Summary: True but general parent of the specific dihydrolipoyl dehydrogenase activity. Reason: Correct but general. GO:0004148 dihydrolipoyl dehydrogenase (NADH) activity, already accepted on this gene, is the supported descendant. Treated the same way in the DLD and E. coli lpd reviews. Proposed replacements: dihydrolipoyl dehydrogenase (NADH) activity Supporting Evidence: file:PSEPK/lpdG/lpdG-uniprot.txt DR NCBIfam; TIGR01350; lipoamide_DH; 1. |
| GO:0050660 flavin adenine dinucleotide binding | IEA GO_REF:0000120 | ACCEPT | Summary: FAD binding is intrinsic to the dihydrolipoyl dehydrogenase catalytic cycle. Reason: FAD is the tightly bound redox cofactor that the E3 reaction cycle uses (FAD to the redox-active disulfide to NAD+); FAD binding is accepted as an intrinsic part of the core catalytic function, consistently across the L-protein reviews of the module. Supporting Evidence: file:PSEPK/lpdG/lpdG-uniprot.txt FT BINDING 15 FT /ligand="FAD" FT /ligand_id="ChEBI:CHEBI:57692" FT /evidence="ECO:0007829|PDB:5TR3, ECO:0007829|PDB:6AWA" |
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Download this section (compressed HTML)Q: Does KT2440 LpdG supply the glycine-cleavage L-protein activity in vivo, as predicted from the experimentally characterized P. putida LPD-glc enzyme?
Q: Should the Q88FB1 UniProt ARBA function text be corrected because it describes the branched-chain complex assigned to LpdV?
Experiment: Compare glycine-dependent growth and native GCS activity across lpdG, lpd, and lpdV mutants, followed by biochemical complementation.
Type: genetics and enzyme-complex reconstitution
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