lpd

Summary: The row captures LpdA's defining E3/L-protein activity.

Reason: Dihydrolipoyl dehydrogenase (NADH) activity is the catalytic function that lets LpdA serve as the E3 enzyme of 2-oxoacid dehydrogenase complexes and the L protein of glycine cleavage.

Summary: The 2-oxoglutarate metabolic process row is correct but broad.

Reason: LpdA participates in 2-oxoglutarate metabolism specifically by reoxidizing the SucB/E2o lipoyl arm during OGDH-catalyzed 2-oxoglutarate decarboxylation to succinyl-CoA.

Proposed replacements: 2-oxoglutarate decarboxylation to succinyl-CoA

Summary: FAD binding is an integral cofactor-binding activity of LpdA.

Reason: LpdA is a FAD-dependent pyridine nucleotide-disulfide oxidoreductase; FAD mediates transfer from the active-site dithiol/disulfide to NAD+.

Summary: The row captures LpdA's defining E3/L-protein activity.

Reason: Dihydrolipoyl dehydrogenase (NADH) activity is the catalytic function that lets LpdA serve as the E3 enzyme of 2-oxoacid dehydrogenase complexes and the L protein of glycine cleavage.

Summary: Cytoplasm is true for this soluble enzyme, but the more specific cytosol location is also retained on this gene.

Reason: Correct but general: GO:0005737 cytoplasm is an ancestor of GO:0005829 cytosol, which this gene already carries with direct support (IDA, HDA). MODIFY to that descendant, following the module-wide rule for true parent terms whose retained child entails them.

Proposed replacements: cytosol

Summary: UniProt and HDA membrane localizations report a minor membrane-associated pool.

Reason: The core LpdA reactions are soluble cytosolic reactions; peripheral membrane association is plausible but not the principal localization.

Summary: Oxidative-stress rows are phenotype-level inferences for a core redox enzyme.

Reason: The deletion/codon-usage data indicate stress sensitivity but do not establish that LpdA itself executes a dedicated oxidative-stress response step.

Summary: oxidoreductase activity is a correct but broader ancestor of LpdA's specific reaction.

Reason: Replace the broad oxidoreductase grouping with the exact EC 1.8.1.4/RHEA:15045 dihydrolipoyl dehydrogenase term.

Proposed replacements: dihydrolipoyl dehydrogenase (NADH) activity

Summary: oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor is a correct but broader ancestor of LpdA's specific reaction.

Reason: Replace the broad oxidoreductase grouping with the exact EC 1.8.1.4/RHEA:15045 dihydrolipoyl dehydrogenase term.

Proposed replacements: dihydrolipoyl dehydrogenase (NADH) activity

Summary: FAD binding is an integral cofactor-binding activity of LpdA.

Reason: LpdA is a FAD-dependent pyridine nucleotide-disulfide oxidoreductase; FAD mediates transfer from the active-site dithiol/disulfide to NAD+.

Summary: A high-throughput IPI row to generic protein binding.

Reason: The reported UvrD interaction is not a known physiological LpdA core function, and bare GO:0005515 is not informative for LpdA curation.

Summary: A high-throughput IPI row to generic protein binding.

Reason: The reported YbaK interaction is not a known physiological LpdA core function, and bare GO:0005515 is not informative for LpdA curation.

Summary: A high-throughput IPI row to generic protein binding.

Reason: SucB/E2o is the physiological lipoyl-domain partner in the OGDH complex, but generic protein binding hides the catalytic E3-in-complex role that should be represented by LpdA's dehydrogenase activity and OGDH process annotations.

Summary: A high-throughput IPI row to generic protein binding.

Reason: The reported IdnD interaction is not a known physiological LpdA core function, and bare GO:0005515 is not informative for LpdA curation.

Summary: A high-throughput IPI row to generic protein binding.

Reason: The reported YgfF interaction is not a known physiological LpdA core function, and bare GO:0005515 is not informative for LpdA curation.

Summary: A high-throughput IPI row to generic protein binding.

Reason: The reported BluR interaction is not a known physiological LpdA core function, and bare GO:0005515 is not informative for LpdA curation.

Summary: A high-throughput IPI row to generic protein binding.

Reason: The reported YdjF interaction is not a known physiological LpdA core function, and bare GO:0005515 is not informative for LpdA curation.

Summary: A high-throughput IPI row to generic protein binding.

Reason: AceF/E2p is the physiological lipoyl-domain partner in the pyruvate dehydrogenase complex, but generic protein binding hides the catalytic E3-in-complex role that should be represented by LpdA's dehydrogenase activity and pyruvate-decarboxylation process annotations.

Summary: A high-throughput IPI row to generic protein binding.

Reason: AceF/E2p is the physiological lipoyl-domain partner in the pyruvate dehydrogenase complex, but generic protein binding hides the catalytic E3-in-complex role that should be represented by LpdA's dehydrogenase activity and pyruvate-decarboxylation process annotations.

Summary: A high-throughput IPI row to generic protein binding.

Reason: AceF/E2p is the physiological lipoyl-domain partner in the pyruvate dehydrogenase complex, but generic protein binding hides the catalytic E3-in-complex role that should be represented by LpdA's dehydrogenase activity and pyruvate-decarboxylation process annotations.

Summary: A high-throughput IPI row to generic protein binding.

Reason: SucB/E2o is the physiological lipoyl-domain partner in the OGDH complex, but generic protein binding hides the catalytic E3-in-complex role that should be represented by LpdA's dehydrogenase activity and OGDH process annotations.

Summary: Identical protein binding reflects the LpdA homodimer.

Reason: Homodimerization is part of the active enzyme architecture, but the catalytic dehydrogenase activity is the informative molecular function.

Summary: Cytoplasm is true for this soluble enzyme, but the more specific cytosol location is also retained on this gene.

Reason: Correct but general: GO:0005737 cytoplasm is an ancestor of GO:0005829 cytosol, which this gene already carries with direct support (IDA, HDA). MODIFY to that descendant, following the module-wide rule for true parent terms whose retained child entails them.

Proposed replacements: cytosol

Summary: LpdA is the L protein of the E. coli glycine cleavage enzyme complex.

Reason: The lpd mutant lacks inducible GCV activity and plasmid-borne lpd restores glycine utilization and enzyme activity, supporting glycine cleavage complex membership.

Summary: LpdA participates directly in the TCA-cycle 2-oxoglutarate dehydrogenase reaction as the shared E3 subunit.

Reason: Correct but general: the E3 takes part in the tricarboxylic acid cycle only through the 2-oxoglutarate dehydrogenase step, reoxidizing the E2 lipoyl arm during oxidative decarboxylation of 2-oxoglutarate to succinyl-CoA. GO:0120551 is part_of the TCA cycle and is the supported refinement, as in the DLD review.

Proposed replacements: 2-oxoglutarate decarboxylation to succinyl-CoA

Summary: The one-carbon process assertion reflects LpdA's glycine-cleavage role.

Reason: GO:0019464 names the specific one-carbon process in which LpdA participates as the GCV L protein.

Proposed replacements: glycine decarboxylation via glycine cleavage system

Summary: LpdA participates in glycine decarboxylation as the GCV L protein.

Reason: LpdA performs the terminal reoxidation of the reduced H-protein lipoyl arm during glycine cleavage.

Summary: LpdA participates in pyruvate catabolism as the E3 enzyme of pyruvate dehydrogenase.

Reason: LpdA directly participates in pyruvate conversion to acetyl-CoA as the PDH E3 enzyme, but GO:0006086 is the more specific process term for this pyruvate dehydrogenase step.

Proposed replacements: pyruvate decarboxylation to acetyl-CoA

Summary: LpdA is the shared E3 enzyme recruited to the 2-oxoglutarate dehydrogenase complex.

Reason: The E. coli 2-oxoglutarate dehydrogenase complex contains the E3 subunit tethered to the SucB/E2o core, reflecting LpdA's physical recruitment to the OGDH complex for SucB lipoyl-arm reoxidation.

Summary: LpdA is also the shared E3 enzyme of the pyruvate dehydrogenase complex.

Reason: LpdA is the E3 dihydrolipoyl dehydrogenase subunit of the E. coli pyruvate dehydrogenase complex, acting with AceE/E1p and AceF/E2p as a core physiological context for its reusable E3 reaction.

Summary: LpdA is the L protein of the E. coli glycine cleavage enzyme complex.

Reason: The lpd mutant lacks inducible GCV activity and plasmid-borne lpd restores glycine utilization and enzyme activity, supporting glycine cleavage complex membership.

Summary: The row captures LpdA's defining E3/L-protein activity.

Reason: Dihydrolipoyl dehydrogenase (NADH) activity is the catalytic function that lets LpdA serve as the E3 enzyme of 2-oxoacid dehydrogenase complexes and the L protein of glycine cleavage.

Summary: Cytoplasmic/cytosolic localization is consistent with the soluble central-metabolism complexes that use LpdA.

Reason: LpdA is a soluble cytoplasmic enzyme that can be recovered from the cytosol in direct proteomics studies.

Summary: Cytoplasmic/cytosolic localization is consistent with the soluble central-metabolism complexes that use LpdA.

Reason: LpdA is a soluble cytoplasmic enzyme that can be recovered from the cytosol in direct proteomics studies.

Summary: Oxidative-stress rows are phenotype-level inferences for a core redox enzyme.

Reason: The deletion/codon-usage data indicate stress sensitivity but do not establish that LpdA itself executes a dedicated oxidative-stress response step.

Summary: The row captures LpdA's defining E3/L-protein activity.

Reason: Dihydrolipoyl dehydrogenase (NADH) activity is the catalytic function that lets LpdA serve as the E3 enzyme of 2-oxoacid dehydrogenase complexes and the L protein of glycine cleavage.

Summary: Zinc binding was detected by a gel-based radioactive Zn(II) screen; no zinc site or zinc role is known for LpdA.

Reason: PMID:11985624 (abstract only in the cache) screened total E. coli proteins on two-dimensional gels for radioactive Zn(II) binding; the abstract does not name LpdA among the assigned spots, so the curated LpdA call rests on full-text data that cannot be checked here. The assay detects Zn(II) retention by denatured, blotted proteins and is prone to non-physiological binding; the E3 fold has no zinc site, and the dihydrolipoyl dehydrogenase mechanism uses FAD and a redox-active disulfide, not zinc. The binding may be real in vitro but is not evidence of a physiological zinc-binding function.

Summary: The membrane-associated pool is the peripheral inner-membrane fraction, which the gene's plasma membrane row already records.

Reason: Correct but general: the cited UniProt line places the membrane pool in the cell inner membrane as a peripheral membrane protein (ECO:0000269, PubMed:16079137). GO:0005886 plasma membrane, already carried by this gene and kept as non-core, is the supported descendant of GO:0016020, so this row is modified to it.

Proposed replacements: plasma membrane

Summary: Cytoplasm is true for this soluble enzyme, but the more specific cytosol location is also retained on this gene.

Reason: Correct but general: GO:0005737 cytoplasm is an ancestor of GO:0005829 cytosol, which this gene already carries with direct support (IDA, HDA). MODIFY to that descendant, following the module-wide rule for true parent terms whose retained child entails them.

Proposed replacements: cytosol

Summary: The 2-oxoglutarate metabolic process row is correct but broad.

Reason: LpdA participates in 2-oxoglutarate metabolism specifically by reoxidizing the SucB/E2o lipoyl arm during OGDH-catalyzed 2-oxoglutarate decarboxylation to succinyl-CoA.

Proposed replacements: 2-oxoglutarate decarboxylation to succinyl-CoA

Summary: The 2-oxoglutarate metabolic process row is correct but broad.

Reason: LpdA participates in 2-oxoglutarate metabolism specifically by reoxidizing the SucB/E2o lipoyl arm during OGDH-catalyzed 2-oxoglutarate decarboxylation to succinyl-CoA.

Proposed replacements: 2-oxoglutarate decarboxylation to succinyl-CoA

Summary: disulfide oxidoreductase activity is a correct but broader ancestor of LpdA's specific reaction.

Reason: Replace the broad oxidoreductase grouping with the exact EC 1.8.1.4/RHEA:15045 dihydrolipoyl dehydrogenase term.

Proposed replacements: dihydrolipoyl dehydrogenase (NADH) activity

Summary: FAD binding is an integral cofactor-binding activity of LpdA.

Reason: LpdA is a FAD-dependent pyridine nucleotide-disulfide oxidoreductase; FAD mediates transfer from the active-site dithiol/disulfide to NAD+.

Summary: Cytoplasmic/cytosolic localization is consistent with the soluble central-metabolism complexes that use LpdA.

Reason: LpdA is a soluble cytoplasmic enzyme that can be recovered from the cytosol in direct proteomics studies.

Summary: LpdA participates in glycine decarboxylation as the GCV L protein.

Reason: LpdA performs the terminal reoxidation of the reduced H-protein lipoyl arm during glycine cleavage.