At3g17240 encodes mtLPD2, one of two mitochondrial dihydrolipoyl dehydrogenases (lipoamide dehydrogenase, E3, EC 1.8.1.4) in Arabidopsis. It should not be confused with the chloroplastic LPD2 encoded by At4g16155. mtLPD2 is a homodimeric FAD-containing flavoprotein of the class-I pyridine nucleotide-disulfide oxidoreductase family. It has a redox-active disulfide and uses NAD+ to reoxidize dihydrolipoyl groups that are covalently attached to the lipoyl domains of its partner enzymes, producing NADH. After import via an N-terminal transit peptide it resides in the mitochondrial matrix. There mitochondrial E3 serves the 2-oxoacid dehydrogenase complexes (pyruvate, 2-oxoglutarate and branched-chain 2-oxoacid dehydrogenases), and it serves as the L protein of the glycine decarboxylase complex. mtLPD2 transcripts are more abundant in roots and less light-responsive than those of its paralog mtLPD1 (At1g48030). On this basis mtLPD2 is proposed to work mainly in the 2-oxoacid dehydrogenase complexes, while mtLPD1 is the main L protein for photorespiratory glycine decarboxylation in leaves. The two proteins are thought to be interchangeable. An mtlpd2 knockout has no visible phenotype under laboratory conditions, but loss-of-function analysis of both genes shows that both mtLPDs contribute to photorespiration, with mtLPD1 predominant, and the leaf glycine decarboxylase complex contains about four times more L1 than L2 protein.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004148 dihydrolipoyl dehydrogenase (NADH) activity | IBA GO_REF:0000033 | ACCEPT | Summary: Dihydrolipoyl dehydrogenase activity inherited from the ancestral E3 node, which is seeded by characterized bacterial, yeast, mammalian and plant LPDs, including At3g17240 itself. Reason: This is the defining catalytic activity of mtLPD2. UniProt records the EC 1.8.1.4 activity with experimental evidence from Lutziger and Oliver (2001). The FAD/NAD binding sites and the redox-active disulfide are conserved. At3g17240 appearing among the IBA sources reflects its own experimental annotation and is not circular. Supporting Evidence: file:ARATH/mtLPD2/mtLPD2-uniprot.txt Reaction=N(6)-[(R)-dihydrolipoyl]-L-lysyl-[protein] + NAD(+) = N(6)-[(R)-lipoyl]-L-lysyl-[protein] + NADH + H(+) PMID:22303256 This reaction is catalyzed by L-protein, a homodimeric dihydrolipoamide dehydrogenase (EC 1.8.1.4). |
| GO:0004148 dihydrolipoyl dehydrogenase (NADH) activity | IEA GO_REF:0000120 | ACCEPT | Summary: Dihydrolipoyl dehydrogenase activity inferred from the InterPro lipoamide dehydrogenase signature and the EC/RHEA mapping. Reason: Consistent with the IBA and IMP rows and with the UniProt curated catalytic activity. Supporting Evidence: file:ARATH/mtLPD2/mtLPD2-uniprot.txt Reaction=N(6)-[(R)-dihydrolipoyl]-L-lysyl-[protein] + NAD(+) = N(6)-[(R)-lipoyl]-L-lysyl-[protein] + NADH + H(+) |
| GO:0004148 dihydrolipoyl dehydrogenase (NADH) activity | IMP PMID:11598235 Characterization of two cDNAs encoding mitochondrial lipoami... | ACCEPT | Summary: Lutziger and Oliver (2001) cloned the two mitochondrial LPD cDNAs and characterized an mtlpd2 T-DNA knockout. Only the abstract is cached. Reason: UniProt attributes the EC 1.8.1.4 catalytic activity to this paper with experimental evidence. The cached abstract covers expression and the knockout phenotype, not the enzyme assays, so we defer to the curator, who read the full text. The activity is in any case well supported by the family and IBA evidence. Supporting Evidence: PMID:11598235 Arabidopsis has two genes encoding for two mitochondrial lipoamide dehydrogenases file:ARATH/mtLPD2/mtLPD2-uniprot.txt EC=1.8.1.4 {ECO:0000269|PubMed:11598235} |
| GO:0005507 copper ion binding | HDA PMID:20018591 Divalent metal ions in plant mitochondria and their role in ... | MARK AS OVER ANNOTATED | Summary: Retained on Cu2+-charged immobilized metal affinity chromatography (IMAC) of mitochondrial proteins. Reason: IMAC retention shows surface affinity for an immobilized metal, which is often due to exposed histidine or cysteine residues. It does not show physiological copper binding. LPD is an FAD/NAD flavoprotein with no known metal cofactor. The study was designed to find proteins susceptible to metal-catalysed oxidative damage, not to define metal-binding functions. Supporting Evidence: PMID:20018591 Immobilized metal affinity chromatography charged with Cu(2+), Zn(2+), and Co(2+) was used to identify over 100 mitochondrial proteins with metal-binding properties. |
| GO:0005524 ATP binding | HDA PMID:17137349 Analysis of the soluble ATP-binding proteome of plant mitoch... | MARK AS OVER ANNOTATED | Summary: Captured on immobilized ATP from the soluble mitochondrial proteome. Reason: ATP-affinity capture also enriches dinucleotide-binding proteins. LPD binds FAD and NAD+ through Rossmann-type folds, which can explain retention on an ATP matrix. ATP is not a known substrate or effector of E3, so ATP binding is not an informative function for this protein. Supporting Evidence: PMID:17137349 including 14-3-3 proteins and RNA binding proteins, as well as proteins known to contain nucleotide binding domains |
| GO:0005739 mitochondrion | HDA PMID:11743115 Analysis of the Arabidopsis mitochondrial proteome. | ACCEPT | Summary: Identified in the Arabidopsis mitochondrial proteome. Reason: Consistent with the experimentally determined mitochondrial transit peptide and the matrix location. Supporting Evidence: PMID:11743115 It has been held that a single product of a single gene encoding lipoamide dehydrogenase was targeted to both organelles and partnered all these multienzyme complexes. file:ARATH/mtLPD2/mtLPD2-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion matrix |
| GO:0005739 mitochondrion | HDA PMID:14671022 Experimental analysis of the Arabidopsis mitochondrial prote... | ACCEPT | Summary: Identified in the LC-MS/MS mitochondrial proteome. UniProt cites this paper for the matrix location. Reason: Consistent with all other localization evidence. Supporting Evidence: file:ARATH/mtLPD2/mtLPD2-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion matrix |
| GO:0005739 mitochondrion | HDA PMID:17137349 Analysis of the soluble ATP-binding proteome of plant mitoch... | ACCEPT | Summary: Identified in the soluble mitochondrial matrix fraction captured on ATP affinity media. Reason: The protein was found in purified mitochondria, which supports the location regardless of the ATP-binding interpretation. Supporting Evidence: PMID:17137349 A range of highly enriched proteins were identified from the mitochondrial proteome |
| GO:0005739 mitochondrion | HDA PMID:18385124 Heterogeneity of the mitochondrial proteome for photosynthet... | ACCEPT | Summary: Detected in shoot and cell-culture mitochondrial proteomes. Reason: Consistent with the transit peptide and matrix location. Supporting Evidence: PMID:18385124 Proteomics comparisons provided a deep insight into the different steady-state abundances of specific mitochondrial proteins. |
| GO:0005739 mitochondrion | HDA PMID:22923678 Putative glycosyltransferases and other plant Golgi apparatu... | ACCEPT | Summary: Assigned to mitochondria by LOPIT organelle proteomics. Reason: LOPIT assignment agrees with the targeted and proteomic evidence. Supporting Evidence: file:ARATH/mtLPD2/mtLPD2-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion matrix |
| GO:0005739 mitochondrion | HDA PMID:25293756 A proteomic strategy for global analysis of plant protein co... | ACCEPT | Summary: Mitochondrial assignment from a leaf protein-complex proteomics study. Reason: Consistent with all other localization evidence. Supporting Evidence: file:ARATH/mtLPD2/mtLPD2-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion matrix |
| GO:0005739 mitochondrion | IBA GO_REF:0000033 | ACCEPT | Summary: Mitochondrial activity location inherited from the eukaryotic mitochondrial E3 node. Reason: mtLPD2 belongs to the mitochondrial E3 clade, not to the plastid LPD clade, and carries an experimentally verified mitochondrial transit peptide. Supporting Evidence: file:ARATH/mtLPD2/mtLPD2-uniprot.txt TRANSIT 1..36 |
| GO:0005739 mitochondrion | IDA PMID:11743114 Proteomic approach to identify novel mitochondrial proteins ... | ACCEPT | Summary: Identified on 2D gels of purified Arabidopsis mitochondria. Reason: Direct detection in purified mitochondria. This is consistent with all other evidence. Supporting Evidence: PMID:11743114 The characterized proteins cooperate in various processes, such as respiration, citric acid cycle, amino acid and nucleotide metabolism |
| GO:0005739 mitochondrion | IDA PMID:14764908 Lipoic acid-dependent oxidative catabolism of alpha-keto aci... | ACCEPT | Summary: E3 lipoamide dehydrogenase identified in Arabidopsis mitochondria during the analysis of lipoic acid-dependent 2-oxoacid dehydrogenase complexes. Reason: Direct identification in mitochondrial extracts. UniProt cites this paper as experimental evidence for the matrix location. Supporting Evidence: PMID:14764908 the bulk of the E3 proteins identified previously in Arabidopsis mitochondria |
| GO:0005739 mitochondrion | ISM GO_REF:0000122 | ACCEPT | Summary: Mitochondrial targeting predicted by AtSubP. Reason: The prediction agrees with the experimental evidence. Supporting Evidence: file:ARATH/mtLPD2/mtLPD2-uniprot.txt TRANSIT 1..36 |
| GO:0005759 mitochondrial matrix | IEA GO_REF:0000044 | ACCEPT | Summary: Mitochondrial matrix location from the UniProt subcellular-location mapping. The underlying UniProt statement has experimental evidence. Reason: E3 is a soluble matrix component of the 2-oxoacid dehydrogenase and glycine decarboxylase complexes. UniProt supports the matrix location with experimental evidence (PubMed 14671022, 14764908). Supporting Evidence: file:ARATH/mtLPD2/mtLPD2-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion matrix PMID:11598235 once in the mitochondrial matrix, are interchangeable among the different multienzyme complexes |
| GO:0005794 Golgi apparatus | RCA NOT PMID:22430844 Isolation and proteomic characterization of the Arabidopsis ... | ACCEPT | Summary: The NOT annotation records that the Golgi proteome analysis classified mtLPD2 as a contaminant rather than a Golgi resident. Reason: The negative claim agrees with the established mitochondrial matrix location of mtLPD2. The Golgi study explicitly estimated a fraction of contaminating proteins from other compartments. Supporting Evidence: PMID:22430844 A composition analysis indicated that approximately 19% of proteins were likely derived from contaminating compartments and ribosomes. |
| GO:0005829 cytosol | HDA PMID:28887381 Global Analysis of Membrane-associated Protein Oligomerizati... | MARK AS OVER ANNOTATED | Summary: Cytosol assignment from membrane-associated protein correlation profiling. Reason: mtLPD2 is imported into mitochondria by an experimentally verified transit peptide and acts in the matrix. The cytosol call from fractionation-based profiling most likely reflects leakage from broken mitochondria. Supporting Evidence: file:ARATH/mtLPD2/mtLPD2-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion matrix |
| GO:0006103 2-oxoglutarate metabolic process | IBA GO_REF:0000033 | ACCEPT | Summary: 2-oxoglutarate metabolism, through the E3 role in the 2-oxoglutarate dehydrogenase complex, inherited from the ancestral E3 node. Reason: Mitochondrial E3 is an obligatory subunit of the 2-oxoglutarate dehydrogenase complex of the TCA cycle. mtLPD2 is proposed to work mainly in the 2-oxoacid dehydrogenase complexes, so this is a core process for the gene. Supporting Evidence: PMID:11598235 mtLPD2 encodes the protein incorporated into alpha-ketoacid dehydrogenase complexes PMID:14764908 Lipoic acid-containing acyltransferases from pyruvate dehydrogenase complex and alpha-ketoglutarate dehydrogenase complex were identified from all three species. |
| GO:0008270 zinc ion binding | HDA PMID:20018591 Divalent metal ions in plant mitochondria and their role in ... | MARK AS OVER ANNOTATED | Summary: Retained on Zn2+-charged IMAC of mitochondrial proteins. Reason: As for copper, IMAC retention does not establish a physiological zinc-binding function. LPD has no known zinc site. Supporting Evidence: PMID:20018591 Immobilized metal affinity chromatography charged with Cu(2+), Zn(2+), and Co(2+) was used to identify over 100 mitochondrial proteins with metal-binding properties. |
| GO:0016491 oxidoreductase activity | IEA GO_REF:0000002 | TOO GENERAL | Summary: Generic oxidoreductase activity from pyridine nucleotide-disulfide oxidoreductase InterPro signatures. Reason: This is true, but it is entailed by the accepted GO:0004148 dihydrolipoyl dehydrogenase (NADH) activity, which is_a oxidoreductase activity. Supporting Evidence: file:ARATH/mtLPD2/mtLPD2-uniprot.txt SIMILARITY: Belongs to the class-I pyridine nucleotide-disulfide oxidoreductase family. |
| GO:0016668 oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor | IEA GO_REF:0000002 | TOO GENERAL | Summary: Oxidoreductase activity on sulfur-group donors with NAD(P) as acceptor, from InterPro. Reason: This is correct, but it is the direct parent of the accepted GO:0004148, which already entails it. Supporting Evidence: file:ARATH/mtLPD2/mtLPD2-uniprot.txt Reaction=N(6)-[(R)-dihydrolipoyl]-L-lysyl-[protein] + NAD(+) = N(6)-[(R)-lipoyl]-L-lysyl-[protein] + NADH + H(+) |
| GO:0045252 oxoglutarate dehydrogenase complex | IBA GO_REF:0000033 | ACCEPT | Summary: Subunit (E3) of the 2-oxoglutarate dehydrogenase complex, inherited from the mitochondrial E3 node. Reason: The mitochondrial E3 is a shared subunit of the 2-oxoacid dehydrogenase complexes. mtLPD2 is proposed to work predominantly in these complexes. There is no Arabidopsis-specific evidence of divergence, and the IBA node placement (mitochondrial eukaryotic E3s) includes mtLPD2. Supporting Evidence: file:ARATH/mtLPD2/mtLPD2-uniprot.txt Lipoamide dehydrogenase is a component of the glycine decarboxylase (GDC) or glycine cleavage system as well as of the alpha-ketoacid dehydrogenase complexes. PMID:11598235 mtLPD2 encodes the protein incorporated into alpha-ketoacid dehydrogenase complexes |
| GO:0045271 respiratory chain complex I | IDA PMID:20197505 Internal architecture of mitochondrial complex I from Arabid... | REMOVE | Summary: A lipoamide dehydrogenase spot was found in complex I preparations from Arabidopsis mitochondria. Reason: The authors of the cited paper list lipoamide dehydrogenase among the contaminating proteins of their complex I preparation, not among its subunits. Nothing suggests that E3 is a structural component of NADH:ubiquinone oxidoreductase. This is a contradiction stated in the source itself, not a second-guess of the curator. Supporting Evidence: PMID:20197505 a few contaminating proteins like prohibitin, the Ξ²-subunit of ATP synthase (complex V), Ser hydroxymethyltransferase, and lipoamide dehydrogenase |
| GO:0045271 respiratory chain complex I | IEA GO_REF:0000117 | REMOVE | Summary: Complex I membership predicted by an ARBA machine-learning rule. Reason: The ARBA rule most likely reflects contaminant-derived complex I annotations of LPDs such as the one above. E3 is a soluble matrix flavoprotein of the 2-oxoacid dehydrogenase and glycine decarboxylase complexes, and the complex I study names it as a contaminant. Supporting Evidence: PMID:20197505 a few contaminating proteins like prohibitin, the Ξ²-subunit of ATP synthase (complex V), Ser hydroxymethyltransferase, and lipoamide dehydrogenase |
| GO:0050660 flavin adenine dinucleotide binding | IBA GO_REF:0000033 | ACCEPT | Summary: FAD binding, the prosthetic group of the E3 flavoprotein. Reason: FAD is the obligatory redox cofactor of lipoamide dehydrogenase, and the FAD-binding residues are conserved in mtLPD2. Supporting Evidence: file:ARATH/mtLPD2/mtLPD2-uniprot.txt Note=Binds 1 FAD per subunit. PMID:22303256 Electrons are first transferred to the co-factor FAD that is re-oxidized by NAD + resulting in the formation of NADH |
| GO:0050660 flavin adenine dinucleotide binding | IEA GO_REF:0000002 | ACCEPT | Summary: FAD binding inferred from the lipoamide dehydrogenase InterPro signature. Reason: Consistent with the IBA row and the conserved FAD-binding residues. Supporting Evidence: file:ARATH/mtLPD2/mtLPD2-uniprot.txt Note=Binds 1 FAD per subunit. |
| GO:0050897 cobalt ion binding | HDA PMID:20018591 Divalent metal ions in plant mitochondria and their role in ... | MARK AS OVER ANNOTATED | Summary: Retained on Co2+-charged IMAC of mitochondrial proteins. Reason: IMAC retention does not establish physiological cobalt binding. Cobalt is present in mitochondria only in trace amounts, and LPD has no known cobalt site. Supporting Evidence: PMID:20018591 revealing a 26:8:6:1 molar ratio for iron:zinc:copper:manganese and trace amounts of cobalt and molybdenum |
| GO:0005960 glycine cleavage complex | IDA PMID:32311173 Stoichiometry of two plant glycine decarboxylase complexes a... | NEW | Summary: Mass-spectrometric stoichiometry of the Arabidopsis leaf glycine decarboxylase complex detects both L-protein isoforms, GCS-L1 (mtLPD1) and GCS-L2 (mtLPD2), as components of the complex. Reason: mtLPD2 has no glycine cleavage complex annotation in GOA. The leaf GDC contains GCS-L2 at about a quarter of the GCS-L1 level, so mtLPD2 is a minor but real L subunit; this mirrors the NEW row on the minor P-protein isoform GLDP2 from the same measurement. The abstract does not give loci; GCS-L2 is mapped to At3g17240 by the same group's nomenclature (PMID:31413204), which is an inference. Supporting Evidence: PMID:32311173 The Arabidopsis GDC contains four times more of the isoforms GCS-P1 and GCS-L1 in comparison with GCS-P2 and GCS-L2 PMID:31413204 GDC-L2 (AT3G17240) |
| GO:0009853 photorespiration | IMP PMID:41990722 Crucial roles of the mitochondrial lipoamide dehydrogenase i... | NEW | Summary: Loss-of-function analysis of both Arabidopsis mtLPDs shows that mtLPD2 contributes to photorespiration, though less than mtLPD1. Reason: Participation test: as the L protein of the glycine decarboxylase complex, mtLPD2 reoxidizes the H-protein lipoyl arm in the photorespiratory glycine decarboxylation step, so it does part of the work of the process. The mutant study reports that both mtLPDs contribute to photorespiration, with mtLPD1 predominant; this matches the NEW photorespiration rows on mtLPD1 and on the minor P-protein isoform GLDP2, and the about 4:1 L1:L2 leaf stoichiometry explains why mtLPD2 is the minor contributor. The earlier mtlpd2 single mutant without a visible phenotype (PMID:11598235) is consistent with redundancy. Abstract-only cache; the abstract states the result directly. Supporting Evidence: PMID:41990722 While the two mtLPDs both contribute to photorespiration, mtLPD1 plays a more predominant role, especially under high-light stress. PMID:32311173 The Arabidopsis GDC contains four times more of the isoforms GCS-P1 and GCS-L1 in comparison with GCS-P2 and GCS-L2 |
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Download this section (compressed HTML)Q: Both mtLPDs contribute to photorespiration, with mtLPD1 predominant (PMID:41990722), and the leaf GDC holds about four times more L1 than L2 (PMID:32311173). Does mtLPD2 occupy GDC in proportion to its abundance, or is it preferentially assembled into the 2-oxoacid dehydrogenase complexes?
Q: Is the proposed division of labour (mtLPD1 for GDC, mtLPD2 for the 2-oxoacid dehydrogenase complexes) reflected at the protein level, or only in transcript abundance?
Experiment: Isoform-specific peptide quantification of the E3 bound to purified GDC versus PDC/OGDC/BCKDC from leaf and root mitochondria.
Hypothesis: mtLPD2 is enriched in the 2-oxoacid dehydrogenase complexes and in root mitochondria, while mtLPD1 dominates leaf GDC.
Type: quantitative proteomics
Experiment: Phenotype the mtlpd1 mtlpd2 combination (for example mtlpd1 knockdown in the mtlpd2 knockout) under ambient and high CO2.
Hypothesis: Combined loss impairs both photorespiration and TCA-cycle 2-oxoacid oxidation, showing redundancy between the two isoforms.
Type: genetic analysis
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