GLDP2 (At2g26080) encodes the second Arabidopsis P protein (glycine dehydrogenase (decarboxylating), EC 1.4.4.2) of the mitochondrial glycine decarboxylase complex (GDC, glycine cleavage system). Like its 91%-identical paralog GLDP1, it is a PLP-dependent enzyme that decarboxylates glycine and transfers the aminomethyl group to the lipoyl arm of the H protein, the first step of the GDC reaction that, with the T and L proteins, converts glycine to 5,10-methylene-tetrahydrofolate, CO2, NH3 and NADH in the mitochondrial matrix. GLDP2 is the minor leaf isoform (about one quarter of GLDP1 in the leaf complex), has weaker catalytic activity than GLDP1 and is relatively more expressed in roots. It is redundant with GLDP1 for photorespiration and one-carbon metabolism: single mutants are near wild type, while loss of both P proteins is seedling lethal even under non-photorespiratory conditions. GLDP2 can form heterodimers with GLDP1 and is selectively degraded via the F-box protein InLYP1.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003729 mRNA binding | IDA PMID:32344669 Discovering the RNA-Binding Proteome of Plant Leaves with an... | MARK AS OVER ANNOTATED | Summary: Leaf RNA interactome capture (ptRIC) recovered glycine dehydrogenase among UV-crosslinked poly(A) RNA-associated proteins. Reason: The paper reports the protein only as one of several metabolic enzymes newly captured in the leaf RBPome, with no follow-up validation, no mapped RNA-binding region and no defined mRNA target. The P protein is a mitochondrial matrix enzyme, and the observation does not establish a biological mRNA-binding function. The detection may be real but is not informative about gene function, so the annotation is kept but flagged as an over-interpretation of a screen. Supporting Evidence: PMID:32344669 Additional moonlighting enzymes were identified in the leaf RBPome, such as COBALAMIN-INDEPENDENT METHIONINE SYNTHASE, (S)-2-HYDROXY-ACID OXIDASE, GLYCINE DEHYDROGENASE and GLUTAMATE-GLYOXYLATE AMINOTRANSFERASE, which, to our knowledge, have not previously been linked to RNA biology |
| GO:0004375 glycine dehydrogenase (decarboxylating) activity | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference from node PTN000206531 (GcvP family) of glycine dehydrogenase (decarboxylating) activity for GLDP2. Reason: GLDP2 (At2g26080) is one of the two Arabidopsis P proteins of the glycine decarboxylase complex, the PLP-dependent enzyme that decarboxylates glycine and transfers the aminomethyl group to the lipoyl arm of the H protein (RHEA:24304, EC 1.4.4.2). It belongs to the GcvP family, and catalytic activity of both Arabidopsis GLDP isoforms is reported (GLDP2 weaker than GLDP1). This is the core molecular function. The IBA node placement is sound: the plant P proteins sit within the eukaryotic mitochondrial GcvP clade and retain the PLP-lysine. Supporting Evidence: PMID:22303256 P-protein (EC 1.4.4.2) is a pyridoxal-5-phosphate-containing homodimer, that catalyzes the actual glycine decarboxylation reaction file:ARATH/GLDP2/GLDP2-uniprot.txt CO(2) is released and the remaining methylamine moiety is then transferred to the lipoamide cofactor of the H protein file:ARATH/GLDP2/GLDP2-uniprot.txt Belongs to the GcvP family. PMID:33506579 GLDP2, a paralog of GLDP1 with weaker catalytic activity |
| GO:0004375 glycine dehydrogenase (decarboxylating) activity | IEA GO_REF:0000120 | ACCEPT | Summary: Combined IEA (InterPro GcvP signatures, RHEA:24304, EC 1.4.4.2) for glycine dehydrogenase (decarboxylating) activity. Reason: GLDP2 (At2g26080) is one of the two Arabidopsis P proteins of the glycine decarboxylase complex, the PLP-dependent enzyme that decarboxylates glycine and transfers the aminomethyl group to the lipoyl arm of the H protein (RHEA:24304, EC 1.4.4.2). It belongs to the GcvP family, and catalytic activity of both Arabidopsis GLDP isoforms is reported (GLDP2 weaker than GLDP1). This is the core molecular function. Supporting Evidence: PMID:22303256 P-protein (EC 1.4.4.2) is a pyridoxal-5-phosphate-containing homodimer, that catalyzes the actual glycine decarboxylation reaction file:ARATH/GLDP2/GLDP2-uniprot.txt CO(2) is released and the remaining methylamine moiety is then transferred to the lipoamide cofactor of the H protein PMID:33506579 GLDP2, a paralog of GLDP1 with weaker catalytic activity |
| GO:0005524 ATP binding | HDA PMID:17137349 Analysis of the soluble ATP-binding proteome of plant mitoch... | MARK AS OVER ANNOTATED | Summary: Captured from the soluble mitochondrial matrix proteome on immobilized ATP. Reason: Abstract-only cache. ATP-affinity capture enriches direct binders but also abundant matrix proteins and partners; the GcvP family has no recognised nucleotide-binding domain, uses PLP rather than ATP, and no ATP-dependent property of GLDP2 has been described. The annotation is not supported as a function of GLDP2. Supporting Evidence: PMID:17137349 A range of highly enriched proteins were identified from the mitochondrial proteome, including 14-3-3 proteins and RNA binding proteins |
| GO:0005739 mitochondrion | HDA PMID:14671022 Experimental analysis of the Arabidopsis mitochondrial prote... | ACCEPT | Summary: Identified in the LC-MS/MS proteome of isolated Arabidopsis mitochondria; this study is the experimental basis of the UniProt mitochondrial location. Reason: The P protein carries a mitochondrial transit peptide and functions in the glycine decarboxylase complex of the mitochondrial matrix; UniProt records an experimental mitochondrial location for GLDP2. Mitochondrion is the compartment established for the Arabidopsis protein itself; the matrix sub-location is inferred from plant GDC biochemistry (largely pea), and the complex-level annotation conveys it, so the general term is kept as the core location. Supporting Evidence: file:ARATH/GLDP2/GLDP2-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:14671022} PMID:11286922 In green leaves, this multienzyme system is present at tremendously high concentrations within the mitochondrial matrix. |
| GO:0005739 mitochondrion | HDA PMID:17137349 Analysis of the soluble ATP-binding proteome of plant mitoch... | ACCEPT | Summary: Identified in the soluble ATP-binding proteome of isolated plant mitochondria (matrix). Reason: The P protein carries a mitochondrial transit peptide and functions in the glycine decarboxylase complex of the mitochondrial matrix; UniProt records an experimental mitochondrial location for GLDP2. Mitochondrion is the compartment established for the Arabidopsis protein itself; the matrix sub-location is inferred from plant GDC biochemistry (largely pea), and the complex-level annotation conveys it, so the general term is kept as the core location. Supporting Evidence: file:ARATH/GLDP2/GLDP2-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:14671022} PMID:11286922 In green leaves, this multienzyme system is present at tremendously high concentrations within the mitochondrial matrix. |
| GO:0005739 mitochondrion | HDA PMID:18385124 Heterogeneity of the mitochondrial proteome for photosynthet... | ACCEPT | Summary: Quantified in the mitochondrial proteome of photosynthetic shoots versus cell culture; the photorespiratory apparatus was elevated in shoot mitochondria. Reason: The P protein carries a mitochondrial transit peptide and functions in the glycine decarboxylase complex of the mitochondrial matrix; UniProt records an experimental mitochondrial location for GLDP2. Mitochondrion is the compartment established for the Arabidopsis protein itself; the matrix sub-location is inferred from plant GDC biochemistry (largely pea), and the complex-level annotation conveys it, so the general term is kept as the core location. Supporting Evidence: PMID:18385124 showed the elevated level of the photorespiratory apparatus file:ARATH/GLDP2/GLDP2-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:14671022} PMID:11286922 In green leaves, this multienzyme system is present at tremendously high concentrations within the mitochondrial matrix. |
| GO:0005739 mitochondrion | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference (PTN000206533) that the P protein is active in mitochondria. Reason: The P protein carries a mitochondrial transit peptide and functions in the glycine decarboxylase complex of the mitochondrial matrix; UniProt records an experimental mitochondrial location for GLDP2. Mitochondrion is the compartment established for the Arabidopsis protein itself; the matrix sub-location is inferred from plant GDC biochemistry (largely pea), and the complex-level annotation conveys it, so the general term is kept as the core location. Supporting Evidence: PMID:25862457 Gly decarboxylase P-protein2 (At2g26080 and At4g33010 file:ARATH/GLDP2/GLDP2-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:14671022} PMID:11286922 In green leaves, this multienzyme system is present at tremendously high concentrations within the mitochondrial matrix. |
| GO:0005739 mitochondrion | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular-location mapping (SL-0173 Mitochondrion). Reason: The P protein carries a mitochondrial transit peptide and functions in the glycine decarboxylase complex of the mitochondrial matrix; UniProt records an experimental mitochondrial location for GLDP2. Mitochondrion is the compartment established for the Arabidopsis protein itself; the matrix sub-location is inferred from plant GDC biochemistry (largely pea), and the complex-level annotation conveys it, so the general term is kept as the core location. Supporting Evidence: file:ARATH/GLDP2/GLDP2-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:14671022} PMID:11286922 In green leaves, this multienzyme system is present at tremendously high concentrations within the mitochondrial matrix. |
| GO:0005739 mitochondrion | ISM GO_REF:0000122 | ACCEPT | Summary: AtSubP sequence-based prediction of mitochondrial targeting, consistent with the N-terminal transit peptide. Reason: The P protein carries a mitochondrial transit peptide and functions in the glycine decarboxylase complex of the mitochondrial matrix; UniProt records an experimental mitochondrial location for GLDP2. Mitochondrion is the compartment established for the Arabidopsis protein itself; the matrix sub-location is inferred from plant GDC biochemistry (largely pea), and the complex-level annotation conveys it, so the general term is kept as the core location. Supporting Evidence: file:ARATH/GLDP2/GLDP2-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:14671022} PMID:11286922 In green leaves, this multienzyme system is present at tremendously high concentrations within the mitochondrial matrix. |
| GO:0005773 vacuole | HDA PMID:28887381 Global Analysis of Membrane-associated Protein Oligomerizati... | MARK AS OVER ANNOTATED | Summary: High-throughput proteomic detection of GLDP2 in a washed microsomal (membrane-associated) fraction assigned to vacuole preparation. Reason: GLDP2 is an abundant mitochondrial matrix enzyme with a mitochondrial transit peptide and an experimentally established mitochondrial location. A single bulk-proteomics detection in a washed microsomal (membrane-associated) fraction assigned to vacuole fraction is best explained by carry-over of this very abundant leaf protein, and no targeted study places the P protein in this compartment. The study itself notes that abundant soluble complexes contaminate the washed microsomes. Under the ARATH corpus convention (projects/ARATH/organelle-audit.md, rule 3) a high-throughput proteomics hit for a protein localized elsewhere is marked as over-annotated rather than removed: the detection is a real observation, most likely contamination, but no targeted experiment excludes the compartment. Supporting Evidence: PMID:28887381 The uncapped proteasome is an abundant, predominantly cytosolic complex that is a likely contaminant in the washed microsomes. file:ARATH/GLDP2/GLDP2-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:14671022} |
| GO:0005829 cytosol | HDA PMID:25293756 A proteomic strategy for global analysis of plant protein co... | MARK AS OVER ANNOTATED | Summary: High-throughput proteomic detection of GLDP2 in a crude leaf cytosolic (size-exclusion) fraction preparation. Reason: GLDP2 is an abundant mitochondrial matrix enzyme with a mitochondrial transit peptide and an experimentally established mitochondrial location. A single bulk-proteomics detection in a crude leaf cytosolic (size-exclusion) fraction fraction is best explained by carry-over of this very abundant leaf protein, and no targeted study places the P protein in this compartment. The crude cytosolic fraction is not depleted of broken-organelle matrix proteins. Under the ARATH corpus convention (projects/ARATH/organelle-audit.md, rule 3) a high-throughput proteomics hit for a protein localized elsewhere is marked as over-annotated rather than removed: the detection is a real observation, most likely contamination, but no targeted experiment excludes the compartment. Supporting Evidence: PMID:25293756 Applying this approach to the crude cytosolic fraction of Arabidopsis thaliana leaves using size exclusion chromatography file:ARATH/GLDP2/GLDP2-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:14671022} |
| GO:0006544 glycine metabolic process | IEA GO_REF:0000002 | TOO GENERAL | Summary: InterPro2GO (IPR003437 GcvP) mapping to glycine metabolic process. Reason: True but uninformative: glycine decarboxylation via glycine cleavage system (GO:0019464) and glycine catabolic process (GO:0006546), both accepted in this review, already entail it. Supporting Evidence: PMID:17496108 The mitochondrial multienzyme glycine decarboxylase (GDC) catalyzes the tetrahydrofolate-dependent catabolism of glycine |
| GO:0006546 glycine catabolic process | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO (GcvP signature) mapping to glycine catabolic process. Reason: The P protein catalyses the first step of glycine catabolism by the glycine cleavage system. The more specific GO:0019464 is also accepted; this broader process term is still informative and consistent with the genetic evidence. Supporting Evidence: PMID:17496108 The mitochondrial multienzyme glycine decarboxylase (GDC) catalyzes the tetrahydrofolate-dependent catabolism of glycine PMID:22303256 P-protein (EC 1.4.4.2) is a pyridoxal-5-phosphate-containing homodimer, that catalyzes the actual glycine decarboxylation reaction |
| GO:0009507 chloroplast | HDA PMID:18431481 Sorting signals, N-terminal modifications and abundance of t... | MARK AS OVER ANNOTATED | Summary: High-throughput proteomic detection of GLDP2 in a chloroplast stroma preparation. Reason: GLDP2 is an abundant mitochondrial matrix enzyme with a mitochondrial transit peptide and an experimentally established mitochondrial location. A single bulk-proteomics detection in a chloroplast stroma fraction is best explained by carry-over of this very abundant leaf protein, and no targeted study places the P protein in this compartment. The authors themselves estimate hundreds of false positives or non-chloroplast contaminants in the unfiltered chloroplast data set. Under the ARATH corpus convention (projects/ARATH/organelle-audit.md, rule 3) a high-throughput proteomics hit for a protein localized elsewhere is marked as over-annotated rather than removed: the detection is a real observation, most likely contamination, but no targeted experiment excludes the compartment. Supporting Evidence: PMID:18431481 proteins likely represent false positive identifications and/or non-chloroplast contaminations file:ARATH/GLDP2/GLDP2-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:14671022} |
| GO:0009941 chloroplast envelope | HDA PMID:12938931 Proteomic study of the Arabidopsis thaliana chloroplastic en... | MARK AS OVER ANNOTATED | Summary: High-throughput proteomic detection of GLDP2 in a chloroplast envelope membrane preparation. Reason: GLDP2 is an abundant mitochondrial matrix enzyme with a mitochondrial transit peptide and an experimentally established mitochondrial location. A single bulk-proteomics detection in a chloroplast envelope membrane fraction is best explained by carry-over of this very abundant leaf protein, and no targeted study places the P protein in this compartment. The P protein is a soluble matrix protein with no membrane anchor. Under the ARATH corpus convention (projects/ARATH/organelle-audit.md, rule 3) a high-throughput proteomics hit for a protein localized elsewhere is marked as over-annotated rather than removed: the detection is a real observation, most likely contamination, but no targeted experiment excludes the compartment. Supporting Evidence: PMID:12938931 membrane proteins localized to the Arabidopsis thaliana chloroplastic envelope membrane file:ARATH/GLDP2/GLDP2-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:14671022} |
| GO:0019464 glycine decarboxylation via glycine cleavage system | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference (PTN000206531) of glycine decarboxylation via glycine cleavage system. Reason: Core process. GLDP2 is the glycine-decarboxylating subunit of the Arabidopsis glycine decarboxylase complex; loss of both P-protein genes abolishes GDC and is lethal even under non-photorespiratory conditions. Supporting Evidence: PMID:17496108 The mitochondrial multienzyme glycine decarboxylase (GDC) catalyzes the tetrahydrofolate-dependent catabolism of glycine PMID:17496108 The presence of all four proteins is necessary for catalytic activity of the complex. PMID:17496108 the double mutant does not develop beyond the cotyledon stage PMID:17496108 The corresponding P proteins, AtGLDP1 and AtGLDP2, can more or less fully substitute each other under standard growth conditions. |
| 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 P-protein isoforms (GCS-P1 = GLDP1, GCS-P2 = GLDP2) as components of the complex. Reason: GLDP2 has no cellular-component annotation to the glycine cleavage complex in GOA, although its paralogous H protein (GDCH) does. The P protein is a defining subunit of the P/H/T/L complex, all four proteins are required for activity, and the Arabidopsis leaf GDC contains GLDP1 and GLDP2 in a 4:1 ratio. Abstract-only cache, but the abstract states the measurement directly. 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:17496108 The presence of all four proteins is necessary for catalytic activity of the complex. |
| GO:0009853 photorespiration | IGI PMID:17496108 Deletion of glycine decarboxylase in Arabidopsis is lethal u... | NEW | Summary: GLDP2 is the minor P protein of the leaf GDC; it substitutes for GLDP1 in gldp1 mutants, and the gldp1 gldp2 double mutant lacks GDC entirely. Reason: Participation test: GLDP2 catalyses a step of the photorespiratory C2 cycle (mitochondrial glycine decarboxylation), so it does part of the work of the process rather than being required for or consumed by it. Comparator check (QuickGO, Arabidopsis, GO:0009853): enzymes catalysing other C2-cycle steps carry the term (SHM1 IMP, GLYK IMP/IBA, HPR TAS, GGAT1 TAS, PLGG1 IMP), whereas none of the GDC subunits (GLDP1, GLDP2, GDCH, GDCST) do; this absence looks like a gap rather than a convention. The term is not an ancestor or descendant of GO:0019464. Supporting Evidence: PMID:22303256 The combined reaction of glycine decarboxylase (GLD) and serine hydroxymethyltransferase (SHM) represents the mitochondrial part of the major photorespiratory pathway. PMID:17496108 The corresponding P proteins, AtGLDP1 and AtGLDP2, can more or less fully substitute each other under standard growth conditions. 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 |
Loading supporting content…
Download this section (compressed HTML)Q: Do GLDP1 and GLDP2 differ in kinetic properties or regulation (e.g. InLYP1-dependent turnover of GLDP2, redox modification) in ways that matter for non-photosynthetic one-carbon metabolism in roots, where GLDP2 transcripts dominate?
Q: Should the GDC subunits (P, H, T, L) be annotated to GO:0009853 photorespiration in Arabidopsis, as other C2-cycle enzymes are, or is GO:0019464 considered sufficient by TAIR curators?
Experiment: Purify recombinant GLDP1, GLDP2 and co-expressed heterodimers and measure H-protein-dependent glycine decarboxylation kinetics.
Hypothesis: GLDP1 and GLDP2 homo- and heterodimers differ in glycine decarboxylase activity and in their interaction with the H protein.
Type: enzyme kinetics
Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)