GDCH (UniProt gene name GDH1; At2g35370) encodes glycine cleavage system H protein 1, one of three Arabidopsis H proteins of the mitochondrial glycine decarboxylase complex (GDC; not to be confused with glutamate dehydrogenase). The small protein carries a lipoyl group covalently attached to a conserved lysine in its lipoyl-binding domain. It has no catalytic activity of its own: the lipoyl arm acts as a mobile carrier that accepts the aminomethyl group of glycine from the P protein, delivers it to the T protein (which releases NH3 and forms 5,10-methylene-tetrahydrofolate), and is then reoxidised by the L protein with formation of NADH. H protein is the most abundant GDC component; in Arabidopsis leaves the H1 (this gene) and H3 isoforms are present in about equal amounts and appear redundant. Expression is light-induced and highest in leaves, consistent with the central role of GDC in the photorespiratory C2 cycle, and GDC also supplies one-carbon units for metabolism. The precursor is imported into mitochondria, where its presequence is removed and the N terminus trimmed by ICP55. GDC activity is inhibited by S-nitrosylation and glutathionylation, which affect the H protein as well.
Definition: Binding a substrate or reaction intermediate via a covalently attached lipoyl (lipoamide) prosthetic group and delivering it between cognate enzymes, as the H protein of the glycine cleavage system does between the P, T and L proteins.
Justification: GO has GO:0140414 phosphopantetheine-dependent carrier activity for ACP-type carriers but no equivalent for lipoyl carriers. H proteins have no catalytic activity, so they currently receive either no MF, the generic GO:0140104 molecular carrier activity, or GO:0031405 lipoic acid binding, which describes cofactor attachment rather than the carrier function.
Parent term: molecular carrier activity
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005634 nucleus | HDA PMID:14617066 Analysis of the Arabidopsis nuclear proteome and its respons... | MARK AS OVER ANNOTATED | Summary: High-throughput proteomic detection of the H protein in a nuclear preparation. Reason: The H protein is a small, extremely abundant leaf mitochondrial matrix protein (about 20 H per GDC unit in Arabidopsis leaves) whose presequence is experimentally shown to be processed in mitochondria. A single bulk-proteomics detection in a nuclear fraction is best explained by carry-over, and no targeted study places GDCH there. The study validated nuclear localization only for six selected proteins, not for GDCH. 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:14617066 Nuclear proteins were isolated and analyzed using two-dimensional (2D) gel electrophoresis PMID:25862457 two glycine decarboxylase (GDC) H proteins (At2g35370 and At1g32470) |
| GO:0005739 mitochondrion | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference (PTN001711613, GcvH family) that the H protein is active in mitochondria. Reason: GDCH (At2g35370) carries a mitochondrial presequence that is processed in mitochondria (cleavage after Phe-34 observed by N-terminal proteomics, with a further ICP55 trimming step), and it functions in the glycine decarboxylase complex of the mitochondrial matrix. Mitochondrion is correct; the matrix sub-location is inferred from plant GDC biochemistry and is conveyed by the accepted glycine cleavage complex annotation, so the general term is kept. Supporting Evidence: PMID:25862457 two glycine decarboxylase (GDC) H proteins (At2g35370 and At1g32470) 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: GDCH (At2g35370) carries a mitochondrial presequence that is processed in mitochondria (cleavage after Phe-34 observed by N-terminal proteomics, with a further ICP55 trimming step), and it functions in the glycine decarboxylase complex of the mitochondrial matrix. Mitochondrion is correct; the matrix sub-location is inferred from plant GDC biochemistry and is conveyed by the accepted glycine cleavage complex annotation, so the general term is kept. Supporting Evidence: PMID:25862457 two glycine decarboxylase (GDC) H proteins (At2g35370 and At1g32470) 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 processed N-terminal presequence. Reason: GDCH (At2g35370) carries a mitochondrial presequence that is processed in mitochondria (cleavage after Phe-34 observed by N-terminal proteomics, with a further ICP55 trimming step), and it functions in the glycine decarboxylase complex of the mitochondrial matrix. Mitochondrion is correct; the matrix sub-location is inferred from plant GDC biochemistry and is conveyed by the accepted glycine cleavage complex annotation, so the general term is kept. Supporting Evidence: PMID:25862457 two glycine decarboxylase (GDC) H proteins (At2g35370 and At1g32470) PMID:11286922 In green leaves, this multienzyme system is present at tremendously high concentrations within the mitochondrial matrix. |
| GO:0005783 endoplasmic reticulum | HDA PMID:28887381 Global Analysis of Membrane-associated Protein Oligomerizati... | MARK AS OVER ANNOTATED | Summary: High-throughput proteomic detection of the H protein in a washed microsomal (membrane-associated) fraction assigned to endoplasmic reticulum preparation. Reason: The H protein is a small, extremely abundant leaf mitochondrial matrix protein (about 20 H per GDC unit in Arabidopsis leaves) whose presequence is experimentally shown to be processed in mitochondria. A single bulk-proteomics detection in a washed microsomal (membrane-associated) fraction assigned to endoplasmic reticulum fraction is best explained by carry-over, and no targeted study places GDCH there. The study itself notes that abundant soluble complexes contaminate the washed microsomes; GDCH has no signal peptide or 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:28887381 The uncapped proteasome is an abundant, predominantly cytosolic complex that is a likely contaminant in the washed microsomes. PMID:25862457 two glycine decarboxylase (GDC) H proteins (At2g35370 and At1g32470) |
| 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 the H protein in a crude leaf cytosolic (size-exclusion) fraction preparation. Reason: The H protein is a small, extremely abundant leaf mitochondrial matrix protein (about 20 H per GDC unit in Arabidopsis leaves) whose presequence is experimentally shown to be processed in mitochondria. A single bulk-proteomics detection in a crude leaf cytosolic (size-exclusion) fraction fraction is best explained by carry-over, and no targeted study places GDCH there. 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 PMID:25862457 two glycine decarboxylase (GDC) H proteins (At2g35370 and At1g32470) |
| GO:0005960 glycine cleavage complex | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference (PTN001711613) that the H protein is part of the glycine cleavage complex. Reason: Core. The H protein is one of the four obligatory components (P, H, T, L) of the glycine decarboxylase complex, and At2g35370 (GCS-H1) is one of the two H isoforms present in about equal amounts in Arabidopsis leaf GDC. The GcvH-family membership underlying the IBA/IEA is secure (HAMAP MF_00272, TIGR00527). Supporting Evidence: PMID:32311173 whereas the H-isoproteins GCS-H1 and GCS-H3 are fully redundant as indicated by their about equal amounts PMID:17496108 The presence of all four proteins is necessary for catalytic activity of the complex. PMID:22303256 H-protein is not an enzyme component of the complex but a cofactor that interacts with all three enzymes of the complex. |
| GO:0005960 glycine cleavage complex | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO (IPR002930 GCV_H, IPR017453 GCV_H_sub) mapping to glycine cleavage complex. Reason: Core. The H protein is one of the four obligatory components (P, H, T, L) of the glycine decarboxylase complex, and At2g35370 (GCS-H1) is one of the two H isoforms present in about equal amounts in Arabidopsis leaf GDC. The GcvH-family membership underlying the IBA/IEA is secure (HAMAP MF_00272, TIGR00527). Supporting Evidence: file:ARATH/GDCH/GDCH-uniprot.txt Belongs to the GcvH family. PMID:32311173 whereas the H-isoproteins GCS-H1 and GCS-H3 are fully redundant as indicated by their about equal amounts |
| GO:0009579 thylakoid | HDA PMID:11826309 Central functions of the lumenal and peripheral thylakoid pr... | MARK AS OVER ANNOTATED | Summary: High-throughput proteomic detection of the H protein in a soluble thylakoid (lumen) fraction preparation. Reason: The H protein is a small, extremely abundant leaf mitochondrial matrix protein (about 20 H per GDC unit in Arabidopsis leaves) whose presequence is experimentally shown to be processed in mitochondria. A single bulk-proteomics detection in a soluble thylakoid (lumen) fraction fraction is best explained by carry-over, and no targeted study places GDCH there. GDCH has no chloroplast transit peptide or lumen-targeting signal. 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:11826309 Soluble thylakoid proteins were separated by two-dimensional electrophoresis and identified by mass spectrometry. PMID:25862457 two glycine decarboxylase (GDC) H proteins (At2g35370 and At1g32470) |
| GO:0019464 glycine decarboxylation via glycine cleavage system | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference (PTN001711613) of glycine decarboxylation via glycine cleavage system. Reason: Core process. The H protein does part of the work of glycine cleavage: its covalently bound lipoyl arm accepts the aminomethyl group from the P protein, delivers it to the T protein, and is reoxidised by the L protein. It is a carrier/cofactor rather than an enzyme, but GO:0019464 is a process term and the H protein is an obligatory participant in it. Supporting Evidence: PMID:17496108 H protein carries no enzymatic activity but interacts as a mobile substrate via its lipoamide arm one after the other with P, T, and L protein PMID:22303256 The remaining amino methylene part of glycine is transferred to the distal sulphur atom of the oxidized lipoamide arm of H-protein file:ARATH/GDCH/GDCH-uniprot.txt The H protein shuttles the methylamine group of glycine from the P protein to the T protein. |
| GO:0019464 glycine decarboxylation via glycine cleavage system | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO (GCV_H signatures) mapping to glycine decarboxylation via glycine cleavage system. Reason: Core process. The H protein does part of the work of glycine cleavage: its covalently bound lipoyl arm accepts the aminomethyl group from the P protein, delivers it to the T protein, and is reoxidised by the L protein. It is a carrier/cofactor rather than an enzyme, but GO:0019464 is a process term and the H protein is an obligatory participant in it. Supporting Evidence: PMID:17496108 H protein carries no enzymatic activity but interacts as a mobile substrate via its lipoamide arm one after the other with P, T, and L protein file:ARATH/GDCH/GDCH-uniprot.txt Belongs to the GcvH family. |
| GO:0140104 molecular carrier activity | TAS PMID:22303256 Photorespiration. | NEW | Summary: The H protein has no catalytic activity; its covalently attached lipoyl arm carries the glycine-derived aminomethyl group (and then the reducing equivalents) between the P, T and L proteins of the glycine decarboxylase complex. Reason: GOA has no molecular-function annotation for GDCH. GO:0140104 (directly binding a molecule and delivering it to an acceptor; a carrier moves with its cargo) describes the swinging-arm role exactly and is the term PomBase uses for the S. pombe H protein gcv3 in its GO-CAM. No catalytic MF should be assigned, because the plant literature is explicit that the H protein is a cofactor/mobile substrate, not an enzyme. GO:0031405 lipoic acid binding (used in earlier human GCSH review and glycine-cleavage module versions) is not proposed: the lipoate is a covalently attached prosthetic group (N6-lipoyllysine), so binding describes cofactor attachment rather than the activity. A more specific lipoyl-dependent carrier term is proposed under proposed_new_terms. Evidence is from plant GDC biochemistry and family membership rather than an assay of At2g35370 itself; recorded as TAS from the Arabidopsis Book review. Supporting Evidence: PMID:22303256 H-protein is not an enzyme component of the complex but a cofactor that interacts with all three enzymes of the complex. PMID:17496108 H protein carries no enzymatic activity but interacts as a mobile substrate via its lipoamide arm one after the other with P, T, and L protein PMID:19860829 H-protein has no catalytic activity itself but is a substrate of the three enzymatically active subunits, P-, T- and L-protein. file:ARATH/GDCH/GDCH-uniprot.txt The H protein shuttles the methylamine group of glycine from the P protein to the T protein. file:ARATH/GDCH/GDCH-uniprot.txt Binds 1 lipoyl cofactor covalently. |
| GO:0009853 photorespiration | IC PMID:32311173 Stoichiometry of two plant glycine decarboxylase complexes a... | NEW | Summary: GCS-H1 (At2g35370) is one of the two H isoforms of the leaf glycine decarboxylase complex, which performs the mitochondrial glycine-to-CO2/NH3 step of the photorespiratory C2 cycle. Reason: Participation test: this is the cofactor case described in CLAUDE.md. The H protein does part of the work of the photorespiratory glycine decarboxylation step by carrying the reaction intermediate between the three GDC enzymes; it is not merely required for, or a substrate of, the process. Comparator check (QuickGO, Arabidopsis, GO:0009853): enzymes for other C2-cycle steps carry the term (SHM1, GLYK, HPR, GGAT1, PLGG1), but no GDC subunit does. Direct genetic evidence for At2g35370 itself is lacking (H1 and H3 are redundant in leaves, and the overexpression studies used a Flaveria H protein), so this rests on the protein's presence in the leaf complex and the established role of GDC. Not an ancestor or descendant of GO:0019464. Supporting Evidence: PMID:32311173 whereas the H-isoproteins GCS-H1 and GCS-H3 are fully redundant as indicated by their about equal amounts PMID:32311173 Photorespiring plant mitochondria contain very high levels of GCS proteins organised as a fragile glycine decarboxylase complex (GDC). PMID:22303256 The combined reaction of glycine decarboxylase (GLD) and serine hydroxymethyltransferase (SHM) represents the mitochondrial part of the major photorespiratory pathway. PMID:7480320 Glycine decarboxylase is a mitochondrial enzyme complex, which is the site of photorespiratory CO2 and NH3 release. |
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Download this section (compressed HTML)Q: Which molecular-function term should GO use for glycine cleavage H proteins: GO:0140104 molecular carrier activity (PomBase GO-CAM and glycine cleavage module), or a new lipoyl-dependent carrier term as also proposed by the human GCSH review? How should these activity terms be reconciled with GO:0031405 lipoic acid binding used for covalently lipoylated proteins in experimental GO annotations?
Q: Are GDCH (H1) and At1g32470 (H3) fully interchangeable in vivo, and does the root/non-photosynthetic one-carbon role of GDC rely on a particular H isoform?
Q: Does the Arabidopsis H protein, like human GCSH, also serve as a lipoyl donor for the E2 subunits of mitochondrial 2-oxoacid dehydrogenases?
Experiment: Generate gdch1 single and gdch1 h3 double mutants (e.g. CRISPR) and test growth in air versus high CO2, leaf glycine/serine ratios and GDC activity of isolated mitochondria.
Hypothesis: GDCH and the H3 isoform are redundant for photorespiratory GDC activity.
Type: genetics / metabolite profiling
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