Aminomethyltransferase (glycine cleavage system T-protein, EC 2.1.2.10) of Saccharomyces cerevisiae. Gcv1 is the T subunit of the mitochondrial glycine decarboxylase complex (P, H, T and L proteins: Gcv2, Gcv3, Gcv1 and Lpd1). It accepts the aminomethyl group carried on the lipoyl arm of the H-protein and transfers the methylene unit to tetrahydrofolate, releasing ammonia and forming 5,10-methylenetetrahydrofolate. Glycine cleavage lets yeast use glycine as sole nitrogen source and supplies mitochondrial one-carbon units; GCV1 expression is induced by glycine and responds to the cytoplasmic level of 5,10-methylenetetrahydrofolate.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004047 aminomethyltransferase activity | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA (PTN000354058) for aminomethyltransferase activity, the T-protein reaction (EC 2.1.2.10). Gcv1 is itself one of the experimentally grounded leaves, and a gcv1 disruption abolishes glycine cleavage activity. Reason: PAINT IBA (GO_REF:0000033) from node PTN000354058, whose experimental seeds include Gcv1 itself (SGD:S000002426) and the bacterial, plant and human T-proteins. Gcv1 is a GcvT-family T-protein, the single such protein in yeast, and its disruption abolishes glycine cleavage activity, so the inherited aminomethyltransferase function is sound. Gcv1's own appearance among the seeds marks experimental grounding on the target, not circularity. Supporting Evidence: PMID:9047339 We have isolated the gene encoding the glycine cleavage T-protein (GCV1) of the yeast Saccharomyces cerevisiae and shown through gene disruption and enzyme assays that inactivation of GCV1 destroys glycine cleavage function. file:yeast/GCV1/GCV1-uniprot.txt InterPro; IPR006223; GcvT. |
| GO:0004047 aminomethyltransferase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Combined IEA (InterPro IPR006223 GcvT, RHEA:16945, EC 2.1.2.10). Correct for Gcv1, which is the sole GcvT-family T-protein in yeast. Reason: UniProt combined-IEA row (GO_REF:0000120) from the GcvT signature IPR006223, RHEA:16945 and EC 2.1.2.10. The reaction (aminomethyl-lipoyl-H-protein + tetrahydrofolate to 5,10-methylenetetrahydrofolate + NH4+) matches the GO:0004047 definition and the T-protein role of Gcv1. Supporting Evidence: file:yeast/GCV1/GCV1-uniprot.txt Reaction=N(6)-[(R)-S(8)-aminomethyldihydrolipoyl]-L-lysyl-[protein] + (6S)-5,6,7,8-tetrahydrofolate = N(6)-[(R)-dihydrolipoyl]-L-lysyl- [protein] + (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + NH4(+); PMID:9047339 We have isolated the gene encoding the glycine cleavage T-protein (GCV1) of the yeast Saccharomyces cerevisiae and shown through gene disruption and enzyme assays that inactivation of GCV1 destroys glycine cleavage function. |
| GO:0004047 aminomethyltransferase activity | IMP PMID:9047339 Cloning, and molecular characterization of the GCV1 gene enc... | ACCEPT | Summary: McNeil et al. disrupted GCV1 and showed loss of glycine cleavage enzyme activity; the gene encodes the T-protein, so loss of the overall GCS activity supports the T-protein aminomethyltransferase function. Curator IMP accepted. Reason: SGD IMP from McNeil et al.: disruption of GCV1 abolished glycine cleavage enzyme activity. The assay measures the whole complex, so the row infers the T-protein step from loss of overall activity together with GcvT family membership; the curator read the full paper and the attribution is consistent with all other evidence. Supporting Evidence: PMID:9047339 We have isolated the gene encoding the glycine cleavage T-protein (GCV1) of the yeast Saccharomyces cerevisiae and shown through gene disruption and enzyme assays that inactivation of GCV1 destroys glycine cleavage function. PMID:9047339 All gcv1 strains studied were unable to grow on glycine as a sole nitrogen source and lacked glycine cleavage enzyme activity. |
| GO:0004047 aminomethyltransferase activity | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways RCA from the glycine cleavage pathway (GLYCLEAV-PWY), assigning Gcv1 to the aminomethyltransferase step (EC 2.1.2.10). Correct pathway assignment for this gene. Reason: SGD YeastPathways-to-GO-CAM conversion (GO_REF:0000123) of GLYCLEAV-PWY, which assigns the EC 2.1.2.10 step to Gcv1. The enzyme assignment is correct and agrees with the experimental and phylogenetic rows. Supporting Evidence: PMID:9047339 We have isolated the gene encoding the glycine cleavage T-protein (GCV1) of the yeast Saccharomyces cerevisiae and shown through gene disruption and enzyme assays that inactivation of GCV1 destroys glycine cleavage function. file:yeast/GCV1/GCV1-uniprot.txt Reaction=N(6)-[(R)-S(8)-aminomethyldihydrolipoyl]-L-lysyl-[protein] + (6S)-5,6,7,8-tetrahydrofolate = N(6)-[(R)-dihydrolipoyl]-L-lysyl- [protein] + (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + NH4(+); |
| GO:0005739 mitochondrion | HDA PMID:14562095 Global analysis of protein localization in budding yeast. | ACCEPT | Summary: Huh et al. genome-wide GFP localisation scored Gcv1 as mitochondrial, consistent with its N-terminal presequence. Reason: Genome-wide GFP-fusion localisation (SGD HDA). The assay resolves the organelle but not the sub-compartment, so the root organelle term is the appropriate, informative location; it agrees with the predicted mitochondrial transit peptide and with organelle proteomics. Supporting Evidence: PMID:14562095 Here we describe the construction and analysis of a collection of yeast strains expressing full-length, chromosomally tagged green fluorescent protein fusion proteins. file:yeast/GCV1/GCV1-uniprot.txt FT TRANSIT 1..? |
| GO:0005739 mitochondrion | HDA PMID:14576278 The proteome of Saccharomyces cerevisiae mitochondria. | ACCEPT | Summary: Gcv1 identified in the highly purified mitochondrial proteome (Sickmann et al.). Reason: Proteomics of highly purified mitochondria (SGD HDA). Whole-organelle proteomics cannot resolve the matrix, so the root term is as precise as this assay allows. Supporting Evidence: PMID:14576278 The proteins of highly pure yeast mitochondria were separated by several independent methods and analyzed by tandem MS. |
| GO:0005739 mitochondrion | HDA PMID:16823961 Toward the complete yeast mitochondrial proteome: multidimen... | ACCEPT | Summary: Gcv1 identified in the PROMITO mitochondrial proteome (Reinders et al.). Reason: PROMITO mitochondrial proteome (SGD HDA); independent organelle proteomics that agrees with the GFP and earlier proteomic data. The root organelle term is as precise as the assay allows. Supporting Evidence: PMID:16823961 A total of 851 different proteins (PROMITO dataset) were identified by use of multidimensional LC-MS/MS, 1D-SDS-PAGE combined with nano-LC-MS/MS and 2D-PAGE with subsequent MALDI-mass fingerprinting. |
| GO:0005739 mitochondrion | HDA PMID:24769239 Quantitative variations of the mitochondrial proteome and ph... | ACCEPT | Summary: Gcv1 quantified in the mitochondrial proteome under fermentative and respiratory growth (Renvoise et al.). Reason: Quantitative proteomics of isolated mitochondria (SGD HDA); a further independent organelle-proteome detection. The root organelle term is as precise as the assay allows. Supporting Evidence: PMID:24769239 we performed an overall quantitative proteomic and phosphoproteomic study of isolated mitochondria extracted from yeast grown on fermentative (glucose or galactose) and respiratory (lactate) media. |
| GO:0005739 mitochondrion | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA placing GcvT proteins in mitochondria; consistent with Gcv1 experimental localisation. Reason: PAINT IBA (GO_REF:0000033) from node PTN000354060, seeded by the Arabidopsis, human and other mitochondrial T-proteins. The eukaryotic T-proteins of this clade are mitochondrial, and Gcv1 carries a predicted transit peptide and is detected by GFP and organelle proteomics, so the inherited organelle claim holds. The row stops at the organelle because its seeds do; no cached assay resolves the matrix for Gcv1, so no sub-compartment is added. Supporting Evidence: PMID:14562095 Here we describe the construction and analysis of a collection of yeast strains expressing full-length, chromosomally tagged green fluorescent protein fusion proteins. PMID:14576278 The proteins of highly pure yeast mitochondria were separated by several independent methods and analyzed by tandem MS. file:yeast/GCV1/GCV1-uniprot.txt FT TRANSIT 1..? |
| GO:0005739 mitochondrion | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular-location mapping (SL-0173 Mitochondrion); correct for Gcv1. Reason: UniProt subcellular-location mapping (GO_REF:0000044, SL-0173 Mitochondrion). The underlying location rests on the predicted transit peptide and agrees with direct GFP and proteomic detection, so the organelle claim holds. Supporting Evidence: file:yeast/GCV1/GCV1-uniprot.txt FT TRANSIT 1..? PMID:14576278 The proteins of highly pure yeast mitochondria were separated by several independent methods and analyzed by tandem MS. |
| GO:0005739 mitochondrion | NAS PMID:8830251 Specific induction by glycine of the gene for the P-subunit ... | ACCEPT | Summary: Author statement in the GCV2 cloning paper that the GDC (including T-protein) is a mitochondrial complex. Weak evidence type but correct; superseded by HDA/IBA evidence. Reason: ComplexPortal NAS citing the GCV2 cloning paper, which describes the four-subunit glycine decarboxylase complex. The mitochondrial location of the complex is an author-level statement; it is correct and is independently established by the HDA rows. Supporting Evidence: PMID:8830251 The glycine decarboxylase complex (GDC) is composed of four subunits referred to as H-, L-, P-, and T-proteins. PMID:14576278 The proteins of highly pure yeast mitochondria were separated by several independent methods and analyzed by tandem MS. |
| GO:0005829 cytosol | RCA GO_REF:0000123 | REMOVE | Summary: YeastPathways RCA (GLYCLEAV-PWY) asserts activity in the cytosol, which is the default compartment used by the YeastPathways-to-GO-CAM conversion. The glycine cleavage system of S. cerevisiae is mitochondrial; Gcv1 carries a mitochondrial presequence and is found in purified mitochondria. There is no evidence for a cytosolic glycine cleavage activity. Reason: SGD YeastPathways-to-GO-CAM conversion (GO_REF:0000123) placed the GLYCLEAV-PWY activity in the cytosol. Gcv1 has a mitochondrial transit peptide and is found by GFP and in purified mitochondria, and the yeast glycine cleavage system is a mitochondrial complex; no cytosolic glycine cleavage activity has been reported. The compartment is wrong for this enzyme. Supporting Evidence: file:yeast/GCV1/GCV1-uniprot.txt FT TRANSIT 1..? PMID:14562095 Here we describe the construction and analysis of a collection of yeast strains expressing full-length, chromosomally tagged green fluorescent protein fusion proteins. PMID:14576278 The proteins of highly pure yeast mitochondria were separated by several independent methods and analyzed by tandem MS. |
| GO:0005960 glycine cleavage complex | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO (IPR006223, GcvT) mapping to glycine cleavage complex; correct for the yeast T-protein. Reason: InterPro2GO (GO_REF:0000002) mapping from the GcvT signature IPR006223. The GcvT family is the T-protein of the glycine cleavage complex, and Gcv1 is the yeast T-protein, so complex membership is correct. Supporting Evidence: file:yeast/GCV1/GCV1-uniprot.txt InterPro; IPR006223; GcvT. file:yeast/GCV1/GCV1-uniprot.txt SUBUNIT: Component of the glycine decarboxylase complex (GDC), which is composed of four proteins: P, T, L and H. PMID:8830251 The glycine decarboxylase complex (GDC) is composed of four subunits referred to as H-, L-, P-, and T-proteins. |
| GO:0005960 glycine cleavage complex | IMP PMID:9047339 Cloning, and molecular characterization of the GCV1 gene enc... | ACCEPT | Summary: gcv1 disruption abolishes GCS activity; Gcv1 is the T-protein subunit of the four-protein complex. Reason: SGD IMP from McNeil et al.; GCV1 encodes the T-protein and its loss abolishes glycine cleavage activity. Loss-of-function does not by itself show complex membership, but the T-protein is by definition a GCS component and the curator's attribution is consistent with all other evidence. Supporting Evidence: PMID:9047339 We have isolated the gene encoding the glycine cleavage T-protein (GCV1) of the yeast Saccharomyces cerevisiae and shown through gene disruption and enzyme assays that inactivation of GCV1 destroys glycine cleavage function. PMID:8830251 The glycine decarboxylase complex (GDC) is composed of four subunits referred to as H-, L-, P-, and T-proteins. |
| GO:0005960 glycine cleavage complex | NAS PMID:7498764 Genetics of the synthesis of serine from glycine and the uti... | ACCEPT | Summary: Sinclair & Dawes describe the yeast GDC; Gcv1 as T-protein is a component. NAS but correct. Reason: ComplexPortal NAS citing Sinclair and Dawes on the yeast glycine decarboxylase multienzyme complex. An author statement rather than an assay on Gcv1, but correct: Gcv1 is the T subunit. Supporting Evidence: PMID:7498764 Saccharomyces cerevisiae can grow on glycine as sole nitrogen source and can convert glycine to serine via the reaction catalyzed by the glycine decarboxylase multienzyme complex (GDC). PMID:8830251 The glycine decarboxylase complex (GDC) is composed of four subunits referred to as H-, L-, P-, and T-proteins. |
| GO:0006546 glycine catabolic process | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO glycine catabolic process for the GcvT family; correct parent of glycine cleavage. Reason: InterPro2GO (GO_REF:0000002) mapping from IPR006223. Glycine catabolism is correct but general: Gcv1 acts specifically in glycine decarboxylation via the glycine cleavage system, GO:0019464, an is_a descendant of GO:0006546 that the gene already carries (IBA, RCA). Proposed replacements: glycine decarboxylation via glycine cleavage system Supporting Evidence: PMID:9047339 All gcv1 strains studied were unable to grow on glycine as a sole nitrogen source and lacked glycine cleavage enzyme activity. |
| GO:0006546 glycine catabolic process | IMP PMID:9047339 Cloning, and molecular characterization of the GCV1 gene enc... | MODIFY | Summary: gcv1 mutants cannot use glycine as sole nitrogen source and lack glycine cleavage activity. Reason: SGD IMP: gcv1 mutants cannot use glycine as sole nitrogen source and lack glycine cleavage activity. The claim is sound, but the supported process is the specific glycine cleavage pathway, GO:0019464, an is_a descendant of GO:0006546 already carried by the gene. Proposed replacements: glycine decarboxylation via glycine cleavage system Supporting Evidence: PMID:9047339 All gcv1 strains studied were unable to grow on glycine as a sole nitrogen source and lacked glycine cleavage enzyme activity. |
| GO:0006546 glycine catabolic process | NAS PMID:7498764 Genetics of the synthesis of serine from glycine and the uti... | MODIFY | Summary: NAS from Sinclair & Dawes on yeast GDC; Gcv1 is part of the glycine catabolic complex. Reason: ComplexPortal NAS on the yeast glycine decarboxylase complex. Correct but general; the process the complex carries out is GO:0019464 glycine decarboxylation via glycine cleavage system, an is_a descendant of GO:0006546 already on the gene. Proposed replacements: glycine decarboxylation via glycine cleavage system Supporting Evidence: PMID:7498764 Saccharomyces cerevisiae can grow on glycine as sole nitrogen source and can convert glycine to serine via the reaction catalyzed by the glycine decarboxylase multienzyme complex (GDC). |
| GO:0006730 one-carbon metabolic process | IGI PMID:10871621 Regulation of the balance of one-carbon metabolism in Saccha... | ACCEPT | Summary: Piper et al. show that the GCV genes are regulated by the cytoplasmic 5,10-CH2-THF level and that GCS supplies mitochondrial one-carbon units. Gcv1 directly produces 5,10-methylene-THF, so one-carbon metabolism is correct, if broad (genetic interaction with SHM2, SGD:S000004048). Reason: SGD IGI (with SHM2, SGD:S000004048) from Piper et al., who show that glycine cleavage is a source of mitochondrial one-carbon units whose balance with cytoplasmic SHMT-derived units is regulated. Gcv1 itself forms 5,10-methylenetetrahydrofolate, so it does the work of this process. GO:0019464 is not a descendant of GO:0006730, so this term adds a distinct, correct claim. Supporting Evidence: PMID:10871621 This control governs the level of 5,10-methylene tetrahydrofolate (5,10-CH(2)-H(4)folate) in the cytoplasm, which has a direct role in signaling transcriptional control of the expression of key genes, particularly those encoding the unique components of the glycine decarboxylase complex (GCV1, GCV2, and GCV3). PMID:10871621 We also propose that under normal conditions, cytoplasmic 5,10-CH(2)-H(4)folate is mainly directed to generating methyl groups via methionine, whereas one-carbon units generated from glycine in mitochondria are more directed to purine biosynthesis. |
| GO:0006730 one-carbon metabolic process | IMP PMID:10871621 Regulation of the balance of one-carbon metabolism in Saccha... | ACCEPT | Summary: IMP from Piper et al.; Gcv1 is the GCS subunit that transfers the methylene unit to THF, a core one-carbon-generating reaction. Reason: SGD IMP from the same study; Gcv1 is the GCS subunit that transfers the methylene unit to tetrahydrofolate, generating one-carbon units in mitochondria. Supporting Evidence: PMID:10871621 We also propose that under normal conditions, cytoplasmic 5,10-CH(2)-H(4)folate is mainly directed to generating methyl groups via methionine, whereas one-carbon units generated from glycine in mitochondria are more directed to purine biosynthesis. file:yeast/GCV1/GCV1-uniprot.txt Reaction=N(6)-[(R)-S(8)-aminomethyldihydrolipoyl]-L-lysyl-[protein] + (6S)-5,6,7,8-tetrahydrofolate = N(6)-[(R)-dihydrolipoyl]-L-lysyl- [protein] + (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + NH4(+); |
| GO:0019464 glycine decarboxylation via glycine cleavage system | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA for glycine decarboxylation via glycine cleavage system; Gcv1 performs the THF-dependent release of the methylene group in this process. Reason: PAINT IBA (GO_REF:0000033) from node PTN000354060, seeded by the human and other T-proteins. Gcv1 is inside the mitochondrial T-protein clade and its disruption abolishes glycine cleavage, so the inherited process is sound and is the specific glycine-catabolic pathway the T-protein catalyses a step of. Supporting Evidence: PMID:9047339 We have isolated the gene encoding the glycine cleavage T-protein (GCV1) of the yeast Saccharomyces cerevisiae and shown through gene disruption and enzyme assays that inactivation of GCV1 destroys glycine cleavage function. PMID:9047339 All gcv1 strains studied were unable to grow on glycine as a sole nitrogen source and lacked glycine cleavage enzyme activity. |
| GO:0019464 glycine decarboxylation via glycine cleavage system | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways RCA (GLYCLEAV-PWY); correct process for the T-protein. Reason: SGD YeastPathways-to-GO-CAM conversion (GO_REF:0000123) of GLYCLEAV-PWY; correct process for the T-protein, matching the experimental and phylogenetic evidence. Supporting Evidence: PMID:9047339 We have isolated the gene encoding the glycine cleavage T-protein (GCV1) of the yeast Saccharomyces cerevisiae and shown through gene disruption and enzyme assays that inactivation of GCV1 destroys glycine cleavage function. |
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Download this section (compressed HTML)Q: How is the flux of glycine-derived one-carbon units from mitochondria (via GCS) partitioned between mitochondrial formate production and direct use, and does Gcv1 abundance limit it?
Experiment: Measure aminomethyltransferase activity of purified Gcv1 with lipoylated aminomethyl-Gcv3 and tetrahydrofolate, and determine its sub-mitochondrial (matrix) localisation by protease protection of isolated mitochondria.
T subunit of the mitochondrial glycine decarboxylase complex; glycine decarboxylase is required for the catabolism of glycine to 5,10-methylene-THF; expression is regulated by levels of levels of 5,10-methylene-THF in the cytoplasm
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