Glyceraldehyde-3-phosphate dehydrogenase 3 (Tdh3, YGR192C) is one of three paralogous NAD+-dependent phosphorylating glyceraldehyde-3-phosphate dehydrogenases (GAPDH, EC 1.2.1.12; TDH1, TDH2, TDH3) of Saccharomyces cerevisiae. These homotetrameric enzymes catalyse the reversible oxidative phosphorylation of D-glyceraldehyde 3-phosphate to 1,3-bisphosphoglycerate with reduction of NAD+ to NADH, the sixth step of glycolysis and an obligatory step of gluconeogenesis. Tdh3 is the dominant isoform, supplying about 50-60% of cellular GAPDH activity although its homotetramer has a 2-3-fold lower apparent Vmax than Tdh2, and it is a highly abundant cytosolic protein. Besides its cytosolic glycolytic role, Tdh3 has experimentally supported moonlighting activities: it binds RNA (including mitochondrial mRNAs and FAS1 mRNA), buffers and allocates labile cytosolic heme to the heme-dependent transcription factor Hap1, and is S-nitrosated during oxidative stress-induced cell death. Tdh3 is also detected in the cell wall, nucleus and in association with mitochondria.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003723 RNA binding | IDA PMID:25288528 Structural insights into RNA recognition properties of glyce... | KEEP AS NON CORE | Summary: Shen et al. solved the Tdh3 crystal structure and characterised its RNA-binding specificity biochemically, supporting moonlighting RNA binding by GAPDH (as for mammalian GAPDH and AU-rich elements). Reason: Experimentally supported moonlighting activity; secondary to glycolytic function. Supporting Evidence: PMID:25288528 Here, we present the first crystal structure of GAPDH3 from Saccharomyces cerevisiae and identify its RNA-binding specificity |
| GO:0003729 mRNA binding | IDA PMID:18959479 Diverse RNA-binding proteins interact with functionally rela... | KEEP AS NON CORE | Summary: Hogan et al. RIP-chip of TAP-tagged Tdh3 identified 155 associated RNAs (1% FDR), including mitochondrial mRNAs, establishing Tdh3 as a non-canonical RBP in yeast. Reason: Moonlighting mRNA binding; non-core. Supporting Evidence: PMID:18959479 Aconitase (Aco1) and glyceraldehyde-3 phosphate dehydrogenase (Tdh3), two metabolic enzymes whose human orthologs also function as RBPs [46,47], but which were not previously known to be RBPs in yeast, associated with 38 and 155 RNAs, respectively, at 1% FDR |
| GO:0003729 mRNA binding | IDA PMID:37792491 Targeting APEX2 to the mRNA encoding fatty acid synthase Ξ² i... | KEEP AS NON CORE | Summary: Using APEX2 targeted to FAS1 mRNA, Blank/Polymenis and colleagues identified Tdh3 as a FAS1 mRNA-binding protein (preferentially late in the cell cycle) required for cell-cycle-dependent changes in Fas1 levels. Reason: Moonlighting mRNA binding; non-core. Supporting Evidence: PMID:37792491 Lastly, while Tdh3p interacted with the FAS1 mRNA preferentially late in the cell cycle, all other proteins did so in the G1 phase (Figure 3E). PMID:37792491 Our results highlight the role of a key glycolytic enzyme (Tdh3p) through its moonlighting RNA-binding properties in the expression of another enzyme (Fas1p) involved in fatty acid biosynthesis. |
| GO:0004365 glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA from GAPDH node PTN000089475, seeded by the three yeast TDH paralogs among other experimentally characterised GAPDHs. TDH3 is an active NAD-dependent phosphorylating GAPDH, so the inherited activity is correct; TDH3 appearing among the donors reflects its own experimental grounding. Supporting Evidence: file:yeast/TDH3/TDH3-uniprot.txt Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) involved in PMID:3905788 The contribution of the TDH1, TDH2, and TDH3 gene products to the total glyceraldehyde-3-phosphate dehydrogenase activity in wild type cells is 10-15, 25-30, and 50-60%, respectively |
| GO:0004365 glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity | IDA PMID:3905788 Differential expression of the three yeast glyceraldehyde-3-... | ACCEPT | Summary: McAlister and Holland used tdh insertion mutants to partition total GAPDH activity among the three genes; TDH3 encodes the dominant (50-60%) isoform of cellular GAPDH activity and the authors conclude all three genes encode catalytically active enzyme. Supporting Evidence: PMID:3905788 The contribution of the TDH1, TDH2, and TDH3 gene products to the total glyceraldehyde-3-phosphate dehydrogenase activity in wild type cells is 10-15, 25-30, and 50-60%, respectively PMID:3905788 These data confirm that the three yeast glyceraldehyde-3-phosphate dehydrogenase genes encode catalytically active enzyme PMID:3905788 The polypeptides encoded by the TDH2 or TDH3 structural genes form catalytically active homotetramers |
| GO:0004365 glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity | IEA GO_REF:0000120 | ACCEPT | Summary: EC 1.2.1.12 / RHEA:10300 mapping from the UniProt catalytic-activity annotation; correct for TDH3. Supporting Evidence: file:yeast/TDH3/TDH3-uniprot.txt Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) involved in PMID:3905788 These data confirm that the three yeast glyceraldehyde-3-phosphate dehydrogenase genes encode catalytically active enzyme |
| GO:0004365 glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways RCA (GLUCFERMEN-PWY, superpathway of glucose fermentation) assigning the reversible GAP + NAD+ + Pi <-> 1,3-bisphosphoglycerate step (EC 1.2.1.12) to TDH3; the activity is experimentally established for TDH3. Supporting Evidence: file:yeast/TDH3/TDH3-uniprot.txt Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) involved in PMID:3905788 These data confirm that the three yeast glyceraldehyde-3-phosphate dehydrogenase genes encode catalytically active enzyme |
| GO:0004365 glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways RCA (GLUCONEO-PWY-1, gluconeogenesis I) assigning the reversible GAP + NAD+ + Pi <-> 1,3-bisphosphoglycerate step (EC 1.2.1.12) to TDH3; the activity is experimentally established for TDH3. Supporting Evidence: file:yeast/TDH3/TDH3-uniprot.txt Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) involved in PMID:3905788 These data confirm that the three yeast glyceraldehyde-3-phosphate dehydrogenase genes encode catalytically active enzyme |
| GO:0004365 glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways RCA (GLYCOLYSIS, glycolysis I) assigning the reversible GAP + NAD+ + Pi <-> 1,3-bisphosphoglycerate step (EC 1.2.1.12) to TDH3; the activity is experimentally established for TDH3. Supporting Evidence: file:yeast/TDH3/TDH3-uniprot.txt Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) involved in PMID:3905788 These data confirm that the three yeast glyceraldehyde-3-phosphate dehydrogenase genes encode catalytically active enzyme |
| GO:0005634 nucleus | HDA PMID:26928762 One library to make them all: streamlining the creation of y... | KEEP AS NON CORE | Summary: SWAT-GFP library imaging assigned a nuclear signal for Tdh3 in addition to cytosol. A nuclear pool is plausible (Tdh3 influences the nuclear heme sensor Hap1, PMID:27247412) but no nuclear catalytic role is established. Reason: HTP localization; secondary pool, non-core. Supporting Evidence: PMID:26928762 we only assigned localizations that could be easily discriminated by eye: ER, nuclear periphery, cytosol, cell periphery, vacuole lumen, vacuole membrane, mitochondria, nucleus, bud/bud neck and punctate |
| GO:0005737 cytoplasm | HDA PMID:11914276 Subcellular localization of the yeast proteome. | ACCEPT | Summary: Kumar et al. genome-wide immunolocalization of tagged proteins placed Tdh3 in the cytoplasm; consistent with its glycolytic role. Supporting Evidence: PMID:11914276 By high-throughput immunolocalization of tagged gene products, we have determined the subcellular localization of 2744 yeast proteins. |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular-location mapping (SL-0086 Cytoplasm); correct for TDH3, which is detected in cytosolic extracts. Supporting Evidence: PMID:11158358 Western immunoblot analysis of cell wall extracts and cytosol showed that Tdh2 and Tdh3 polypeptides are present in the cell wall, as well as in the cytosol, of exponentially growing cells |
| GO:0005739 mitochondrion | HDA PMID:16823961 Toward the complete yeast mitochondrial proteome: multidimen... | KEEP AS NON CORE | Summary: Reinders et al. PROMITO proteomics of purified mitochondria detected Tdh3 (UniProt cites this for its mitochondrion location). Abundant glycolytic enzymes co-purify with mitochondria; a genuine outer-surface pool exists (PMID:16962558). Reason: HTP proteomic detection; peripheral, non-core. 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. PMID:16962558 we show that all glycolytic enzymes are associated with mitochondria in yeast |
| GO:0005739 mitochondrion | HDA PMID:24769239 Quantitative variations of the mitochondrial proteome and ph... | KEEP AS NON CORE | Summary: High-throughput mitochondrial proteomics detected TDH3 in purified mitochondria. Abundant glycolytic enzymes are frequent co-purifying passengers of mitochondrial preparations, although a genuine outer-surface pool exists (PMID:16962558). Reason: HTP proteomic detection; peripheral, non-core. 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 PMID:16962558 we show that all glycolytic enzymes are associated with mitochondria in yeast |
| GO:0005739 mitochondrion | IDA PMID:16962558 Enolase takes part in a macromolecular complex associated to... | KEEP AS NON CORE | Summary: Brandina et al. report that all glycolytic enzyme activities, including GAPDH, are partly associated with purified mitochondria and that glycolytic enzymes co-purify with an enolase-containing complex at the mitochondrial surface. This is a peripheral association of a small pool of TDH3; the abstract does not resolve individual TDH isoforms, but the curator had full text. Reason: Experimental, not removed; peripheral pool, not the site of core glycolytic activity. Supporting Evidence: PMID:16962558 we show that all glycolytic enzymes are associated with mitochondria in yeast PMID:16962558 The identified components included additional glycolytic enzymes |
| GO:0005739 mitochondrion | IEA GO_REF:0000120 | KEEP AS NON CORE | Summary: Combined IEA from UniProt subcellular location (SL-0173 Mitochondrion, itself based on PMID:16823961 proteomics) and ARBA. Reflects a peripheral, mitochondria-associated pool of Tdh3. Reason: Peripheral location; non-core. Supporting Evidence: file:yeast/TDH3/TDH3-uniprot.txt Mitochondrion {ECO:0000269|PubMed:16823961}. PMID:16962558 we show that all glycolytic enzymes are associated with mitochondria in yeast |
| GO:0005811 lipid droplet | IDA PMID:10515935 Identification and characterization of major lipid particle ... | KEEP AS NON CORE | Summary: Athenstaedt et al. identified GAPDH by MS as a minor component in a gel band of highly purified lipid particles (less abundant than Yju3p). A minor co-purifying pool of an abundant cytosolic enzyme; no role at lipid droplets is described. Reason: Experimental but minor co-fractionation; non-core. Supporting Evidence: PMID:10515935 glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and Yju3p (the amount of Yju3p was greater than GAPDH) |
| GO:0005811 lipid droplet | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: ARBA rule propagating lipid droplet location to GAPDHs, derived from proteomic detection of GAPDH in lipid-particle fractions; consistent with the experimental row but a minor co-fractionating pool, not a characteristic location. Reason: Minor co-fractionation location; non-core. Supporting Evidence: PMID:10515935 glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and Yju3p (the amount of Yju3p was greater than GAPDH) |
| GO:0005829 cytosol | HDA PMID:26928762 One library to make them all: streamlining the creation of y... | ACCEPT | Summary: SWAT-GFP library imaging (Meurer/Weill et al.) assigned TDH3 to the cytosol; consistent with its glycolytic role. Supporting Evidence: PMID:26928762 we only assigned localizations that could be easily discriminated by eye: ER, nuclear periphery, cytosol, cell periphery, vacuole lumen, vacuole membrane, mitochondria, nucleus, bud/bud neck and punctate |
| GO:0005829 cytosol | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA is_active_in cytosol for glycolytic GAPDHs; correct for TDH3. Supporting Evidence: PMID:11158358 Western immunoblot analysis of cell wall extracts and cytosol showed that Tdh2 and Tdh3 polypeptides are present in the cell wall, as well as in the cytosol, of exponentially growing cells |
| GO:0005829 cytosol | IDA PMID:11158358 The glyceraldehyde-3-phosphate dehydrogenase polypeptides en... | ACCEPT | Summary: Delgado et al. detected Tdh3 polypeptide by Western blot in the cytosol of exponentially growing cells; cytosol is where Tdh3 carries out glycolytic GAPDH activity (is_active_in). Supporting Evidence: PMID:11158358 Western immunoblot analysis of cell wall extracts and cytosol showed that Tdh2 and Tdh3 polypeptides are present in the cell wall, as well as in the cytosol, of exponentially growing cells PMID:11158358 By immunoelectron microscopy, the GAPDH protein was detected at the outer surface of the cell wall of wild-type cells, as well as in the cytoplasm |
| GO:0005829 cytosol | IDA PMID:11158358 The glyceraldehyde-3-phosphate dehydrogenase polypeptides en... | ACCEPT | Summary: Delgado et al. detected Tdh3 polypeptide by Western blot in the cytosol of exponentially growing cells; cytosol is where Tdh3 carries out glycolytic GAPDH activity (located_in). Supporting Evidence: PMID:11158358 Western immunoblot analysis of cell wall extracts and cytosol showed that Tdh2 and Tdh3 polypeptides are present in the cell wall, as well as in the cytosol, of exponentially growing cells PMID:11158358 By immunoelectron microscopy, the GAPDH protein was detected at the outer surface of the cell wall of wild-type cells, as well as in the cytoplasm |
| GO:0005829 cytosol | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA mapping to cytosol; correct for TDH3. Supporting Evidence: PMID:11158358 Western immunoblot analysis of cell wall extracts and cytosol showed that Tdh2 and Tdh3 polypeptides are present in the cell wall, as well as in the cytosol, of exponentially growing cells |
| GO:0005829 cytosol | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways RCA is_active_in cytosol for the GAPDH step of superpathway of glucose fermentation; TDH3 is a soluble cytosolic glycolytic/gluconeogenic enzyme. Supporting Evidence: PMID:11158358 Western immunoblot analysis of cell wall extracts and cytosol showed that Tdh2 and Tdh3 polypeptides are present in the cell wall, as well as in the cytosol, of exponentially growing cells file:yeast/TDH3/TDH3-uniprot.txt Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) involved in |
| GO:0005829 cytosol | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways RCA is_active_in cytosol for the GAPDH step of gluconeogenesis I; TDH3 is a soluble cytosolic glycolytic/gluconeogenic enzyme. Supporting Evidence: PMID:11158358 Western immunoblot analysis of cell wall extracts and cytosol showed that Tdh2 and Tdh3 polypeptides are present in the cell wall, as well as in the cytosol, of exponentially growing cells file:yeast/TDH3/TDH3-uniprot.txt Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) involved in |
| GO:0005829 cytosol | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways RCA is_active_in cytosol for the GAPDH step of glycolysis I; TDH3 is a soluble cytosolic glycolytic/gluconeogenic enzyme. Supporting Evidence: PMID:11158358 Western immunoblot analysis of cell wall extracts and cytosol showed that Tdh2 and Tdh3 polypeptides are present in the cell wall, as well as in the cytosol, of exponentially growing cells file:yeast/TDH3/TDH3-uniprot.txt Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) involved in |
| GO:0005886 plasma membrane | HDA PMID:16622836 The plasma membrane proteome of Saccharomyces cerevisiae and... | KEEP AS NON CORE | Summary: Delom et al. identified ~90 proteins in a stripped plasma-membrane fraction by IEC/LDS-PAGE MS, including TDH3. Abundant glycolytic enzymes are common contaminants of membrane fractions, although yeast GAPDH is also found at the cell surface/cell wall (PMID:11158358). Reason: HTP proteomic detection; plausible peripheral pool, non-core. Supporting Evidence: PMID:16622836 Proteins from a stripped plasma membrane fraction were solubilized with the neutral and non-denaturing detergent, the n-dodecyl beta-D-maltoside. PMID:11158358 By immunoelectron microscopy, the GAPDH protein was detected at the outer surface of the cell wall of wild-type cells, as well as in the cytoplasm |
| GO:0006006 glucose metabolic process | IEA GO_REF:0000002 | TOO GENERAL | Summary: InterPro IPR006424 (type I GAPDH) mapping to glucose metabolic process. Correct but very general; the specific processes glycolysis and gluconeogenesis are annotated separately. Reason: Correct, general parent-level process; redundant with glycolysis/gluconeogenesis. Supporting Evidence: file:yeast/TDH3/TDH3-uniprot.txt Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) involved in |
| GO:0006094 gluconeogenesis | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA mapping to gluconeogenesis. GAPDH catalyses the reversible step used in both glycolysis and gluconeogenesis, and TDH3 is expressed on ethanol as well as glucose. Supporting Evidence: file:yeast/TDH3/TDH3-uniprot.txt Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) involved in PMID:3905788 The relative proportions of expression of each gene is the same in cells grown in the presence of glucose or ethanol as carbon source |
| GO:0006094 gluconeogenesis | IEP PMID:3905788 Differential expression of the three yeast glyceraldehyde-3-... | ACCEPT | Summary: McAlister and Holland measured TDH3 expression/activity in ethanol-grown (gluconeogenic) as well as glucose-grown cells. IEP is weak evidence for participation, but the reversible GAPDH step is an obligatory part of gluconeogenesis, so the process assignment is correct. Supporting Evidence: PMID:3905788 The relative proportions of expression of each gene is the same in cells grown in the presence of glucose or ethanol as carbon source |
| GO:0006094 gluconeogenesis | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways RCA (gluconeogenesis I) for TDH3; the GAPDH step operates in the gluconeogenic direction during growth on non-fermentable carbon sources. Supporting Evidence: file:yeast/TDH3/TDH3-uniprot.txt Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) involved in PMID:3905788 The relative proportions of expression of each gene is the same in cells grown in the presence of glucose or ethanol as carbon source |
| GO:0006096 glycolysis | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA for glycolysis from the GAPDH clade; TDH3 contributes the dominant (50-60%) isoform of the glycolytic GAPDH activity. Supporting Evidence: file:yeast/TDH3/TDH3-uniprot.txt glyceraldehyde 3-phosphate: step 1/5. {ECO:0000269|PubMed:3905788}. PMID:3905788 The contribution of the TDH1, TDH2, and TDH3 gene products to the total glyceraldehyde-3-phosphate dehydrogenase activity in wild type cells is 10-15, 25-30, and 50-60%, respectively |
| GO:0006096 glycolysis | IEA GO_REF:0000120 | ACCEPT | Summary: UniPathway UPA00109 / ARBA mapping to glycolysis; correct for TDH3. Supporting Evidence: file:yeast/TDH3/TDH3-uniprot.txt glyceraldehyde 3-phosphate: step 1/5. {ECO:0000269|PubMed:3905788}. |
| GO:0006096 glycolysis | IEP PMID:3905788 Differential expression of the three yeast glyceraldehyde-3-... | ACCEPT | Summary: McAlister and Holland: total GAPDH activity is 2-fold higher in glucose-grown cells, and TDH3 supplies the dominant (50-60%) isoform of it. IEP is indirect, but the glycolytic role of TDH3 is well established. Supporting Evidence: PMID:3905788 The contribution of the TDH1, TDH2, and TDH3 gene products to the total glyceraldehyde-3-phosphate dehydrogenase activity in wild type cells is 10-15, 25-30, and 50-60%, respectively PMID:3905788 The relative proportions of expression of each gene is the same in cells grown in the presence of glucose or ethanol as carbon source |
| GO:0006915 apoptotic process | IMP PMID:17726063 NO-mediated apoptosis in yeast. | KEEP AS NON CORE | Summary: Almeida et al. linked H2O2-induced, NO-dependent yeast apoptosis to GAPDH S-nitrosation and proteolysis; the IMP presumably reflects altered death/survival of a tdh mutant (full text not available here). GAPDH appears as a target/mediator of the death programme rather than a dedicated apoptotic effector, and the phenotype may be partly metabolic. Reason: Experimental (curator saw full text), not removed; stress/death role is peripheral to the core glycolytic function. Supporting Evidence: PMID:17726063 yeast GAPDH is a target of extensive proteolysis upon H2O2-induced apoptosis and undergoes S-nitrosation PMID:17726063 NO signalling and GAPDH S-nitrosation are linked with H2O2-induced apoptotic cell death |
| GO:0009277 fungal-type cell wall | IDA PMID:11158358 The glyceraldehyde-3-phosphate dehydrogenase polypeptides en... | KEEP AS NON CORE | Summary: Delgado et al. detected catalytically active GAPDH at the outer surface of the cell wall by immunofluorescence, immuno-EM and Western blotting of cell-wall extracts; TDH3 polypeptide was specifically detected in cell-wall extracts. Reason: Experimentally supported secondary (moonlighting) location; function there unknown. Supporting Evidence: PMID:11158358 Western immunoblot analysis of cell wall extracts and cytosol showed that Tdh2 and Tdh3 polypeptides are present in the cell wall, as well as in the cytosol, of exponentially growing cells PMID:11158358 By immunoelectron microscopy, the GAPDH protein was detected at the outer surface of the cell wall of wild-type cells, as well as in the cytoplasm |
| GO:0009277 fungal-type cell wall | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: ARBA mapping to fungal-type cell wall; consistent with direct experimental detection of TDH3 in cell-wall extracts. Reason: Secondary location, non-core. Supporting Evidence: PMID:11158358 Western immunoblot analysis of cell wall extracts and cytosol showed that Tdh2 and Tdh3 polypeptides are present in the cell wall, as well as in the cytosol, of exponentially growing cells |
| GO:0015886 heme transport | IMP PMID:27247412 Heme dynamics and trafficking factors revealed by geneticall... | KEEP AS NON CORE | Summary: Hanna et al. used genetically encoded heme sensors: tdh3 deletion (but not tdh1 or tdh2) raises labile cytosolic heme ~4-fold and reduces activity of the nuclear heme-dependent factor Hap1, indicating Tdh3 buffers and allocates labile heme. 'Heme transport' (intracellular movement) captures this chaperone-like allocation loosely. Reason: Experimentally supported moonlighting role in heme allocation; secondary to glycolysis. Supporting Evidence: PMID:27247412 In total, our data indicate GAPDH is involved in buffering cytosolic heme and regulates the activity of Hap1p, presumably by acting as a source for heme. PMID:27247412 Deletion of TDH3 homologs TDH1 and TDH2 does not affect LH pools |
| GO:0016620 oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor | IEA GO_REF:0000002 | MODIFY | Summary: InterPro GAPDH signatures mapped to the generic parent oxidoreductase activity acting on aldehyde/oxo donors with NAD(P) acceptor. Correct but uninformative; the specific child term GAPDH (NAD+) (phosphorylating) activity is supported. Reason: Too general; replace with the specific activity. Proposed replacements: glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity Supporting Evidence: file:yeast/TDH3/TDH3-uniprot.txt Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) involved in PMID:3905788 These data confirm that the three yeast glyceraldehyde-3-phosphate dehydrogenase genes encode catalytically active enzyme |
| GO:0019658 bifid shunt | RCA GO_REF:0000123 | REMOVE | Summary: YeastPathways RCA from GLUCFERMEN-PWY mapped to GO bifid shunt, the Bifidobacterium phosphoketolase pathway converting glucose to lactate and acetate. S. cerevisiae has no bifid shunt; TDH3 acts in glycolysis/alcoholic fermentation. Reason: Mis-mapped pathway: bifid shunt does not occur in S. cerevisiae. Supporting Evidence: file:yeast/TDH3/TDH3-uniprot.txt glyceraldehyde 3-phosphate: step 1/5. {ECO:0000269|PubMed:3905788}. |
| GO:0020037 heme binding | IMP PMID:30012884 Glyceraldehyde-3-phosphate dehydrogenase is a chaperone that... | KEEP AS NON CORE | Summary: Sweeny et al. identified a conserved GAPDH histidine required for robust heme binding; substituting it impaired heme delivery to Hap1 in yeast. The IMP code reflects the yeast mutant analysis of the conserved heme-binding residue. Reason: Moonlighting heme-chaperone binding; non-core. Supporting Evidence: PMID:30012884 We identified a conserved histidine in GAPDH that is needed for its robust heme binding both in vitro and in mammalian cells. PMID:30012884 Substitution of this histidine, and the consequent decreases in GAPDH heme binding, antagonized heme delivery to both cytosolic and nuclear hemeprotein targets, including inducible nitric-oxide synthase (iNOS) in murine macrophages and the nuclear transcription factor Hap1 in yeast |
| GO:0050661 NADP binding | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: InterPro IPR006424 (type I GAPDH family, which includes NADP-dependent plant/cyanobacterial GapB/GapC) mapped to NADP binding. Yeast TDH3 is the NAD+-specific phosphorylating GAPDH (EC 1.2.1.12); the only NADP(H) interaction recorded is a slow NAD(P)H-hydratase side activity, so NADP binding is not a meaningful functional description. Reason: Family-level mapping that over-states cofactor specificity of an NAD-dependent GAPDH. Supporting Evidence: file:yeast/TDH3/TDH3-uniprot.txt FUNCTION: As a side activity, catalyzes the hydration of the file:yeast/TDH3/TDH3-uniprot.txt Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) involved in |
| GO:0051287 NAD binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro GAPDH NAD(P)-binding domain mapped to NAD binding; correct, NAD+ is the cosubstrate of TDH3. Part of the catalytic activity rather than a separate function. Reason: Cosubstrate binding; non-core. Supporting Evidence: file:yeast/TDH3/TDH3-uniprot.txt Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) involved in file:yeast/TDH3/TDH3-uniprot.txt KM=0.32 uM for NAD(+) |
| GO:0061620 obsolete glycolytic process through glucose-6-phosphate | RCA GO_REF:0000123 | MODIFY | Summary: YeastPathways RCA (GLYCOLYSIS) to glycolytic process through glucose-6-phosphate, now obsolete and replaced by glycolysis (GO:0006096). TDH3 does act in glycolysis. Reason: Obsolete term; use replaced_by GO:0006096. Proposed replacements: glycolysis Supporting Evidence: file:yeast/TDH3/TDH3-uniprot.txt glyceraldehyde 3-phosphate: step 1/5. {ECO:0000269|PubMed:3905788}. |
| GO:0072593 reactive oxygen species metabolic process | IMP PMID:17726063 NO-mediated apoptosis in yeast. | KEEP AS NON CORE | Summary: Almeida et al.: blocking NO synthesis decreases GAPDH S-nitrosation and intracellular ROS accumulation; the curator's IMP links TDH3 loss to altered ROS levels. Likely an indirect consequence of redox/metabolic perturbation rather than a dedicated ROS-metabolising activity. Reason: Indirect/pleiotropic effect; non-core. Supporting Evidence: PMID:17726063 Blockage of NO synthesis with Nomega-nitro-L-arginine methyl ester leads to a decrease of GAPDH S-nitrosation and of intracellular reactive oxygen species (ROS) accumulation, increasing survival PMID:17726063 NO signalling and GAPDH S-nitrosation are linked with H2O2-induced apoptotic cell death |
| GO:1904408 melatonin binding | IDA PMID:31708896 Glycolytic Proteins Interact With Intracellular Melatonin in... | MARK AS OVER ANNOTATED | Summary: Morcillo-Parra et al. immunopurified melatonin-associated proteins from fermenting cells with anti-melatonin IgG beads and identified Tdh1/2/3 by MS in one gel band. This is an affinity co-purification without a defined binding site, stoichiometry or physiological effect on TDH3. Reason: Affinity co-purification of abundant GAPDH paralogs is weak support for a specific melatonin-binding activity; the experimental report is retained but likely overstates a physiologic molecular function. Supporting Evidence: PMID:31708896 Surprisingly, most of the proteins identified participate in the glycolytic pathway: pyruvate kinase 1 (Pyk2p; band a), enolase (Eno1p, Eno2p; band c), fructose biphosphate aldolase (Fba1p; band d), and glyceraldehyde-3-phosphate dehydrogenase (Tdh1p, Tdh2p, Tdh3p; band f). PMID:31708896 We subsequently performed immunopurification melatonin-IgG-Dynabeads and identified a set of proteins that interact with melatonin inside the cell. |
| GO:1904408 melatonin binding | IEA GO_REF:0000117 | MARK AS OVER ANNOTATED | Summary: ARBA rule propagating melatonin binding to GAPDHs, derived from a single affinity pull-down study in yeast that did identify this protein; physiological significance is unknown. Reason: ARBA propagates the same weak affinity-capture result as a molecular-function assertion; the interaction lacks a binding constant, site, or demonstrated physiologic effect. Supporting Evidence: PMID:31708896 We subsequently performed immunopurification melatonin-IgG-Dynabeads and identified a set of proteins that interact with melatonin inside the cell. |
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Download this section (compressed HTML)Q: Are the heme-buffering and RNA-binding activities of Tdh3 mutually exclusive with catalysis (e.g. via NAD+ site occupancy or S-nitrosation of the catalytic cysteine)?
Q: Why does tdh3 but not tdh1 or tdh2 deletion affect labile heme pools: abundance only, or isoform-specific sequence features?
Experiment: Replace TDH3 with TDH2 coding sequence at the TDH3 locus and measure labile heme (heme sensor) and Hap1 reporter activity, to separate dosage from isoform-specific heme handling.
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), isozyme 3; involved in glycolysis and gluconeogenesis; tetramer that catalyzes the reaction of glyceraldehyde-3-phosphate to 1,3 bis-phosphoglycerate; detected in the cytoplasm and cell wall; GAPDH-derived antimicrobial peptides secreted by S. cerevisiae are active against a wide variety of wine-related yeasts and bacteria; moonlighting role as an AU-rich mRNA binding protein that binds to the FAS1 mRNA and controls periodic abundance of Fas1p
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