GDB1 (YPR184W) encodes the glycogen debranching enzyme of Saccharomyces cerevisiae, a 1536-residue cytosolic bifunctional protein homologous to mammalian AGL. Its N-terminal alpha-amylase (GH13) region carries 4-alpha-glucanotransferase activity (EC 2.4.1.25), which moves maltosyl/maltotriosyl units from the short outer chains left by glycogen phosphorylase (Gph1) onto another chain, and its C-terminal GH133 region carries amylo-alpha-1,6-glucosidase activity (EC 3.2.1.33), which releases the remaining alpha-1,6-linked glucose stub as free glucose. Together with Gph1 it completes cytosolic glycogenolysis; gdb1 deletion blocks glycogen degradation. GDB1 is co-regulated with the other glycogen genes (induced at the diauxic shift and by stress) and its activity is inhibited by the small fermentation-stress protein Igd1.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004134 4-alpha-glucanotransferase activity | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT node PTN000060165 (glycogen debranching enzyme family, PTHR10569) propagates 4-alpha-glucanotransferase activity from human AGL (P35573), mouse/rat Agl and Gdb1 itself. Gdb1 has the conserved GH13 N-terminal transferase region and direct biochemical evidence, so the inherited function is sound. Supporting Evidence: PMID:11094287 Reliable measurement of alpha-1,4-glucanotransferase and alpha-1, 6-glucosidase activity of the yeast debranching enzyme was determined in strains overexpressing YPR184w PMID:11094287 is 34-39% identical to the mammal, Drosophila melanogaster and Caenorhabditis elegans glycogen debranching enzyme |
| GO:0004134 4-alpha-glucanotransferase activity | IDA PMID:11094287 The Saccharomyces cerevisiae YPR184w gene encodes the glycog... | ACCEPT | Summary: Teste et al. measured alpha-1,4-glucanotransferase activity in extracts of Gdb1-overexpressing strains and in a partially purified enzyme preparation, which preferentially transferred maltosyl units. Direct evidence for the transferase half-reaction. Supporting Evidence: PMID:11094287 Reliable measurement of alpha-1,4-glucanotransferase and alpha-1, 6-glucosidase activity of the yeast debranching enzyme was determined in strains overexpressing YPR184w PMID:11094287 The alpha-1, 4-glucanotransferase activity of a partially purified preparation of debranching enzyme preferentially transferred maltosyl units than maltotriosyl |
| GO:0004134 4-alpha-glucanotransferase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Combined IEA from InterPro IPR006421/IPR010401 (glycogen debranching enzyme domains) and EC 2.4.1.25 in the UniProt entry. Correct for Gdb1 and redundant with the IDA. Supporting Evidence: file:yeast/GDB1/GDB1-uniprot.txt Reaction=Transfers a segment of a (1->4)-alpha-D-glucan to a new |
| GO:0004134 4-alpha-glucanotransferase activity | IMP PMID:11094287 The Saccharomyces cerevisiae YPR184w gene encodes the glycog... | ACCEPT | Summary: gdb1 deletion abolishes glycogen degradation and overexpression raises measurable transferase activity; the curator used the loss/gain-of-function data from the same paper. Consistent with the IDA. Supporting Evidence: PMID:11094287 Reliable measurement of alpha-1,4-glucanotransferase and alpha-1, 6-glucosidase activity of the yeast debranching enzyme was determined in strains overexpressing YPR184w PMID:11094287 Deletion of YPR184w prevents glycogen degradation, whereas overexpression had no effect on the rate of glycogen breakdown |
| GO:0004135 amylo-alpha-1,6-glucosidase activity | IBA GO_REF:0000033 | ACCEPT | Summary: Same PAINT node (PTN000060165) as the transferase IBA, propagating amylo-alpha-1,6-glucosidase activity; Gdb1 retains the C-terminal GDE_C (GH133) glucosidase domain and has direct activity data. Supporting Evidence: PMID:11094287 Reliable measurement of alpha-1,4-glucanotransferase and alpha-1, 6-glucosidase activity of the yeast debranching enzyme was determined in strains overexpressing YPR184w |
| GO:0004135 amylo-alpha-1,6-glucosidase activity | IDA PMID:11094287 The Saccharomyces cerevisiae YPR184w gene encodes the glycog... | ACCEPT | Summary: Alpha-1,6-glucosidase activity was assayed directly in Gdb1-overexpressing strains (Teste et al. 2000). Core catalytic activity. Supporting Evidence: PMID:11094287 Reliable measurement of alpha-1,4-glucanotransferase and alpha-1, 6-glucosidase activity of the yeast debranching enzyme was determined in strains overexpressing YPR184w |
| GO:0004135 amylo-alpha-1,6-glucosidase activity | IEA GO_REF:0000120 | ACCEPT | Summary: IEA from InterPro debranching-enzyme signatures and EC 3.2.1.33; correct and redundant with the experimental annotation. Supporting Evidence: file:yeast/GDB1/GDB1-uniprot.txt Reaction=Hydrolysis of (1->6)-alpha-D-glucosidic branch linkages in |
| GO:0004135 amylo-alpha-1,6-glucosidase activity | IMP PMID:11094287 The Saccharomyces cerevisiae YPR184w gene encodes the glycog... | ACCEPT | Summary: Mutant/overexpression analysis in Teste et al.: deletion prevents glycogen breakdown, overexpression increases measurable glucosidase activity. Supports the activity assignment. Supporting Evidence: PMID:11094287 Reliable measurement of alpha-1,4-glucanotransferase and alpha-1, 6-glucosidase activity of the yeast debranching enzyme was determined in strains overexpressing YPR184w PMID:11094287 Deletion of YPR184w prevents glycogen degradation, whereas overexpression had no effect on the rate of glycogen breakdown |
| GO:0004135 amylo-alpha-1,6-glucosidase activity | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways glycogen catabolism (GLYCOCAT-YEAST-PWY) assigns Gdb1 to the EC 3.2.1.33 limit-dextrin debranching step; this matches the biochemistry. (The pathway also lists the EC 2.4.1.25 transferase step, covered by GO:0004134 rows.) Supporting Evidence: PMID:11094287 Reliable measurement of alpha-1,4-glucanotransferase and alpha-1, 6-glucosidase activity of the yeast debranching enzyme was determined in strains overexpressing YPR184w |
| GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds | IEA GO_REF:0000117 | MODIFY | Summary: ARBA machine-learning rule assigns the generic glycosidase parent 'hydrolase activity, hydrolyzing O-glycosyl compounds'. Not wrong (the C-terminal domain is a glucosidase) but uninformative given the specific, experimentally supported amylo-alpha-1,6-glucosidase term. Reason: Replace generic parent with the specific glucosidase activity already supported by IDA. Proposed replacements: amylo-alpha-1,6-glucosidase activity Supporting Evidence: PMID:11094287 Reliable measurement of alpha-1,4-glucanotransferase and alpha-1, 6-glucosidase activity of the yeast debranching enzyme was determined in strains overexpressing YPR184w |
| GO:0005737 cytoplasm | HDA PMID:14562095 Global analysis of protein localization in budding yeast. | ACCEPT | Summary: Genome-wide GFP localization (Huh et al. 2003) placed Gdb1-GFP in the cytoplasm, consistent with its role in cytosolic glycogenolysis. Supporting Evidence: PMID:38832010 Accumulated glycogen is subsequently broken down into glucose-1-phosphate via glycogenolysis by glycogen phosphorylases (Gph1) and glycogen debranching enzyme (Gdb1) in the cytosol according to cellular needs |
| GO:0005737 cytoplasm | HDA PMID:22842922 Dissecting DNA damage response pathways by analysing protein... | ACCEPT | Summary: High-throughput GFP imaging (Tkach et al. 2012) recorded Gdb1 in the cytoplasm; consistent with the known cytosolic site of glycogen breakdown. Supporting Evidence: PMID:38832010 Accumulated glycogen is subsequently broken down into glucose-1-phosphate via glycogenolysis by glycogen phosphorylases (Gph1) and glycogen debranching enzyme (Gdb1) in the cytosol according to cellular needs |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular-location mapping (SL-0086, cytoplasm), itself derived from the Huh et al. GFP data. Correct. Supporting Evidence: PMID:38832010 Accumulated glycogen is subsequently broken down into glucose-1-phosphate via glycogenolysis by glycogen phosphorylases (Gph1) and glycogen debranching enzyme (Gdb1) in the cytosol according to cellular needs |
| GO:0005739 mitochondrion | HDA PMID:14576278 The proteome of Saccharomyces cerevisiae mitochondria. | MARK AS OVER ANNOTATED | Summary: Detection in the mass-spectrometry proteome of purified mitochondria (Sickmann et al. 2003). Gdb1 has no mitochondrial targeting signal or known intramitochondrial role; glycogen and its enzymes are cytosolic, and abundant cytosolic proteins are frequent co-purifying contaminants in organelle proteomics. Reason: Proteomic co-purification only; not a site of Gdb1 function. Not removed because it is an experimental dataset whose full details are not available here. Supporting Evidence: PMID:38832010 Accumulated glycogen is subsequently broken down into glucose-1-phosphate via glycogenolysis by glycogen phosphorylases (Gph1) and glycogen debranching enzyme (Gdb1) in the cytosol according to cellular needs |
| GO:0005739 mitochondrion | HDA PMID:16823961 Toward the complete yeast mitochondrial proteome: multidimen... | MARK AS OVER ANNOTATED | Summary: Second mitochondrial proteome dataset (Reinders et al. 2006) from the same group; same caveat that cytosolic glycogen enzymes are not expected in the matrix and no functional evidence supports a mitochondrial pool. Reason: Proteomic detection only; Gdb1 acts in cytosolic glycogenolysis. Supporting Evidence: PMID:38832010 Accumulated glycogen is subsequently broken down into glucose-1-phosphate via glycogenolysis by glycogen phosphorylases (Gph1) and glycogen debranching enzyme (Gdb1) in the cytosol according to cellular needs |
| GO:0005739 mitochondrion | IEA GO_REF:0000044 | MARK AS OVER ANNOTATED | Summary: UniProt SubCell mapping (SL-0173). The UniProt 'Mitochondrion' line is attributed to the Huh et al. GFP screen, which GOA itself records only as cytoplasm; no targeting sequence or mitochondrial activity is known. Reason: Electronic propagation of a weak large-scale localization; functional site is the cytosol. Supporting Evidence: PMID:38832010 Accumulated glycogen is subsequently broken down into glucose-1-phosphate via glycogenolysis by glycogen phosphorylases (Gph1) and glycogen debranching enzyme (Gdb1) in the cytosol according to cellular needs |
| GO:0005829 cytosol | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways places glycogen catabolism by Gph1/Gdb1 in the cytosol; consistent with literature describing cytosolic glycogenolysis by these two enzymes. Supporting Evidence: PMID:38832010 Accumulated glycogen is subsequently broken down into glucose-1-phosphate via glycogenolysis by glycogen phosphorylases (Gph1) and glycogen debranching enzyme (Gdb1) in the cytosol according to cellular needs |
| GO:0005975 carbohydrate metabolic process | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO (six-hairpin glycosidase / glycoside hydrolase superfamily signatures) gives the root carbohydrate metabolic process term; correct but far less informative than glycogen catabolic process. Reason: Use the specific process supported by IMP. Proposed replacements: glycogen catabolic process Supporting Evidence: PMID:11094287 Deletion of YPR184w prevents glycogen degradation, whereas overexpression had no effect on the rate of glycogen breakdown |
| GO:0005978 glycogen biosynthetic process | IEA GO_REF:0000002 | REMOVE | Summary: InterPro2GO mapping of IPR006421 (glycogen debranching enzyme, metazoa) to glycogen biosynthetic process. Debranching enzyme degrades glycogen; gdb1 deletion blocks glycogen breakdown and has no reported biosynthetic defect. The mapping is not appropriate for this enzyme. Reason: Debranching enzyme acts in glycogen catabolism, not synthesis; InterPro2GO mapping is wrong for this family member. Supporting Evidence: PMID:11094287 Deletion of YPR184w prevents glycogen degradation, whereas overexpression had no effect on the rate of glycogen breakdown |
| GO:0005980 glycogen catabolic process | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference from AGL orthologs (human, mouse, rat, Candida) and Gdb1 itself; in agreement with the yeast deletion phenotype. Supporting Evidence: PMID:11094287 Deletion of YPR184w prevents glycogen degradation, whereas overexpression had no effect on the rate of glycogen breakdown |
| GO:0005980 glycogen catabolic process | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO from IPR010401 (glycogen debranching enzyme C-terminal domain); correct for Gdb1. Supporting Evidence: PMID:11094287 Deletion of YPR184w prevents glycogen degradation, whereas overexpression had no effect on the rate of glycogen breakdown |
| GO:0005980 glycogen catabolic process | IMP PMID:11094287 The Saccharomyces cerevisiae YPR184w gene encodes the glycog... | ACCEPT | Summary: Deletion of GDB1 prevents glycogen degradation (Teste et al. 2000); direct genetic evidence for participation in glycogen catabolism, where Gdb1 itself catalyses the debranching steps. Supporting Evidence: PMID:11094287 Deletion of YPR184w prevents glycogen degradation, whereas overexpression had no effect on the rate of glycogen breakdown |
| GO:0005980 glycogen catabolic process | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways glycogen catabolism pathway assignment; Gdb1 catalyses the transferase and debranching steps of this pathway. Correct. Supporting Evidence: PMID:38832010 Accumulated glycogen is subsequently broken down into glucose-1-phosphate via glycogenolysis by glycogen phosphorylases (Gph1) and glycogen debranching enzyme (Gdb1) in the cytosol according to cellular needs |
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Download this section (compressed HTML)Q: Does Igd1 inhibition of Gdb1 act on both catalytic half-reactions or only one, and is it the main post-translational control on yeast debranching?
Q: Is the mitochondrial detection of Gdb1 in proteomic surveys a co-purification artefact of glycogen particles, or is there a genuine organelle-associated pool?
Experiment: Assay separated transferase and glucosidase activities of purified Gdb1 point mutants (GH13 vs GH133 catalytic residues) with and without Igd1 to map the inhibited site.
Hypothesis: Igd1 inhibits only one of the two Gdb1 catalytic sites.
Glycogen debranching enzyme; contains glucanotranferase and alpha-1,6-amyloglucosidase activities; required for glycogen degradation; phosphorylated in mitochondria; activity is inhibited by Igd1p; protein abundance increases in response to DNA replication stress
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