Glycogen catabolism

WikiPathways:WP478

Glycogen catabolism in Saccharomyces cerevisiae covers the WikiPathways GPH1 phosphorolysis branch from glycogen to glucose-1-phosphate and the downstream PGM1/PGM2 phosphoglucomutase conversion to glucose-6-phosphate.

Pathway type

glycogen catabolism

Organism scope

Saccharomyces cerevisiae NCBITaxon:4932

Read the source YAML

Pathway network

13 nodes · 13 asserted directed edges

Arrows show recorded subject → object relationships, not necessarily metabolic flow. Select a node for details or an arrow for evidence. Scroll, zoom or find a node to explore.

Reaction / activity
Chemical / cofactor
Protein / complex
Solid arrow: mechanistic relation
Dashed arrow: membership, location or cofactor relation

Show at full size (scroll to explore)

Components and activities

Declared biological components and source reaction directions
Node	Kind or role	Source direction
Saccharomyces cerevisiae `NCBITaxon:4932`	taxon
glycogens `CHEBI:24384`	small molecule
PGM2 `SGD:S000004711`	protein
maltodextrin `CHEBI:25140`	small molecule
glucose-6-phosphate (closed form) `CHEBI:4170`	small molecule
hydrogenphosphate `CHEBI:43474`	small molecule
PGM1 `SGD:S000001610`	protein
GPH1 `SGD:S000006364`	protein
glucose-1-phosphate (closed form) `CHEBI:16077`	small molecule
magnesium(2+) `CHEBI:18420`	cofactor
zinc(2+) `CHEBI:29105`	cofactor
pyridoxal 5'-phosphate(2-) `CHEBI:597326`	cofactor
glycogen phosphorolysis branch to glucose-1-phosphate `WikiPathways:WP478/id16beba20`	molecular activity	left to right
glucose-1-phosphate to glucose-6-phosphate `WikiPathways:WP478/id5442c585`	molecular activity	left to right

Mechanistic edges

Mechanistic edges and their cited evidence
Subject	Predicate and description	Object	Evidence
glycogens `CHEBI:24384`	consumes	glycogen phosphorolysis branch to glucose-1-phosphate `WikiPathways:WP478/id16beba20`	WikiPathways:WP478 Source assertion: GPML id16beba20 connects normalized CHEBI:24384 as an input of interaction id16beba20. Source location `/Pathway/Interaction[@GraphId='id16beba20']/Graphics; /Pathway/DataNode[@GraphId='ff246']`
glycogen phosphorolysis branch to glucose-1-phosphate `WikiPathways:WP478/id16beba20`	produces	maltodextrin `CHEBI:25140`	WikiPathways:WP478 Source assertion: GPML id16beba20 connects normalized CHEBI:25140 as an output of interaction id16beba20. Source location `/Pathway/Interaction[@GraphId='id16beba20']/Graphics; /Pathway/DataNode[@GraphId='c16']`
glucose-1-phosphate (closed form) `CHEBI:16077`	consumes	glucose-1-phosphate to glucose-6-phosphate `WikiPathways:WP478/id5442c585`	WikiPathways:WP478 Source assertion: GPML id5442c585 connects normalized CHEBI:16077 as an input of interaction id5442c585. Source location `/Pathway/Interaction[@GraphId='id5442c585']/Graphics; /Pathway/DataNode[@GraphId='f0d']`
glucose-1-phosphate to glucose-6-phosphate `WikiPathways:WP478/id5442c585`	produces	glucose-6-phosphate (closed form) `CHEBI:4170`	WikiPathways:WP478 Source assertion: GPML id5442c585 connects normalized CHEBI:4170 as an output of interaction id5442c585. Source location `/Pathway/Interaction[@GraphId='id5442c585']/Graphics; /Pathway/DataNode[@GraphId='c69']`
hydrogenphosphate `CHEBI:43474`	consumes	glycogen phosphorolysis branch to glucose-1-phosphate `WikiPathways:WP478/id16beba20`	WikiPathways:WP478 Source assertion: GPML id2d319881 connects normalized CHEBI:43474 as an input of interaction id16beba20. Source location `/Pathway/Interaction[@GraphId='id2d319881']/Graphics; /Pathway/DataNode[@GraphId='d18']`
PGM2 `SGD:S000004711`	catalyzes	glucose-1-phosphate to glucose-6-phosphate `WikiPathways:WP478/id5442c585`	WikiPathways:WP478 Source assertion: GPML id62f35795 connects normalized SGD:S000004711 as a catalyst of interaction id5442c585. Source location `/Pathway/Interaction[@GraphId='id62f35795']/Graphics; /Pathway/DataNode[@GraphId='a35']`
PGM1 `SGD:S000001610`	catalyzes	glucose-1-phosphate to glucose-6-phosphate `WikiPathways:WP478/id5442c585`	WikiPathways:WP478 Source assertion: GPML id62f35795 connects normalized SGD:S000001610 as a catalyst of interaction id5442c585. Source location `/Pathway/Interaction[@GraphId='id62f35795']/Graphics; /Pathway/DataNode[@GraphId='d6a']`
glycogen phosphorolysis branch to glucose-1-phosphate `WikiPathways:WP478/id16beba20`	produces	glucose-1-phosphate (closed form) `CHEBI:16077`	WikiPathways:WP478 Source assertion: GPML ida7682afa connects normalized CHEBI:16077 as an output of interaction id16beba20. Source location `/Pathway/Interaction[@GraphId='ida7682afa']/Graphics; /Pathway/DataNode[@GraphId='f0d']`
GPH1 `SGD:S000006364`	catalyzes	glycogen phosphorolysis branch to glucose-1-phosphate `WikiPathways:WP478/id16beba20`	WikiPathways:WP478 Source assertion: GPML idc3547a63 connects normalized SGD:S000006364 as a catalyst of interaction id16beba20. Source location `/Pathway/Interaction[@GraphId='idc3547a63']/Graphics; /Pathway/DataNode[@GraphId='ef0']`
PGM2 `SGD:S000004711`	has_cofactor UniProtKB reviewed (Swiss-Prot) annotation. UniProt evidence: ECO:0000269 (PubMed:1100398); ECO:0000269 (PubMed:4628805) Binds 1 magnesium ion per subunit. Can also use Zn(2+) as cofactor. UniProt note evidence: ECO:0000269 (PubMed:1100398); ECO:0000269 (PubMed:4628805)	magnesium(2+) `CHEBI:18420`	UniProtKB:P37012 Source assertion: UniProtKB:P37012 annotates CHEBI:18420 as a cofactor of this protein. Source location `https://rest.uniprot.org/uniprotkb/stream?query=taxonomy_id%3A559292+AND+reviewed%3Atrue&format=json&fields=accession%2Cprotein_name%2Cxref_sgd%2Ccc_cofactor%2Corganism_id%2Ccc_caution [sha256:1378282d22c5518215707964664b55946f468ba74a227a6ea1bbf27db69ddbc4] #/results/1251/comments/0/cofactors/0; /results/1251/comments/0/note` UniProtKB:P37012 Source assertion: UniProtKB:P37012 has the exact SGD cross-reference SGD:S000004711. Source location `https://rest.uniprot.org/uniprotkb/stream?query=taxonomy_id%3A559292+AND+reviewed%3Atrue&format=json&fields=accession%2Cprotein_name%2Cxref_sgd%2Ccc_cofactor%2Corganism_id%2Ccc_caution [sha256:1378282d22c5518215707964664b55946f468ba74a227a6ea1bbf27db69ddbc4] #/results/1251/uniProtKBCrossReferences/0`
PGM2 `SGD:S000004711`	has_cofactor UniProtKB reviewed (Swiss-Prot) annotation. UniProt evidence: ECO:0000269 (PubMed:1100398); ECO:0000269 (PubMed:4628805) Binds 1 magnesium ion per subunit. Can also use Zn(2+) as cofactor. UniProt note evidence: ECO:0000269 (PubMed:1100398); ECO:0000269 (PubMed:4628805)	zinc(2+) `CHEBI:29105`	UniProtKB:P37012 Source assertion: UniProtKB:P37012 annotates CHEBI:29105 as a cofactor of this protein. Source location `https://rest.uniprot.org/uniprotkb/stream?query=taxonomy_id%3A559292+AND+reviewed%3Atrue&format=json&fields=accession%2Cprotein_name%2Cxref_sgd%2Ccc_cofactor%2Corganism_id%2Ccc_caution [sha256:1378282d22c5518215707964664b55946f468ba74a227a6ea1bbf27db69ddbc4] #/results/1251/comments/0/cofactors/1; /results/1251/comments/0/note` UniProtKB:P37012 Source assertion: UniProtKB:P37012 has the exact SGD cross-reference SGD:S000004711. Source location `https://rest.uniprot.org/uniprotkb/stream?query=taxonomy_id%3A559292+AND+reviewed%3Atrue&format=json&fields=accession%2Cprotein_name%2Cxref_sgd%2Ccc_cofactor%2Corganism_id%2Ccc_caution [sha256:1378282d22c5518215707964664b55946f468ba74a227a6ea1bbf27db69ddbc4] #/results/1251/uniProtKBCrossReferences/0`
PGM1 `SGD:S000001610`	has_cofactor UniProtKB reviewed (Swiss-Prot) annotation. UniProt evidence: ECO:0000250 (UniProtKB:P00949) Binds 1 Mg(2+) ion per subunit. UniProt note evidence: ECO:0000250 (UniProtKB:P00949)	magnesium(2+) `CHEBI:18420`	UniProtKB:P33401 Source assertion: UniProtKB:P33401 annotates CHEBI:18420 as a cofactor of this protein. Source location `https://rest.uniprot.org/uniprotkb/stream?query=taxonomy_id%3A559292+AND+reviewed%3Atrue&format=json&fields=accession%2Cprotein_name%2Cxref_sgd%2Ccc_cofactor%2Corganism_id%2Ccc_caution [sha256:1378282d22c5518215707964664b55946f468ba74a227a6ea1bbf27db69ddbc4] #/results/1085/comments/0/cofactors/0; /results/1085/comments/0/note` UniProtKB:P33401 Source assertion: UniProtKB:P33401 has the exact SGD cross-reference SGD:S000001610. Source location `https://rest.uniprot.org/uniprotkb/stream?query=taxonomy_id%3A559292+AND+reviewed%3Atrue&format=json&fields=accession%2Cprotein_name%2Cxref_sgd%2Ccc_cofactor%2Corganism_id%2Ccc_caution [sha256:1378282d22c5518215707964664b55946f468ba74a227a6ea1bbf27db69ddbc4] #/results/1085/uniProtKBCrossReferences/0`
GPH1 `SGD:S000006364`	has_cofactor UniProtKB reviewed (Swiss-Prot) annotation. UniProt evidence: not specified	pyridoxal 5'-phosphate(2-) `CHEBI:597326`	UniProtKB:P06738 Source assertion: UniProtKB:P06738 annotates CHEBI:597326 as a cofactor of this protein. Source location `https://rest.uniprot.org/uniprotkb/stream?query=taxonomy_id%3A559292+AND+reviewed%3Atrue&format=json&fields=accession%2Cprotein_name%2Cxref_sgd%2Ccc_cofactor%2Corganism_id%2Ccc_caution [sha256:1378282d22c5518215707964664b55946f468ba74a227a6ea1bbf27db69ddbc4] #/results/139/comments/0/cofactors/0` UniProtKB:P06738 Source assertion: UniProtKB:P06738 has the exact SGD cross-reference SGD:S000006364. Source location `https://rest.uniprot.org/uniprotkb/stream?query=taxonomy_id%3A559292+AND+reviewed%3Atrue&format=json&fields=accession%2Cprotein_name%2Cxref_sgd%2Ccc_cofactor%2Corganism_id%2Ccc_caution [sha256:1378282d22c5518215707964664b55946f468ba74a227a6ea1bbf27db69ddbc4] #/results/139/uniProtKBCrossReferences/0`

References

WikiPathways:WP478 WP478 native structured pathway source (source version: WP478_r139587)
UniProtKB:P37012 UniProtKB P37012 cofactor annotations (source version: 2026_03)
UniProtKB:P33401 UniProtKB P33401 cofactor annotations (source version: 2026_03)
UniProtKB:P06738 UniProtKB P06738 cofactor annotations (source version: 2026_03)

Curation history

2026-10-05T04:31:23Z codex
- EDIT — Correct upstream glucose-6-phosphate identifier in WP478
  The original WP478_r139587 GPML node c69 labels glucose-6-phosphate (closed form) but directly cross-references CHEBI:75150, which ChEBI255 identifies as the different oxidized compound 3-dehydro-D-glucose 6-phosphate. Replaced the participant ID and edge-005 product with CHEBI:4170 (neutral, anomer-unspecified D-glucopyranose 6-phosphate), preserving display text, charge scope, and unspecified anomer. Independent YeastCyc PHOSPHOGLUCMUT-RXN evidence confirms the PGM1/PGM2 substrate/product pair. Original GPML SHA256 c02b28bb6136df307e48c26d6b79ad15acb251555772b64f86715f8333530586. Recorded the upstream correction in curation/decisions.tsv; no exactMatch is asserted between different molecules. Reviewed all 108 CHEBI participant occurrences across 12 WikiPathways records; no other definite different-molecule conflict found.
Read this curation session
2026-10-05T06:16:40Z Codex
- EDIT — Review complete causal graph against native sources and correct unsupported or omitted relationships
  Retained the explicitly scoped GPH1/PGM branch, including prior glucose-6-phosphate correction; restored shortened glucan product and phosphate. Ambiguous GDB1 debranching and SGA1 peripheral branches are not reinterpreted as complete reactions. Every native record was inspected; see reports/causal-graph-diagram-review.json for native-object counts, exclusions and identity corrections. Semantic validation and native GraphId locator checks passed; authority snapshots and full corpus gates are coordinated separately.
Read this curation session