phosphatidylcholine biosynthesis I

gomodel:YeastPathways_PWY3O-450

Phosphatidylcholine biosynthesis I in Saccharomyces cerevisiae S288C phosphorylates choline to choline phosphate, converts choline phosphate and CTP to CDP-choline, and transfers phosphocholine from CDP-choline to 1,2-diacyl-sn-glycerol to form 1,2-diacyl-sn-glycero-3-phosphocholine.

Pathway type

lipid biosynthesis

Organism scope

Saccharomyces cerevisiae S288C NCBITaxon:559292

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Pathway network

24 nodes · 28 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
Cell / process context
Solid arrow: mechanistic relation
Dashed arrow: membership, location or cofactor relation

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Components and activities

Declared biological components and source reaction directions
Node	Kind or role	Source direction
Saccharomyces cerevisiae S288C `NCBITaxon:559292`	taxon
ATP(4-) `CHEBI:30616`	small molecule
CPT1 Scer `SGD:S000005074`	protein
cytidine 5'-monophosphate(2-) `CHEBI:60377`	small molecule
CDP-choline(1-) `CHEBI:58779`	small molecule
1,2-diacyl-sn-glycero-3-phosphocholine(1+) `CHEBI:16110`	small molecule
CDP-choline pathway `GO:0006657`	biological process
hydron `CHEBI:15378`	small molecule
CTP(4-) `CHEBI:37563`	small molecule
1,2-diacyl-sn-glycerol `CHEBI:17815`	lipid
cytosol `GO:0005829`	cellular component
diphosphoric acid `CHEBI:29888`	small molecule
PCT1 Scer `SGD:S000003434`	protein
choline phosphate(1-) `CHEBI:295975`	small molecule
CKI1 Scer `SGD:S000004123`	protein
ADP(3-) `CHEBI:456216`	small molecule
choline `CHEBI:15354`	small molecule
endoplasmic reticulum membrane `GO:0005789`	cellular component
mitochondrial outer membrane `GO:0005741`	cellular component
membrane `GO:0016020`	cellular component
cytoplasm `GO:0005737`	cellular component
magnesium(2+) `CHEBI:18420`	cofactor
CTP + phosphocholine + H⁺ -> CDP-choline + diphosphate `gomodel:2.7.7.15-RXN`	molecular activity
choline + ATP -> phosphocholine + ADP + H⁺ `gomodel:CHOLINE-KINASE-RXN`	molecular activity
a 1,2-diacyl-sn-glycerol + CDP-choline <=> a phosphatidylcholine + CMP + H⁺ `gomodel:RXN-5781`	molecular activity

Mechanistic edges

Mechanistic edges and their cited evidence
Subject	Predicate and description	Object	Evidence
choline + ATP -> phosphocholine + ADP + H⁺ `gomodel:CHOLINE-KINASE-RXN`	has_input	ATP(4-) `CHEBI:30616`	gomodel:YeastPathways_PWY3O-450 Source assertion: The model asserts gomodel:CHOLINE-KINASE-RXN RO:0002233 gomodel:CHEBI_30616_CHOLINE-KINASE-RXN. Source location `./YeastPathways_PWY3O-450.json#/facts/0; endpoint types: /individuals/13/type; /individuals/8/type`
CPT1 Scer `SGD:S000005074`	enables	a 1,2-diacyl-sn-glycerol + CDP-choline <=> a phosphatidylcholine + CMP + H⁺ `gomodel:RXN-5781`	gomodel:YeastPathways_PWY3O-450 Source assertion: The model asserts gomodel:RXN-5781 RO:0002333 gomodel:YNL130C-MONOMER_RXN-5781_controller. Source location `./YeastPathways_PWY3O-450.json#/facts/1; endpoint types: /individuals/14/type; /individuals/17/type`
a 1,2-diacyl-sn-glycerol + CDP-choline <=> a phosphatidylcholine + CMP + H⁺ `gomodel:RXN-5781`	has_output	cytidine 5'-monophosphate(2-) `CHEBI:60377`	gomodel:YeastPathways_PWY3O-450 Source assertion: The model asserts gomodel:RXN-5781 RO:0002234 gomodel:CHEBI_60377_RXN-5781. Source location `./YeastPathways_PWY3O-450.json#/facts/2; endpoint types: /individuals/14/type; /individuals/12/type`
CTP + phosphocholine + H⁺ -> CDP-choline + diphosphate `gomodel:2.7.7.15-RXN`	has_output	CDP-choline(1-) `CHEBI:58779`	gomodel:YeastPathways_PWY3O-450 Source assertion: The model asserts gomodel:2.7.7.15-RXN RO:0002234 gomodel:CHEBI_58779_2.7.7.15-RXN. Source location `./YeastPathways_PWY3O-450.json#/facts/3; endpoint types: /individuals/42/type; /individuals/11/type`
a 1,2-diacyl-sn-glycerol + CDP-choline <=> a phosphatidylcholine + CMP + H⁺ `gomodel:RXN-5781`	has_output	1,2-diacyl-sn-glycero-3-phosphocholine(1+) `CHEBI:16110`	gomodel:YeastPathways_PWY3O-450 Source assertion: The model asserts gomodel:RXN-5781 RO:0002234 gomodel:CHEBI_16110_RXN-5781. Source location `./YeastPathways_PWY3O-450.json#/facts/4; endpoint types: /individuals/14/type; /individuals/4/type`
choline + ATP -> phosphocholine + ADP + H⁺ `gomodel:CHOLINE-KINASE-RXN`	part_of	CDP-choline pathway `GO:0006657`	gomodel:YeastPathways_PWY3O-450 Source assertion: The model asserts gomodel:CHOLINE-KINASE-RXN BFO:0000050 gomodel:YeastPathways_PWY3O-450/YeastPathways_PWY3O-450. Source location `./YeastPathways_PWY3O-450.json#/facts/5; endpoint types: /individuals/13/type; /individuals/43/type`
a 1,2-diacyl-sn-glycerol + CDP-choline <=> a phosphatidylcholine + CMP + H⁺ `gomodel:RXN-5781`	has_output	hydron `CHEBI:15378`	gomodel:YeastPathways_PWY3O-450 Source assertion: The model asserts gomodel:RXN-5781 RO:0002234 gomodel:CHEBI_15378_RXN-5781. Source location `./YeastPathways_PWY3O-450.json#/facts/6; endpoint types: /individuals/14/type; /individuals/3/type`
CTP + phosphocholine + H⁺ -> CDP-choline + diphosphate `gomodel:2.7.7.15-RXN`	has_input	CTP(4-) `CHEBI:37563`	gomodel:YeastPathways_PWY3O-450 Source assertion: The model asserts gomodel:2.7.7.15-RXN RO:0002233 gomodel:CHEBI_37563_2.7.7.15-RXN. Source location `./YeastPathways_PWY3O-450.json#/facts/7; endpoint types: /individuals/42/type; /individuals/9/type`
a 1,2-diacyl-sn-glycerol + CDP-choline <=> a phosphatidylcholine + CMP + H⁺ `gomodel:RXN-5781`	has_input	1,2-diacyl-sn-glycerol `CHEBI:17815`	gomodel:YeastPathways_PWY3O-450 Source assertion: The model asserts gomodel:RXN-5781 RO:0002233 gomodel:CHEBI_17815_RXN-5781. Source location `./YeastPathways_PWY3O-450.json#/facts/8; endpoint types: /individuals/14/type; /individuals/5/type`
CTP + phosphocholine + H⁺ -> CDP-choline + diphosphate `gomodel:2.7.7.15-RXN`	part_of	CDP-choline pathway `GO:0006657`	gomodel:YeastPathways_PWY3O-450 Source assertion: The model asserts gomodel:2.7.7.15-RXN BFO:0000050 gomodel:YeastPathways_PWY3O-450/YeastPathways_PWY3O-450. Source location `./YeastPathways_PWY3O-450.json#/facts/9; endpoint types: /individuals/42/type; /individuals/43/type`
CTP + phosphocholine + H⁺ -> CDP-choline + diphosphate `gomodel:2.7.7.15-RXN`	has_output	diphosphoric acid `CHEBI:29888`	gomodel:YeastPathways_PWY3O-450 Source assertion: The model asserts gomodel:2.7.7.15-RXN RO:0002234 gomodel:CHEBI_29888_2.7.7.15-RXN. Source location `./YeastPathways_PWY3O-450.json#/facts/11; endpoint types: /individuals/42/type; /individuals/7/type`
CTP + phosphocholine + H⁺ -> CDP-choline + diphosphate `gomodel:2.7.7.15-RXN`	has_input	hydron `CHEBI:15378`	gomodel:YeastPathways_PWY3O-450 Source assertion: The model asserts gomodel:2.7.7.15-RXN RO:0002233 gomodel:CHEBI_15378_2.7.7.15-RXN. Source location `./YeastPathways_PWY3O-450.json#/facts/12; endpoint types: /individuals/42/type; /individuals/1/type`
PCT1 Scer `SGD:S000003434`	enables	CTP + phosphocholine + H⁺ -> CDP-choline + diphosphate `gomodel:2.7.7.15-RXN`	gomodel:YeastPathways_PWY3O-450 Source assertion: The model asserts gomodel:2.7.7.15-RXN RO:0002333 gomodel:YGR202C-MONOMER_2.7.7.15-RXN_controller. Source location `./YeastPathways_PWY3O-450.json#/facts/13; endpoint types: /individuals/42/type; /individuals/15/type`
CTP + phosphocholine + H⁺ -> CDP-choline + diphosphate `gomodel:2.7.7.15-RXN`	has_input	choline phosphate(1-) `CHEBI:295975`	gomodel:YeastPathways_PWY3O-450 Source assertion: The model asserts gomodel:2.7.7.15-RXN RO:0002233 gomodel:CHEBI_295975_CHOLINE-KINASE-RXN. Source location `./YeastPathways_PWY3O-450.json#/facts/14; endpoint types: /individuals/42/type; /individuals/6/type`
CKI1 Scer `SGD:S000004123`	enables	choline + ATP -> phosphocholine + ADP + H⁺ `gomodel:CHOLINE-KINASE-RXN`	gomodel:YeastPathways_PWY3O-450 Source assertion: The model asserts gomodel:CHOLINE-KINASE-RXN RO:0002333 gomodel:YLR133W-MONOMER_CHOLINE-KINASE-RXN_controller. Source location `./YeastPathways_PWY3O-450.json#/facts/16; endpoint types: /individuals/13/type; /individuals/16/type`
choline + ATP -> phosphocholine + ADP + H⁺ `gomodel:CHOLINE-KINASE-RXN`	occurs_in	cytosol `GO:0005829`	gomodel:YeastPathways_PWY3O-450 Source assertion: The model asserts gomodel:CHOLINE-KINASE-RXN BFO:0000066 gomodel:reaction_CHOLINE-KINASE-RXN_location_lociGO_0005829. Source location `./YeastPathways_PWY3O-450.json#/facts/17; endpoint types: /individuals/13/type; /individuals/40/type`
a 1,2-diacyl-sn-glycerol + CDP-choline <=> a phosphatidylcholine + CMP + H⁺ `gomodel:RXN-5781`	part_of	CDP-choline pathway `GO:0006657`	gomodel:YeastPathways_PWY3O-450 Source assertion: The model asserts gomodel:RXN-5781 BFO:0000050 gomodel:YeastPathways_PWY3O-450/YeastPathways_PWY3O-450. Source location `./YeastPathways_PWY3O-450.json#/facts/18; endpoint types: /individuals/14/type; /individuals/43/type`
a 1,2-diacyl-sn-glycerol + CDP-choline <=> a phosphatidylcholine + CMP + H⁺ `gomodel:RXN-5781`	has_input	CDP-choline(1-) `CHEBI:58779`	gomodel:YeastPathways_PWY3O-450 Source assertion: The model asserts gomodel:RXN-5781 RO:0002233 gomodel:CHEBI_58779_2.7.7.15-RXN. Source location `./YeastPathways_PWY3O-450.json#/facts/19; endpoint types: /individuals/14/type; /individuals/11/type`
choline + ATP -> phosphocholine + ADP + H⁺ `gomodel:CHOLINE-KINASE-RXN`	has_output	hydron `CHEBI:15378`	gomodel:YeastPathways_PWY3O-450 Source assertion: The model asserts gomodel:CHOLINE-KINASE-RXN RO:0002234 gomodel:CHEBI_15378_CHOLINE-KINASE-RXN. Source location `./YeastPathways_PWY3O-450.json#/facts/20; endpoint types: /individuals/13/type; /individuals/2/type`
choline + ATP -> phosphocholine + ADP + H⁺ `gomodel:CHOLINE-KINASE-RXN`	has_output	ADP(3-) `CHEBI:456216`	gomodel:YeastPathways_PWY3O-450 Source assertion: The model asserts gomodel:CHOLINE-KINASE-RXN RO:0002234 gomodel:CHEBI_456216_CHOLINE-KINASE-RXN. Source location `./YeastPathways_PWY3O-450.json#/facts/21; endpoint types: /individuals/13/type; /individuals/10/type`
choline + ATP -> phosphocholine + ADP + H⁺ `gomodel:CHOLINE-KINASE-RXN`	has_input	choline `CHEBI:15354`	gomodel:YeastPathways_PWY3O-450 Source assertion: The model asserts gomodel:CHOLINE-KINASE-RXN RO:0002233 gomodel:CHEBI_15354_CHOLINE-KINASE-RXN. Source location `./YeastPathways_PWY3O-450.json#/facts/22; endpoint types: /individuals/13/type; /individuals/0/type`
choline + ATP -> phosphocholine + ADP + H⁺ `gomodel:CHOLINE-KINASE-RXN`	has_output	choline phosphate(1-) `CHEBI:295975`	gomodel:YeastPathways_PWY3O-450 Source assertion: The model asserts gomodel:CHOLINE-KINASE-RXN RO:0002234 gomodel:CHEBI_295975_CHOLINE-KINASE-RXN. Source location `./YeastPathways_PWY3O-450.json#/facts/23; endpoint types: /individuals/13/type; /individuals/6/type`
CPT1 Scer `SGD:S000005074`	located_in Physical protein location from reviewed UniProt. evidence code not specified by source Topology: Multi-pass membrane protein.	endoplasmic reticulum membrane `GO:0005789`	UniProtKB:P17898 Source assertion: UniProtKB:P17898 annotates location Endoplasmic reticulum membrane (SL-0097). Source location `https://rest.uniprot.org/uniprotkb/stream?query=taxonomy_id%3A559292+AND+reviewed%3Atrue&format=json&fields=accession%2Cprotein_name%2Cxref_sgd%2Ccc_subcellular_location%2Ccc_function%2Ccc_caution%2Corganism_id#/results/474/comments/1/subcellularLocations/1; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d` UniProtKB:P17898 Source assertion: UniProtKB:P17898 has the exact SGD cross-reference SGD:S000005074. Source location `https://rest.uniprot.org/uniprotkb/stream?query=taxonomy_id%3A559292+AND+reviewed%3Atrue&format=json&fields=accession%2Cprotein_name%2Cxref_sgd%2Ccc_subcellular_location%2Ccc_function%2Ccc_caution%2Corganism_id#/results/474/uniProtKBCrossReferences/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
CPT1 Scer `SGD:S000005074`	located_in Physical protein location from reviewed UniProt. evidence code not specified by source Topology: Multi-pass membrane protein.	mitochondrial outer membrane `GO:0005741`	UniProtKB:P17898 Source assertion: UniProtKB:P17898 annotates location Mitochondrion outer membrane (SL-0172). Source location `https://rest.uniprot.org/uniprotkb/stream?query=taxonomy_id%3A559292+AND+reviewed%3Atrue&format=json&fields=accession%2Cprotein_name%2Cxref_sgd%2Ccc_subcellular_location%2Ccc_function%2Ccc_caution%2Corganism_id#/results/474/comments/1/subcellularLocations/2; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d` UniProtKB:P17898 Source assertion: UniProtKB:P17898 has the exact SGD cross-reference SGD:S000005074. Source location `https://rest.uniprot.org/uniprotkb/stream?query=taxonomy_id%3A559292+AND+reviewed%3Atrue&format=json&fields=accession%2Cprotein_name%2Cxref_sgd%2Ccc_subcellular_location%2Ccc_function%2Ccc_caution%2Corganism_id#/results/474/uniProtKBCrossReferences/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
PCT1 Scer `SGD:S000003434`	located_in Physical protein location from reviewed UniProt. evidence code not specified by source Source qualification: Most of its activity is membrane-associated	membrane `GO:0016020`	UniProtKB:P13259 Source assertion: UniProtKB:P13259 annotates location Membrane (SL-0162). Source location `https://rest.uniprot.org/uniprotkb/stream?query=taxonomy_id%3A559292+AND+reviewed%3Atrue&format=json&fields=accession%2Cprotein_name%2Cxref_sgd%2Ccc_subcellular_location%2Ccc_function%2Ccc_caution%2Corganism_id#/results/364/comments/1/subcellularLocations/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d` UniProtKB:P13259 Source assertion: UniProtKB:P13259 has the exact SGD cross-reference SGD:S000003434. Source location `https://rest.uniprot.org/uniprotkb/stream?query=taxonomy_id%3A559292+AND+reviewed%3Atrue&format=json&fields=accession%2Cprotein_name%2Cxref_sgd%2Ccc_subcellular_location%2Ccc_function%2Ccc_caution%2Corganism_id#/results/364/uniProtKBCrossReferences/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
CKI1 Scer `SGD:S000004123`	located_in Physical protein location from reviewed UniProt. ECO:0000269 (PubMed:14562095)	cytoplasm `GO:0005737`	UniProtKB:P20485 Source assertion: UniProtKB:P20485 annotates location Cytoplasm (SL-0086). Source location `https://rest.uniprot.org/uniprotkb/stream?query=taxonomy_id%3A559292+AND+reviewed%3Atrue&format=json&fields=accession%2Cprotein_name%2Cxref_sgd%2Ccc_subcellular_location%2Ccc_function%2Ccc_caution%2Corganism_id#/results/531/comments/1/subcellularLocations/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d` UniProtKB:P20485 Source assertion: UniProtKB:P20485 has the exact SGD cross-reference SGD:S000004123. Source location `https://rest.uniprot.org/uniprotkb/stream?query=taxonomy_id%3A559292+AND+reviewed%3Atrue&format=json&fields=accession%2Cprotein_name%2Cxref_sgd%2Ccc_subcellular_location%2Ccc_function%2Ccc_caution%2Corganism_id#/results/531/uniProtKBCrossReferences/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
CPT1 Scer `SGD:S000005074`	has_cofactor UniProtKB reviewed (Swiss-Prot) annotation. UniProt evidence: ECO:0000269 (PubMed:1847919)	magnesium(2+) `CHEBI:18420`	UniProtKB:P17898 Source assertion: UniProtKB:P17898 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/474/comments/0/cofactors/0` UniProtKB:P17898 Source assertion: UniProtKB:P17898 has the exact SGD cross-reference SGD:S000005074. 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/474/uniProtKBCrossReferences/0`
CKI1 Scer `SGD:S000004123`	has_cofactor UniProtKB reviewed (Swiss-Prot) annotation. UniProt evidence: ECO:0000269 (PubMed:9506987)	magnesium(2+) `CHEBI:18420`	UniProtKB:P20485 Source assertion: UniProtKB:P20485 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/531/comments/0/cofactors/0` UniProtKB:P20485 Source assertion: UniProtKB:P20485 has the exact SGD cross-reference SGD:S000004123. 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/531/uniProtKBCrossReferences/0`

References

gomodel:YeastPathways_PWY3O-450 SGD GO-CAM phosphatidylcholine biosynthesis I pathway PWY3O-450 (source version: Pinned Noctua JSON archive; model date 2024-07-15; member ./YeastPathways_PWY3O-450.json)
UniProtKB:P17898 Reviewed UniProtKB P17898 location annotations (source version: UniProt release 2026_03)
UniProtKB:P13259 Reviewed UniProtKB P13259 location annotations (source version: UniProt release 2026_03)
UniProtKB:P20485 Reviewed UniProtKB P20485 location annotations (source version: UniProt release 2026_03)

Curation history

2026-10-05T06:05:08Z Codex; review-causal-graph; Reviewed every native GO-CAM fact; preserved precise input/output, causal, location, membership and complex-part relations with traceable structured source evidence. Kept distinct generic physical instances and recorded source-scope exclusions in the cohort review ledger.
2026-10-05T06:43:56Z Codex
- EDIT — Audit causal activity compartments and preserve scoped protein location evidence
  Reviewed all 3 activity location assignments and 3 mapped physical proteins against reviewed S288C UniProt release2026_03 location/function/caution batch SHA256 95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d. Added 4 independently supported location edges and quarantined 2 generic cytosol source assertions. Mapped physical protein locations via exact SGD cross-references; retained source ECO grades, molecular form and conditional notes. Physical protein location alone never generates activity location. Explicitly inspected functional assertions support bounded activity projections. Every original activity location and exclusion is recorded in reports/causal_graph_review/gocam-location-review.json. No independent location annotation is treated as an evidence gap, not a negative result. Cytoplasm is not narrowed to cytosol. Microsome fractions are not projected as in-vivo organelles. Semantic validation passed all85 records;4 independent source-role acceptance tests passed.
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