L-homocysteine biosynthesis

gomodel:YeastPathways_PWY-5344

L-homocysteine biosynthesis in Saccharomyces cerevisiae S288C uses MET2 to acetylate L-homoserine with acetyl-CoA, forming O-acetyl-L-homoserine and coenzyme A, then uses MET17 to condense O-acetyl-L-homoserine with hydrogen sulfide to produce L-homocysteine, acetate, and hydron.

Pathway type

amino acid biosynthesis

Organism scope

Saccharomyces cerevisiae S288C NCBITaxon:559292

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Pathway network

16 nodes · 19 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
acetate `CHEBI:30089`	small molecule
O-acetyl-L-homoserine zwitterion `CHEBI:57716`	small molecule
MET2 Scer `SGD:S000005221`	protein
L-homoserine zwitterion `CHEBI:57476`	small molecule
hydron `CHEBI:15378`	small molecule
acetyl-CoA(4-) `CHEBI:57288`	small molecule
hydrogen sulfide `CHEBI:16136`	small molecule
L-homocysteine biosynthetic process `GO:0071269`	biological process
L-homocysteine zwitterion `CHEBI:58199`	small molecule
cytosol `GO:0005829`	cellular component
coenzyme A(4-) `CHEBI:57287`	small molecule
MET17 Scer `SGD:S000004294`	protein
cytoplasm `GO:0005737`	cellular component
pyridoxal 5'-phosphate(2-) `CHEBI:597326`	cofactor
O-acetyl-L-homoserine + hydrogen sulfide -> L-homocysteine + acetate + H⁺ `gomodel:ACETYLHOMOSER-CYS-RXN`	molecular activity
L-homoserine + acetyl-CoA -> O-acetyl-L-homoserine + coenzyme A `gomodel:HOMOSERINE-O-ACETYLTRANSFERASE-RXN`	molecular activity

Mechanistic edges

Mechanistic edges and their cited evidence
Subject	Predicate and description	Object	Evidence
O-acetyl-L-homoserine + hydrogen sulfide -> L-homocysteine + acetate + H⁺ `gomodel:ACETYLHOMOSER-CYS-RXN`	has_output	acetate `CHEBI:30089`	gomodel:YeastPathways_PWY-5344 Source assertion: The model asserts gomodel:ACETYLHOMOSER-CYS-RXN RO:0002234 gomodel:CHEBI_30089_ACETYLHOMOSER-CYS-RXN. Source location `./YeastPathways_PWY-5344.json#/facts/0; endpoint types: /individuals/0/type; /individuals/3/type`
L-homoserine + acetyl-CoA -> O-acetyl-L-homoserine + coenzyme A `gomodel:HOMOSERINE-O-ACETYLTRANSFERASE-RXN`	has_output	O-acetyl-L-homoserine zwitterion `CHEBI:57716`	gomodel:YeastPathways_PWY-5344 Source assertion: The model asserts gomodel:HOMOSERINE-O-ACETYLTRANSFERASE-RXN RO:0002234 gomodel:CHEBI_57716_HOMOSERINE-O-ACETYLTRANSFERASE-RXN. Source location `./YeastPathways_PWY-5344.json#/facts/1; endpoint types: /individuals/9/type; /individuals/7/type`
MET2 Scer `SGD:S000005221`	enables	L-homoserine + acetyl-CoA -> O-acetyl-L-homoserine + coenzyme A `gomodel:HOMOSERINE-O-ACETYLTRANSFERASE-RXN`	gomodel:YeastPathways_PWY-5344 Source assertion: The model asserts gomodel:HOMOSERINE-O-ACETYLTRANSFERASE-RXN RO:0002333 gomodel:YNL277W-MONOMER_HOMOSERINE-O-ACETYLTRANSFERASE-RXN_controller. Source location `./YeastPathways_PWY-5344.json#/facts/2; endpoint types: /individuals/9/type; /individuals/11/type`
O-acetyl-L-homoserine + hydrogen sulfide -> L-homocysteine + acetate + H⁺ `gomodel:ACETYLHOMOSER-CYS-RXN`	has_input	O-acetyl-L-homoserine zwitterion `CHEBI:57716`	gomodel:YeastPathways_PWY-5344 Source assertion: The model asserts gomodel:ACETYLHOMOSER-CYS-RXN RO:0002233 gomodel:CHEBI_57716_HOMOSERINE-O-ACETYLTRANSFERASE-RXN. Source location `./YeastPathways_PWY-5344.json#/facts/3; endpoint types: /individuals/0/type; /individuals/7/type`
L-homoserine + acetyl-CoA -> O-acetyl-L-homoserine + coenzyme A `gomodel:HOMOSERINE-O-ACETYLTRANSFERASE-RXN`	has_input	L-homoserine zwitterion `CHEBI:57476`	gomodel:YeastPathways_PWY-5344 Source assertion: The model asserts gomodel:HOMOSERINE-O-ACETYLTRANSFERASE-RXN RO:0002233 gomodel:CHEBI_57476_HOMOSERINE-O-ACETYLTRANSFERASE-RXN. Source location `./YeastPathways_PWY-5344.json#/facts/4; endpoint types: /individuals/9/type; /individuals/6/type`
O-acetyl-L-homoserine + hydrogen sulfide -> L-homocysteine + acetate + H⁺ `gomodel:ACETYLHOMOSER-CYS-RXN`	has_output	hydron `CHEBI:15378`	gomodel:YeastPathways_PWY-5344 Source assertion: The model asserts gomodel:ACETYLHOMOSER-CYS-RXN RO:0002234 gomodel:CHEBI_15378_ACETYLHOMOSER-CYS-RXN. Source location `./YeastPathways_PWY-5344.json#/facts/5; endpoint types: /individuals/0/type; /individuals/1/type`
L-homoserine + acetyl-CoA -> O-acetyl-L-homoserine + coenzyme A `gomodel:HOMOSERINE-O-ACETYLTRANSFERASE-RXN`	has_input	acetyl-CoA(4-) `CHEBI:57288`	gomodel:YeastPathways_PWY-5344 Source assertion: The model asserts gomodel:HOMOSERINE-O-ACETYLTRANSFERASE-RXN RO:0002233 gomodel:CHEBI_57288_HOMOSERINE-O-ACETYLTRANSFERASE-RXN. Source location `./YeastPathways_PWY-5344.json#/facts/6; endpoint types: /individuals/9/type; /individuals/5/type`
O-acetyl-L-homoserine + hydrogen sulfide -> L-homocysteine + acetate + H⁺ `gomodel:ACETYLHOMOSER-CYS-RXN`	has_input	hydrogen sulfide `CHEBI:16136`	gomodel:YeastPathways_PWY-5344 Source assertion: The model asserts gomodel:ACETYLHOMOSER-CYS-RXN RO:0002233 gomodel:CHEBI_16136_ACETYLHOMOSER-CYS-RXN. Source location `./YeastPathways_PWY-5344.json#/facts/7; endpoint types: /individuals/0/type; /individuals/2/type`
L-homoserine + acetyl-CoA -> O-acetyl-L-homoserine + coenzyme A `gomodel:HOMOSERINE-O-ACETYLTRANSFERASE-RXN`	part_of	L-homocysteine biosynthetic process `GO:0071269`	gomodel:YeastPathways_PWY-5344 Source assertion: The model asserts gomodel:HOMOSERINE-O-ACETYLTRANSFERASE-RXN BFO:0000050 gomodel:YeastPathways_PWY-5344/YeastPathways_PWY-5344. Source location `./YeastPathways_PWY-5344.json#/facts/8; endpoint types: /individuals/9/type; /individuals/27/type`
O-acetyl-L-homoserine + hydrogen sulfide -> L-homocysteine + acetate + H⁺ `gomodel:ACETYLHOMOSER-CYS-RXN`	has_output	L-homocysteine zwitterion `CHEBI:58199`	gomodel:YeastPathways_PWY-5344 Source assertion: The model asserts gomodel:ACETYLHOMOSER-CYS-RXN RO:0002234 gomodel:CHEBI_58199_ACETYLHOMOSER-CYS-RXN. Source location `./YeastPathways_PWY-5344.json#/facts/9; endpoint types: /individuals/0/type; /individuals/8/type`
O-acetyl-L-homoserine + hydrogen sulfide -> L-homocysteine + acetate + H⁺ `gomodel:ACETYLHOMOSER-CYS-RXN`	occurs_in	cytosol `GO:0005829`	gomodel:YeastPathways_PWY-5344 Source assertion: The model asserts gomodel:ACETYLHOMOSER-CYS-RXN BFO:0000066 gomodel:reaction_ACETYLHOMOSER-CYS-RXN_location_lociGO_0005829. Source location `./YeastPathways_PWY-5344.json#/facts/10; endpoint types: /individuals/0/type; /individuals/25/type`
L-homoserine + acetyl-CoA -> O-acetyl-L-homoserine + coenzyme A `gomodel:HOMOSERINE-O-ACETYLTRANSFERASE-RXN`	has_output	coenzyme A(4-) `CHEBI:57287`	gomodel:YeastPathways_PWY-5344 Source assertion: The model asserts gomodel:HOMOSERINE-O-ACETYLTRANSFERASE-RXN RO:0002234 gomodel:CHEBI_57287_HOMOSERINE-O-ACETYLTRANSFERASE-RXN. Source location `./YeastPathways_PWY-5344.json#/facts/11; endpoint types: /individuals/9/type; /individuals/4/type`
O-acetyl-L-homoserine + hydrogen sulfide -> L-homocysteine + acetate + H⁺ `gomodel:ACETYLHOMOSER-CYS-RXN`	part_of	L-homocysteine biosynthetic process `GO:0071269`	gomodel:YeastPathways_PWY-5344 Source assertion: The model asserts gomodel:ACETYLHOMOSER-CYS-RXN BFO:0000050 gomodel:YeastPathways_PWY-5344/YeastPathways_PWY-5344. Source location `./YeastPathways_PWY-5344.json#/facts/12; endpoint types: /individuals/0/type; /individuals/27/type`
MET17 Scer `SGD:S000004294`	enables	O-acetyl-L-homoserine + hydrogen sulfide -> L-homocysteine + acetate + H⁺ `gomodel:ACETYLHOMOSER-CYS-RXN`	gomodel:YeastPathways_PWY-5344 Source assertion: The model asserts gomodel:ACETYLHOMOSER-CYS-RXN RO:0002333 gomodel:YLR303W-MONOMER_ACETYLHOMOSER-CYS-RXN_controller. Source location `./YeastPathways_PWY-5344.json#/facts/13; endpoint types: /individuals/0/type; /individuals/10/type`
L-homoserine + acetyl-CoA -> O-acetyl-L-homoserine + coenzyme A `gomodel:HOMOSERINE-O-ACETYLTRANSFERASE-RXN`	provides_input_for	O-acetyl-L-homoserine + hydrogen sulfide -> L-homocysteine + acetate + H⁺ `gomodel:ACETYLHOMOSER-CYS-RXN`	gomodel:YeastPathways_PWY-5344 Source assertion: The model asserts gomodel:HOMOSERINE-O-ACETYLTRANSFERASE-RXN RO:0002413 gomodel:ACETYLHOMOSER-CYS-RXN. Source location `./YeastPathways_PWY-5344.json#/facts/14; endpoint types: /individuals/9/type; /individuals/0/type`
L-homoserine + acetyl-CoA -> O-acetyl-L-homoserine + coenzyme A `gomodel:HOMOSERINE-O-ACETYLTRANSFERASE-RXN`	occurs_in	cytosol `GO:0005829`	gomodel:YeastPathways_PWY-5344 Source assertion: The model asserts gomodel:HOMOSERINE-O-ACETYLTRANSFERASE-RXN BFO:0000066 gomodel:reaction_HOMOSERINE-O-ACETYLTRANSFERASE-RXN_location_lociGO_0005829. Source location `./YeastPathways_PWY-5344.json#/facts/15; endpoint types: /individuals/9/type; /individuals/26/type`
MET2 Scer `SGD:S000005221`	located_in Physical protein location from reviewed UniProt. ECO:0000269 (PubMed:11914276); ECO:0000269 (PubMed:14562095)	cytoplasm `GO:0005737`	UniProtKB:P08465 Source assertion: UniProtKB:P08465 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/3255/comments/1/subcellularLocations/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d` UniProtKB:P08465 Source assertion: UniProtKB:P08465 has the exact SGD cross-reference SGD:S000005221. 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/3255/uniProtKBCrossReferences/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
MET17 Scer `SGD:S000004294`	located_in Physical protein location from reviewed UniProt. ECO:0000269 (PubMed:11914276)	cytoplasm `GO:0005737`	UniProtKB:P06106 Source assertion: UniProtKB:P06106 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/125/comments/1/subcellularLocations/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d` UniProtKB:P06106 Source assertion: UniProtKB:P06106 has the exact SGD cross-reference SGD:S000004294. 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/125/uniProtKBCrossReferences/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
MET17 Scer `SGD:S000004294`	has_cofactor UniProtKB reviewed (Swiss-Prot) annotation. UniProt evidence: ECO:0000269 (PubMed:4609980); ECO:0000269 (PubMed:4947307); ECO:0000269 (PubMed:7765825); ECO:0000269 (PubMed:795806)	pyridoxal 5'-phosphate(2-) `CHEBI:597326`	UniProtKB:P06106 Source assertion: UniProtKB:P06106 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/125/comments/0/cofactors/0` UniProtKB:P06106 Source assertion: UniProtKB:P06106 has the exact SGD cross-reference SGD:S000004294. 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/125/uniProtKBCrossReferences/0`

References

gomodel:YeastPathways_PWY-5344 SGD GO-CAM L-homocysteine biosynthesis pathway PWY-5344 (source version: Pinned Noctua JSON archive; model date 2026-07-31; member ./YeastPathways_PWY-5344.json)
UniProtKB:P08465 Reviewed UniProtKB P08465 location annotations (source version: UniProt release 2026_03)
UniProtKB:P06106 Reviewed UniProtKB P06106 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 2 activity location assignments and 2 mapped physical proteins against reviewed S288C UniProt release2026_03 location/function/caution batch SHA256 95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d. Added 2 independently supported location edges and quarantined 0 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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