siroheme biosynthesis

gomodel:YeastPathways_PWY-5194-1

Siroheme biosynthesis in Saccharomyces cerevisiae S288C methylates uroporphyrinogen III to precorrin-2, oxidizes precorrin-2 to sirohydrochlorin, and inserts iron into sirohydrochlorin to form siroheme.

Pathway type

Organism scope

Saccharomyces cerevisiae S288C NCBITaxon:559292

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Pathway network

17 nodes · 25 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
iron(2+) `CHEBI:29033`	small molecule
NADH(2-) `CHEBI:57945`	small molecule
hydron `CHEBI:15378`	small molecule
sirohydrochlorin(8-) `CHEBI:58351`	small molecule
cytosol `GO:0005829`	cellular component
NAD(1-) `CHEBI:57540`	small molecule
S-adenosyl-L-homocysteine zwitterion `CHEBI:57856`	small molecule
siroheme biosynthetic process `GO:0019354`	biological process
precorrin-2(7-) `CHEBI:58827`	small molecule
uroporphyrinogen III(8-) `CHEBI:57308`	small molecule
siroheme(8-) `CHEBI:60052`	small molecule
S-adenosyl-L-methionine zwitterion `CHEBI:59789`	small molecule
MET1 Scer `SGD:S000001777`	protein
MET8 Scer `SGD:S000000417`	protein
precorrin-2 dehydrogenase activity `gomodel:DIMETHUROPORDEHYDROG-RXN`	molecular activity
uroporphyrin-III C-methyltransferase activity `gomodel:RXN-13403`	molecular activity
sirohydrochlorin ferrochelatase activity `gomodel:SIROHEME-FERROCHELAT-RXN`	molecular activity

Mechanistic edges

Mechanistic edges and their cited evidence
Subject	Predicate and description	Object	Evidence
uroporphyrin-III C-methyltransferase activity `gomodel:RXN-13403`	provides_input_for	precorrin-2 dehydrogenase activity `gomodel:DIMETHUROPORDEHYDROG-RXN`	gomodel:YeastPathways_PWY-5194-1 Source assertion: The model asserts gomodel:RXN-13403 RO:0002413 gomodel:DIMETHUROPORDEHYDROG-RXN. Source location `./YeastPathways_PWY-5194-1.json#/facts/0; endpoint types: /individuals/16/type; /individuals/12/type`
sirohydrochlorin ferrochelatase activity `gomodel:SIROHEME-FERROCHELAT-RXN`	has_input	iron(2+) `CHEBI:29033`	gomodel:YeastPathways_PWY-5194-1 Source assertion: The model asserts gomodel:SIROHEME-FERROCHELAT-RXN RO:0002233 gomodel:CHEBI_29033_SIROHEME-FERROCHELAT-RXN. Source location `./YeastPathways_PWY-5194-1.json#/facts/1; endpoint types: /individuals/17/type; /individuals/3/type`
precorrin-2 dehydrogenase activity `gomodel:DIMETHUROPORDEHYDROG-RXN`	has_output	NADH(2-) `CHEBI:57945`	gomodel:YeastPathways_PWY-5194-1 Source assertion: The model asserts gomodel:DIMETHUROPORDEHYDROG-RXN RO:0002234 gomodel:CHEBI_57945_DIMETHUROPORDEHYDROG-RXN. Source location `./YeastPathways_PWY-5194-1.json#/facts/2; endpoint types: /individuals/12/type; /individuals/7/type`
uroporphyrin-III C-methyltransferase activity `gomodel:RXN-13403`	has_output	hydron `CHEBI:15378`	gomodel:YeastPathways_PWY-5194-1 Source assertion: The model asserts gomodel:RXN-13403 RO:0002234 gomodel:CHEBI_15378_RXN-13403. Source location `./YeastPathways_PWY-5194-1.json#/facts/3; endpoint types: /individuals/16/type; /individuals/1/type`
precorrin-2 dehydrogenase activity `gomodel:DIMETHUROPORDEHYDROG-RXN`	has_output	sirohydrochlorin(8-) `CHEBI:58351`	gomodel:YeastPathways_PWY-5194-1 Source assertion: The model asserts gomodel:DIMETHUROPORDEHYDROG-RXN RO:0002234 gomodel:CHEBI_58351_DIMETHUROPORDEHYDROG-RXN. Source location `./YeastPathways_PWY-5194-1.json#/facts/4; endpoint types: /individuals/12/type; /individuals/8/type`
uroporphyrin-III C-methyltransferase activity `gomodel:RXN-13403`	occurs_in	cytosol `GO:0005829`	gomodel:YeastPathways_PWY-5194-1 Source assertion: The model asserts gomodel:RXN-13403 BFO:0000066 gomodel:reaction_RXN-13403_location_lociGO_0005829. Source location `./YeastPathways_PWY-5194-1.json#/facts/5; endpoint types: /individuals/16/type; /individuals/39/type`
precorrin-2 dehydrogenase activity `gomodel:DIMETHUROPORDEHYDROG-RXN`	has_input	NAD(1-) `CHEBI:57540`	gomodel:YeastPathways_PWY-5194-1 Source assertion: The model asserts gomodel:DIMETHUROPORDEHYDROG-RXN RO:0002233 gomodel:CHEBI_57540_DIMETHUROPORDEHYDROG-RXN. Source location `./YeastPathways_PWY-5194-1.json#/facts/6; endpoint types: /individuals/12/type; /individuals/5/type`
sirohydrochlorin ferrochelatase activity `gomodel:SIROHEME-FERROCHELAT-RXN`	has_input	sirohydrochlorin(8-) `CHEBI:58351`	gomodel:YeastPathways_PWY-5194-1 Source assertion: The model asserts gomodel:SIROHEME-FERROCHELAT-RXN RO:0002233 gomodel:CHEBI_58351_DIMETHUROPORDEHYDROG-RXN. Source location `./YeastPathways_PWY-5194-1.json#/facts/7; endpoint types: /individuals/17/type; /individuals/8/type`
uroporphyrin-III C-methyltransferase activity `gomodel:RXN-13403`	has_output	S-adenosyl-L-homocysteine zwitterion `CHEBI:57856`	gomodel:YeastPathways_PWY-5194-1 Source assertion: The model asserts gomodel:RXN-13403 RO:0002234 gomodel:CHEBI_57856_RXN-13403. Source location `./YeastPathways_PWY-5194-1.json#/facts/8; endpoint types: /individuals/16/type; /individuals/6/type`
precorrin-2 dehydrogenase activity `gomodel:DIMETHUROPORDEHYDROG-RXN`	part_of	siroheme biosynthetic process `GO:0019354`	gomodel:YeastPathways_PWY-5194-1 Source assertion: The model asserts gomodel:DIMETHUROPORDEHYDROG-RXN BFO:0000050 gomodel:YeastPathways_PWY-5194-1/YeastPathways_PWY-5194-1. Source location `./YeastPathways_PWY-5194-1.json#/facts/9; endpoint types: /individuals/12/type; /individuals/41/type`
sirohydrochlorin ferrochelatase activity `gomodel:SIROHEME-FERROCHELAT-RXN`	has_output	hydron `CHEBI:15378`	gomodel:YeastPathways_PWY-5194-1 Source assertion: The model asserts gomodel:SIROHEME-FERROCHELAT-RXN RO:0002234 gomodel:CHEBI_15378_SIROHEME-FERROCHELAT-RXN. Source location `./YeastPathways_PWY-5194-1.json#/facts/10; endpoint types: /individuals/17/type; /individuals/2/type`
precorrin-2 dehydrogenase activity `gomodel:DIMETHUROPORDEHYDROG-RXN`	has_input	precorrin-2(7-) `CHEBI:58827`	gomodel:YeastPathways_PWY-5194-1 Source assertion: The model asserts gomodel:DIMETHUROPORDEHYDROG-RXN RO:0002233 gomodel:CHEBI_58827_RXN-13403. Source location `./YeastPathways_PWY-5194-1.json#/facts/11; endpoint types: /individuals/12/type; /individuals/9/type`
uroporphyrin-III C-methyltransferase activity `gomodel:RXN-13403`	has_input	uroporphyrinogen III(8-) `CHEBI:57308`	gomodel:YeastPathways_PWY-5194-1 Source assertion: The model asserts gomodel:RXN-13403 RO:0002233 gomodel:CHEBI_57308_RXN-13403. Source location `./YeastPathways_PWY-5194-1.json#/facts/12; endpoint types: /individuals/16/type; /individuals/4/type`
sirohydrochlorin ferrochelatase activity `gomodel:SIROHEME-FERROCHELAT-RXN`	has_output	siroheme(8-) `CHEBI:60052`	gomodel:YeastPathways_PWY-5194-1 Source assertion: The model asserts gomodel:SIROHEME-FERROCHELAT-RXN RO:0002234 gomodel:CHEBI_60052_SIROHEME-FERROCHELAT-RXN. Source location `./YeastPathways_PWY-5194-1.json#/facts/13; endpoint types: /individuals/17/type; /individuals/11/type`
precorrin-2 dehydrogenase activity `gomodel:DIMETHUROPORDEHYDROG-RXN`	has_output	hydron `CHEBI:15378`	gomodel:YeastPathways_PWY-5194-1 Source assertion: The model asserts gomodel:DIMETHUROPORDEHYDROG-RXN RO:0002234 gomodel:CHEBI_15378_DIMETHUROPORDEHYDROG-RXN. Source location `./YeastPathways_PWY-5194-1.json#/facts/14; endpoint types: /individuals/12/type; /individuals/0/type`
uroporphyrin-III C-methyltransferase activity `gomodel:RXN-13403`	has_input	S-adenosyl-L-methionine zwitterion `CHEBI:59789`	gomodel:YeastPathways_PWY-5194-1 Source assertion: The model asserts gomodel:RXN-13403 RO:0002233 gomodel:CHEBI_59789_RXN-13403. Source location `./YeastPathways_PWY-5194-1.json#/facts/15; endpoint types: /individuals/16/type; /individuals/10/type`
precorrin-2 dehydrogenase activity `gomodel:DIMETHUROPORDEHYDROG-RXN`	occurs_in	cytosol `GO:0005829`	gomodel:YeastPathways_PWY-5194-1 Source assertion: The model asserts gomodel:DIMETHUROPORDEHYDROG-RXN BFO:0000066 gomodel:reaction_DIMETHUROPORDEHYDROG-RXN_location_lociGO_0005829. Source location `./YeastPathways_PWY-5194-1.json#/facts/16; endpoint types: /individuals/12/type; /individuals/38/type`
MET1 Scer `SGD:S000001777`	enables	uroporphyrin-III C-methyltransferase activity `gomodel:RXN-13403`	gomodel:YeastPathways_PWY-5194-1 Source assertion: The model asserts gomodel:RXN-13403 RO:0002333 gomodel:MONOMER3O-47_RXN-13403_controller. Source location `./YeastPathways_PWY-5194-1.json#/facts/17; endpoint types: /individuals/16/type; /individuals/15/type`
uroporphyrin-III C-methyltransferase activity `gomodel:RXN-13403`	part_of	siroheme biosynthetic process `GO:0019354`	gomodel:YeastPathways_PWY-5194-1 Source assertion: The model asserts gomodel:RXN-13403 BFO:0000050 gomodel:YeastPathways_PWY-5194-1/YeastPathways_PWY-5194-1. Source location `./YeastPathways_PWY-5194-1.json#/facts/18; endpoint types: /individuals/16/type; /individuals/41/type`
sirohydrochlorin ferrochelatase activity `gomodel:SIROHEME-FERROCHELAT-RXN`	part_of	siroheme biosynthetic process `GO:0019354`	gomodel:YeastPathways_PWY-5194-1 Source assertion: The model asserts gomodel:SIROHEME-FERROCHELAT-RXN BFO:0000050 gomodel:YeastPathways_PWY-5194-1/YeastPathways_PWY-5194-1. Source location `./YeastPathways_PWY-5194-1.json#/facts/19; endpoint types: /individuals/17/type; /individuals/41/type`
MET8 Scer `SGD:S000000417`	enables	precorrin-2 dehydrogenase activity `gomodel:DIMETHUROPORDEHYDROG-RXN`	gomodel:YeastPathways_PWY-5194-1 Source assertion: The model asserts gomodel:DIMETHUROPORDEHYDROG-RXN RO:0002333 gomodel:MONOMER3O-106_DIMETHUROPORDEHYDROG-RXN_controller. Source location `./YeastPathways_PWY-5194-1.json#/facts/20; endpoint types: /individuals/12/type; /individuals/13/type`
sirohydrochlorin ferrochelatase activity `gomodel:SIROHEME-FERROCHELAT-RXN`	occurs_in	cytosol `GO:0005829`	gomodel:YeastPathways_PWY-5194-1 Source assertion: The model asserts gomodel:SIROHEME-FERROCHELAT-RXN BFO:0000066 gomodel:reaction_SIROHEME-FERROCHELAT-RXN_location_lociGO_0005829. Source location `./YeastPathways_PWY-5194-1.json#/facts/21; endpoint types: /individuals/17/type; /individuals/40/type`
MET8 Scer `SGD:S000000417`	enables	sirohydrochlorin ferrochelatase activity `gomodel:SIROHEME-FERROCHELAT-RXN`	gomodel:YeastPathways_PWY-5194-1 Source assertion: The model asserts gomodel:SIROHEME-FERROCHELAT-RXN RO:0002333 gomodel:MONOMER3O-106_SIROHEME-FERROCHELAT-RXN_controller. Source location `./YeastPathways_PWY-5194-1.json#/facts/22; endpoint types: /individuals/17/type; /individuals/14/type`
precorrin-2 dehydrogenase activity `gomodel:DIMETHUROPORDEHYDROG-RXN`	provides_input_for	sirohydrochlorin ferrochelatase activity `gomodel:SIROHEME-FERROCHELAT-RXN`	gomodel:YeastPathways_PWY-5194-1 Source assertion: The model asserts gomodel:DIMETHUROPORDEHYDROG-RXN RO:0002413 gomodel:SIROHEME-FERROCHELAT-RXN. Source location `./YeastPathways_PWY-5194-1.json#/facts/23; endpoint types: /individuals/12/type; /individuals/17/type`
uroporphyrin-III C-methyltransferase activity `gomodel:RXN-13403`	has_output	precorrin-2(7-) `CHEBI:58827`	gomodel:YeastPathways_PWY-5194-1 Source assertion: The model asserts gomodel:RXN-13403 RO:0002234 gomodel:CHEBI_58827_RXN-13403. Source location `./YeastPathways_PWY-5194-1.json#/facts/24; endpoint types: /individuals/16/type; /individuals/9/type`

References

gomodel:YeastPathways_PWY-5194-1 GO-CAM siroheme biosynthesis model YeastPathways_PWY-5194-1 (source version: Pinned Noctua JSON archive; model date 2026-08-04; member ./YeastPathways_PWY-5194-1.json)

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
- REVIEW — Audit causal activity compartments and preserve scoped protein location evidence
  Reviewed all 3 activity location assignments and 2 mapped physical proteins against reviewed S288C UniProt release2026_03 location/function/caution batch SHA256 95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d. Added 0 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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