adenosine deoxyribonucleotides de novo biosynthesis II

gomodel:YeastPathways_PWY-7220-1

Adenosine deoxyribonucleotide biosynthesis in Saccharomyces cerevisiae S288C reduces ADP to dADP through the represented ribonucleoside-diphosphate reductase complexes and phosphorylates dADP to dATP through YNK1. The imported formate-dependent ATP-to-dATP branch has no yeast enzyme assignment and is excluded: it describes class III anaerobic ribonucleotide reductase chemistry, whereas the independently characterized yeast system reduces ribonucleoside diphosphates.

Pathway type

nucleotide biosynthesis

Organism scope

Saccharomyces cerevisiae S288C NCBITaxon:559292

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Pathway network

24 nodes · 42 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
thioredoxin dithiol `CHEBI:15967`	protein
ADP(3-) `CHEBI:456216`	small molecule
dADP(3-) `CHEBI:57667`	small molecule
thioredoxin disulfide `CHEBI:18191`	protein
ATP(4-) `CHEBI:30616`	small molecule
water `CHEBI:15377`	small molecule
CPX-1102 Scer `SGD:S000217933`	complex
CPX-1103 Scer `SGD:S000217934`	complex
YNK1 Scer `SGD:S000001550`	protein
cytosol `GO:0005829`	cellular component
adenosine metabolic process `GO:0046085`	biological process
dATP(4-) `CHEBI:61404`	small molecule
iron cation `CHEBI:24875`	cofactor
Ribonucleoside-diphosphate reductase large chain 1 `UniProtKB:P21524`	protein
Ribonucleoside-diphosphate reductase small chain 1 `UniProtKB:P09938`	protein
Ribonucleoside-diphosphate reductase small chain 2 `UniProtKB:P49723`	protein
cytoplasm `GO:0005737`	cellular component
Ribonucleoside-diphosphate reductase large chain 2 `UniProtKB:P21672`	protein
mitochondrial intermembrane space `GO:0005758`	cellular component
nucleus `GO:0005634`	cellular component
magnesium(2+) `CHEBI:18420`	cofactor
ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor `gomodel:ADPREDUCT-RXN`	molecular activity
nucleoside diphosphate kinase activity `gomodel:DADPKIN-RXN`	molecular activity
ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor `gomodel:YeastPathways_PWY-7220-1/6a2b236300005372`	molecular activity

Mechanistic edges

Mechanistic edges and their cited evidence
Subject	Predicate and description	Object	Evidence
ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor `gomodel:YeastPathways_PWY-7220-1/6a2b236300005372`	has_input	thioredoxin dithiol `CHEBI:15967`	gomodel:YeastPathways_PWY-7220-1 Source assertion: The model asserts gomodel:YeastPathways_PWY-7220-1/6a2b236300005372 RO:0002233 gomodel:YeastPathways_PWY-7220-1/6a2b236300005373. Source location `./YeastPathways_PWY-7220-1.json#/facts/0; endpoint types: /individuals/38/type; /individuals/39/type`
ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor `gomodel:YeastPathways_PWY-7220-1/6a2b236300005372`	has_input	ADP(3-) `CHEBI:456216`	gomodel:YeastPathways_PWY-7220-1 Source assertion: The model asserts gomodel:YeastPathways_PWY-7220-1/6a2b236300005372 RO:0002233 gomodel:YeastPathways_PWY-7220-1/6a2b236300005374. Source location `./YeastPathways_PWY-7220-1.json#/facts/1; endpoint types: /individuals/38/type; /individuals/40/type`
ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor `gomodel:ADPREDUCT-RXN`	has_output	dADP(3-) `CHEBI:57667`	gomodel:YeastPathways_PWY-7220-1 Source assertion: The model asserts gomodel:ADPREDUCT-RXN RO:0002234 gomodel:CHEBI_57667_ADPREDUCT-RXN. Source location `./YeastPathways_PWY-7220-1.json#/facts/2; endpoint types: /individuals/0/type; /individuals/10/type`
ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor `gomodel:ADPREDUCT-RXN`	has_output	thioredoxin disulfide `CHEBI:18191`	gomodel:YeastPathways_PWY-7220-1 Source assertion: The model asserts gomodel:ADPREDUCT-RXN RO:0002234 gomodel:YeastPathways_PWY-7220-1/66a3e0bb00000654. Source location `./YeastPathways_PWY-7220-1.json#/facts/3; endpoint types: /individuals/0/type; /individuals/55/type`
ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor `gomodel:ADPREDUCT-RXN`	has_output	water `CHEBI:15377`	gomodel:YeastPathways_PWY-7220-1 Source assertion: The model asserts gomodel:ADPREDUCT-RXN RO:0002234 gomodel:CHEBI_15377_ADPREDUCT-RXN. Source location `./YeastPathways_PWY-7220-1.json#/facts/7; endpoint types: /individuals/0/type; /individuals/1/type`
ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor `gomodel:YeastPathways_PWY-7220-1/6a2b236300005372`	has_output	dADP(3-) `CHEBI:57667`	gomodel:YeastPathways_PWY-7220-1 Source assertion: The model asserts gomodel:YeastPathways_PWY-7220-1/6a2b236300005372 RO:0002234 gomodel:CHEBI_57667_ADPREDUCT-RXN. Source location `./YeastPathways_PWY-7220-1.json#/facts/8; endpoint types: /individuals/38/type; /individuals/10/type`
CPX-1102 Scer `SGD:S000217933`	enables	ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor `gomodel:ADPREDUCT-RXN`	gomodel:YeastPathways_PWY-7220-1 Source assertion: The model asserts gomodel:ADPREDUCT-RXN RO:0002333 gomodel:YeastPathways_PWY-7220-1/66a3e0bb00000651. Source location `./YeastPathways_PWY-7220-1.json#/facts/10; endpoint types: /individuals/0/type; /individuals/53/type` PMID:6370695 Source assertion: The characterized yeast ribonucleotide reductase reduces all four natural ribonucleoside diphosphates; ADP reduction yields the dADP precursor used in this route. Source location `https://pubmed.ncbi.nlm.nih.gov/6370695/#abstract`
CPX-1103 Scer `SGD:S000217934`	enables	ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor `gomodel:YeastPathways_PWY-7220-1/6a2b236300005372`	gomodel:YeastPathways_PWY-7220-1 Source assertion: The model asserts gomodel:YeastPathways_PWY-7220-1/6a2b236300005372 RO:0002333 gomodel:YeastPathways_PWY-7220-1/6a2b236300005378. Source location `./YeastPathways_PWY-7220-1.json#/facts/11; endpoint types: /individuals/38/type; /individuals/43/type` PMID:6370695 Source assertion: The characterized yeast ribonucleotide reductase reduces all four natural ribonucleoside diphosphates; ADP reduction yields the dADP precursor used in this route. Source location `https://pubmed.ncbi.nlm.nih.gov/6370695/#abstract`
nucleoside diphosphate kinase activity `gomodel:DADPKIN-RXN`	has_output	ADP(3-) `CHEBI:456216`	gomodel:YeastPathways_PWY-7220-1 Source assertion: The model asserts gomodel:DADPKIN-RXN RO:0002234 gomodel:CHEBI_456216_DADPKIN-RXN. Source location `./YeastPathways_PWY-7220-1.json#/facts/13; endpoint types: /individuals/13/type; /individuals/9/type`
ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor `gomodel:YeastPathways_PWY-7220-1/6a2b236300005372`	has_output	thioredoxin disulfide `CHEBI:18191`	gomodel:YeastPathways_PWY-7220-1 Source assertion: The model asserts gomodel:YeastPathways_PWY-7220-1/6a2b236300005372 RO:0002234 gomodel:YeastPathways_PWY-7220-1/6a2b236300005375. Source location `./YeastPathways_PWY-7220-1.json#/facts/14; endpoint types: /individuals/38/type; /individuals/41/type`
YNK1 Scer `SGD:S000001550`	enables	nucleoside diphosphate kinase activity `gomodel:DADPKIN-RXN`	gomodel:YeastPathways_PWY-7220-1 Source assertion: The model asserts gomodel:DADPKIN-RXN RO:0002333 gomodel:YKL067W-MONOMER_DADPKIN-RXN_controller. Source location `./YeastPathways_PWY-7220-1.json#/facts/15; endpoint types: /individuals/13/type; /individuals/15/type`
ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor `gomodel:YeastPathways_PWY-7220-1/6a2b236300005372`	has_output	water `CHEBI:15377`	gomodel:YeastPathways_PWY-7220-1 Source assertion: The model asserts gomodel:YeastPathways_PWY-7220-1/6a2b236300005372 RO:0002234 gomodel:YeastPathways_PWY-7220-1/6a2b236300005376. Source location `./YeastPathways_PWY-7220-1.json#/facts/16; endpoint types: /individuals/38/type; /individuals/42/type`
nucleoside diphosphate kinase activity `gomodel:DADPKIN-RXN`	has_input	dADP(3-) `CHEBI:57667`	gomodel:YeastPathways_PWY-7220-1 Source assertion: The model asserts gomodel:DADPKIN-RXN RO:0002233 gomodel:CHEBI_57667_ADPREDUCT-RXN. Source location `./YeastPathways_PWY-7220-1.json#/facts/17; endpoint types: /individuals/13/type; /individuals/10/type`
nucleoside diphosphate kinase activity `gomodel:DADPKIN-RXN`	occurs_in	cytosol `GO:0005829`	gomodel:YeastPathways_PWY-7220-1 Source assertion: The model asserts gomodel:DADPKIN-RXN BFO:0000066 gomodel:reaction_DADPKIN-RXN_location_lociGO_0005829. Source location `./YeastPathways_PWY-7220-1.json#/facts/18; endpoint types: /individuals/13/type; /individuals/35/type`
ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor `gomodel:YeastPathways_PWY-7220-1/6a2b236300005372`	occurs_in	cytosol `GO:0005829`	gomodel:YeastPathways_PWY-7220-1 Source assertion: The model asserts gomodel:YeastPathways_PWY-7220-1/6a2b236300005372 BFO:0000066 gomodel:YeastPathways_PWY-7220-1/6a2b236300005379. Source location `./YeastPathways_PWY-7220-1.json#/facts/19; endpoint types: /individuals/38/type; /individuals/44/type`
ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor `gomodel:ADPREDUCT-RXN`	occurs_in	cytosol `GO:0005829`	gomodel:YeastPathways_PWY-7220-1 Source assertion: The model asserts gomodel:ADPREDUCT-RXN BFO:0000066 gomodel:reaction_ADPREDUCT-RXN_location_lociGO_0005829. Source location `./YeastPathways_PWY-7220-1.json#/facts/21; endpoint types: /individuals/0/type; /individuals/34/type`
ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor `gomodel:YeastPathways_PWY-7220-1/6a2b236300005372`	part_of	adenosine metabolic process `GO:0046085`	gomodel:YeastPathways_PWY-7220-1 Source assertion: The model asserts gomodel:YeastPathways_PWY-7220-1/6a2b236300005372 BFO:0000050 gomodel:YeastPathways_PWY-7220-1/YeastPathways_PWY-7220-1. Source location `./YeastPathways_PWY-7220-1.json#/facts/22; endpoint types: /individuals/38/type; /individuals/37/type`
nucleoside diphosphate kinase activity `gomodel:DADPKIN-RXN`	part_of	adenosine metabolic process `GO:0046085`	gomodel:YeastPathways_PWY-7220-1 Source assertion: The model asserts gomodel:DADPKIN-RXN BFO:0000050 gomodel:YeastPathways_PWY-7220-1/YeastPathways_PWY-7220-1. Source location `./YeastPathways_PWY-7220-1.json#/facts/24; endpoint types: /individuals/13/type; /individuals/37/type`
ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor `gomodel:ADPREDUCT-RXN`	part_of	adenosine metabolic process `GO:0046085`	gomodel:YeastPathways_PWY-7220-1 Source assertion: The model asserts gomodel:ADPREDUCT-RXN BFO:0000050 gomodel:YeastPathways_PWY-7220-1/YeastPathways_PWY-7220-1. Source location `./YeastPathways_PWY-7220-1.json#/facts/25; endpoint types: /individuals/0/type; /individuals/37/type`
nucleoside diphosphate kinase activity `gomodel:DADPKIN-RXN`	has_input	ATP(4-) `CHEBI:30616`	gomodel:YeastPathways_PWY-7220-1 Source assertion: The model asserts gomodel:DADPKIN-RXN RO:0002233 gomodel:CHEBI_30616_DADPKIN-RXN. Source location `./YeastPathways_PWY-7220-1.json#/facts/26; endpoint types: /individuals/13/type; /individuals/6/type`
ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor `gomodel:ADPREDUCT-RXN`	has_input	thioredoxin dithiol `CHEBI:15967`	gomodel:YeastPathways_PWY-7220-1 Source assertion: The model asserts gomodel:ADPREDUCT-RXN RO:0002233 gomodel:YeastPathways_PWY-7220-1/66a3e0bb00000653. Source location `./YeastPathways_PWY-7220-1.json#/facts/27; endpoint types: /individuals/0/type; /individuals/54/type`
ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor `gomodel:ADPREDUCT-RXN`	has_input	ADP(3-) `CHEBI:456216`	gomodel:YeastPathways_PWY-7220-1 Source assertion: The model asserts gomodel:ADPREDUCT-RXN RO:0002233 gomodel:CHEBI_456216_ADPREDUCT-RXN. Source location `./YeastPathways_PWY-7220-1.json#/facts/29; endpoint types: /individuals/0/type; /individuals/8/type`
nucleoside diphosphate kinase activity `gomodel:DADPKIN-RXN`	has_output	dATP(4-) `CHEBI:61404`	gomodel:YeastPathways_PWY-7220-1 Source assertion: The model asserts gomodel:DADPKIN-RXN RO:0002234 gomodel:CHEBI_61404_DADPKIN-RXN. Source location `./YeastPathways_PWY-7220-1.json#/facts/31; endpoint types: /individuals/13/type; /individuals/11/type`
CPX-1102 Scer `SGD:S000217933`	has_part ECO:0000353: physical interaction evidence; source stoichiometry minValue: 2, maxValue: 2	iron cation `CHEBI:24875`	SGD:S000217933 Source assertion: Complex Portal CPX-1102 lists CHEBI:24875 as a small molecule component; complex evidence is ECO:0000353: physical interaction evidence. Source location `Complex Portal JSON #/participants/0; /evidenceType`
CPX-1102 Scer `SGD:S000217933`	has_part ECO:0000353: physical interaction evidence; source stoichiometry minValue: 2, maxValue: 2	Ribonucleoside-diphosphate reductase large chain 1 `UniProtKB:P21524`	SGD:S000217933 Source assertion: Complex Portal CPX-1102 lists P21524 as a protein component; complex evidence is ECO:0000353: physical interaction evidence. Source location `Complex Portal JSON #/participants/1; /evidenceType`
CPX-1102 Scer `SGD:S000217933`	has_part ECO:0000353: physical interaction evidence; source stoichiometry minValue: 1, maxValue: 1	Ribonucleoside-diphosphate reductase small chain 1 `UniProtKB:P09938`	SGD:S000217933 Source assertion: Complex Portal CPX-1102 lists P09938 as a protein component; complex evidence is ECO:0000353: physical interaction evidence. Source location `Complex Portal JSON #/participants/2; /evidenceType`
CPX-1102 Scer `SGD:S000217933`	has_part ECO:0000353: physical interaction evidence; source stoichiometry minValue: 1, maxValue: 1	Ribonucleoside-diphosphate reductase small chain 2 `UniProtKB:P49723`	SGD:S000217933 Source assertion: Complex Portal CPX-1102 lists P49723 as a protein component; complex evidence is ECO:0000353: physical interaction evidence. Source location `Complex Portal JSON #/participants/3; /evidenceType`
CPX-1102 Scer `SGD:S000217933`	located_in Complex location from the independent composition source; original GO-CAM activity locations are retained with their own provenance.	cytoplasm `GO:0005737`	SGD:S000217933 Source assertion: Complex Portal CPX-1102 records cellular location GO:0005737 (cytoplasm); its evidence classification is ECO:0000353: physical interaction evidence. Source location `Complex Portal JSON #/crossReferences/11; /evidenceType`
CPX-1103 Scer `SGD:S000217934`	has_part ECO:0005546: inferred by paralogy; source stoichiometry minValue: 2, maxValue: 2	iron cation `CHEBI:24875`	SGD:S000217934 Source assertion: Complex Portal CPX-1103 lists CHEBI:24875 as a small molecule component; complex evidence is ECO:0005546: inferred by paralogy. Source location `Complex Portal JSON #/participants/0; /evidenceType`
CPX-1103 Scer `SGD:S000217934`	has_part ECO:0005546: inferred by paralogy; source stoichiometry minValue: 1, maxValue: 1	Ribonucleoside-diphosphate reductase large chain 1 `UniProtKB:P21524`	SGD:S000217934 Source assertion: Complex Portal CPX-1103 lists P21524 as a protein component; complex evidence is ECO:0005546: inferred by paralogy. Source location `Complex Portal JSON #/participants/1; /evidenceType`
CPX-1103 Scer `SGD:S000217934`	has_part ECO:0005546: inferred by paralogy; source stoichiometry minValue: 1, maxValue: 1	Ribonucleoside-diphosphate reductase small chain 1 `UniProtKB:P09938`	SGD:S000217934 Source assertion: Complex Portal CPX-1103 lists P09938 as a protein component; complex evidence is ECO:0005546: inferred by paralogy. Source location `Complex Portal JSON #/participants/2; /evidenceType`
CPX-1103 Scer `SGD:S000217934`	has_part ECO:0005546: inferred by paralogy; source stoichiometry minValue: 1, maxValue: 1	Ribonucleoside-diphosphate reductase large chain 2 `UniProtKB:P21672`	SGD:S000217934 Source assertion: Complex Portal CPX-1103 lists P21672 as a protein component; complex evidence is ECO:0005546: inferred by paralogy. Source location `Complex Portal JSON #/participants/3; /evidenceType`
CPX-1103 Scer `SGD:S000217934`	has_part ECO:0005546: inferred by paralogy; source stoichiometry minValue: 1, maxValue: 1	Ribonucleoside-diphosphate reductase small chain 2 `UniProtKB:P49723`	SGD:S000217934 Source assertion: Complex Portal CPX-1103 lists P49723 as a protein component; complex evidence is ECO:0005546: inferred by paralogy. Source location `Complex Portal JSON #/participants/4; /evidenceType`
CPX-1103 Scer `SGD:S000217934`	located_in Complex location from the independent composition source; original GO-CAM activity locations are retained with their own provenance.	cytoplasm `GO:0005737`	SGD:S000217934 Source assertion: Complex Portal CPX-1103 records cellular location GO:0005737 (cytoplasm); its evidence classification is ECO:0005546: inferred by paralogy. Source location `Complex Portal JSON #/crossReferences/5; /evidenceType`
YNK1 Scer `SGD:S000001550`	located_in Physical protein location from reviewed UniProt. ECO:0000269 (PubMed:12472466) Source qualification: Localizes predominantly to the cytoplasm. A small fraction is present in the mitochondrial intermembrane space	cytoplasm `GO:0005737`	UniProtKB:P36010 Source assertion: UniProtKB:P36010 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/1183/comments/1/subcellularLocations/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d` UniProtKB:P36010 Source assertion: UniProtKB:P36010 has the exact SGD cross-reference SGD:S000001550. 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/1183/uniProtKBCrossReferences/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
YNK1 Scer `SGD:S000001550`	located_in Physical protein location from reviewed UniProt. ECO:0000269 (PubMed:12472466); ECO:0000269 (PubMed:16823961); ECO:0000269 (PubMed:22984289) Source qualification: Localizes predominantly to the cytoplasm. A small fraction is present in the mitochondrial intermembrane space	mitochondrial intermembrane space `GO:0005758`	UniProtKB:P36010 Source assertion: UniProtKB:P36010 annotates location Mitochondrion intermembrane space (SL-0169). 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/1183/comments/1/subcellularLocations/1; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d` UniProtKB:P36010 Source assertion: UniProtKB:P36010 has the exact SGD cross-reference SGD:S000001550. 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/1183/uniProtKBCrossReferences/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
Ribonucleoside-diphosphate reductase large chain 1 `UniProtKB:P21524`	located_in Physical protein location from reviewed UniProt. ECO:0000269 (PubMed:12732713)	cytoplasm `GO:0005737`	UniProtKB:P21524 Source assertion: UniProtKB:P21524 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/551/comments/1/subcellularLocations/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
Ribonucleoside-diphosphate reductase small chain 1 `UniProtKB:P09938`	located_in Physical protein location from reviewed UniProt. ECO:0000269 (PubMed:12732713); ECO:0000269 (PubMed:18851834) Source qualification: Found predominantly in the nucleus under normal growth conditions and is redistributed to the cytoplasm in damaged cells in a DNA replication and damage checkpoint-dependent manner. Nuclear localization is mediated by DIF1	nucleus `GO:0005634`	UniProtKB:P09938 Source assertion: UniProtKB:P09938 annotates location Nucleus (SL-0191). 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/232/comments/1/subcellularLocations/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
Ribonucleoside-diphosphate reductase small chain 2 `UniProtKB:P49723`	located_in Physical protein location from reviewed UniProt. ECO:0000269 (PubMed:12732713); ECO:0000269 (PubMed:18851834) Source qualification: Found predominantly in the nucleus under normal growth conditions and is redistributed to the cytoplasm in damaged cells in a DNA replication and damage checkpoint-dependent manner. Nuclear localization is mediated by DIF1	nucleus `GO:0005634`	UniProtKB:P49723 Source assertion: UniProtKB:P49723 annotates location Nucleus (SL-0191). 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/2032/comments/1/subcellularLocations/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
Ribonucleoside-diphosphate reductase large chain 2 `UniProtKB:P21672`	located_in Physical protein location from reviewed UniProt. ECO:0000269 (PubMed:12732713)	cytoplasm `GO:0005737`	UniProtKB:P21672 Source assertion: UniProtKB:P21672 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/557/comments/1/subcellularLocations/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
YNK1 Scer `SGD:S000001550`	has_cofactor UniProtKB reviewed (Swiss-Prot) annotation. UniProt evidence: ECO:0000269 (PubMed:5793714)	magnesium(2+) `CHEBI:18420`	UniProtKB:P36010 Source assertion: UniProtKB:P36010 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/1183/comments/0/cofactors/0` UniProtKB:P36010 Source assertion: UniProtKB:P36010 has the exact SGD cross-reference SGD:S000001550. 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/1183/uniProtKBCrossReferences/0`
Ribonucleoside-diphosphate reductase small chain 1 `UniProtKB:P09938`	has_cofactor UniProtKB reviewed (Swiss-Prot) annotation. UniProt evidence: not specified Binds 2 iron ions per subunit.	iron cation `CHEBI:24875`	UniProtKB:P09938 Source assertion: UniProtKB:P09938 annotates CHEBI:24875 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/232/comments/0/cofactors/0; /results/232/comments/0/note`

References

gomodel:YeastPathways_PWY-7220-1 GO-CAM adenosine deoxyribonucleotides de novo biosynthesis II model YeastPathways_PWY-7220-1 (source version: Pinned Noctua JSON archive; model date 2026-07-02; member ./YeastPathways_PWY-7220-1.json)
SGD:S000217933 Complex Portal CPX-1102: Ribonucleoside-diphosphate reductase variant 1 (source version: Inspected API snapshot 2026-10-05; release dates 2014-10-16)
SGD:S000217934 Complex Portal CPX-1103: Ribonucleoside-diphosphate reductase variant 2 (source version: Inspected API snapshot 2026-10-05; release dates 2014-10-16)
UniProtKB:P36010 Reviewed UniProtKB P36010 location annotations (source version: UniProt release 2026_03)
UniProtKB:P21524 Reviewed UniProtKB P21524 location annotations (source version: UniProt release 2026_03)
UniProtKB:P09938 Reviewed UniProtKB P09938 location annotations (source version: UniProt release 2026_03)
UniProtKB:P49723 Reviewed UniProtKB P49723 location annotations (source version: UniProt release 2026_03)
UniProtKB:P21672 Reviewed UniProtKB P21672 location annotations (source version: UniProt release 2026_03)
PMID:6370695 Deoxyribonucleotide biosynthesis in yeast (Saccharomyces cerevisiae). A ribonucleotide reductase system of sufficient activity for DNA synthesis

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. Reviewed exact Complex Portal composition, source evidence grades, and independent physical complex locations.
2026-10-05T06:17:04Z Codex; review-complex-composition; Reviewed exact Complex Portal composition, source evidence grades, and independent physical complex locations; reused existing proteins through reviewed UniProt SGD cross-references.
2026-10-05T07:05:26Z Codex; edited; Exclude unenabled class III formate-dependent ATP reduction from the yeast graph. Native source inclusion alone does not establish yeast activity; the directly characterized yeast reductase and exact yeast UniProt entries support diphosphate reduction.
2026-10-05T06:43:56Z Codex
- EDIT — Audit causal activity compartments and preserve scoped protein location evidence
  Reviewed all 4 activity location assignments and 5 mapped physical proteins against reviewed S288C UniProt release2026_03 location/function/caution batch SHA256 95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d. Added 6 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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2026-10-05T07:05:26Z Codex
- EDIT — Exclude unenabled class III formate-dependent ATP reduction from the yeast graph. Native source inclusion alone does not establish yeast activity; the directly characterized yeast reductase and exact yeast UniProt entries support diphosphate reduction.
  User-authorized full causal graph curation. Exclude unenabled class III formate-dependent ATP reduction from the yeast graph. Native source inclusion alone does not establish yeast activity; the directly characterized yeast reductase and exact yeast UniProt entries support diphosphate reduction. Independent UniProt release2026_03 annotations, Rhea139 and ChEBI255 were inspected; primary literature was checked for the taxon/function distinctions. Exact source pointers and superseded edge assertions are retained in reports/causal_graph_review/gocam-chemical-final-supplement.json. Native schema validation and focused biochemical regression tests were run. Shared final rendering and full gates are performed by the coordinating agent.
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