periplasmic NAD degradation

gomodel:YeastPathways_PERIPLASMA-NAD-DEGRADATION

Periplasmic NAD degradation in Saccharomyces cerevisiae S288C hydrolyzes NAD to AMP and NMN, then dephosphorylates AMP to adenosine and hydrogenphosphate.

Pathway type

cofactor degradation

Organism scope

Saccharomyces cerevisiae S288C NCBITaxon:559292

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Pathway network

18 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
adenosine `CHEBI:16335`	small molecule
cytosol `GO:0005829`	cellular component
adenosine 5'-monophosphate(2-) `CHEBI:456215`	small molecule
water `CHEBI:15377`	small molecule
NPY1 Scer `SGD:S000003035`	protein
NAD+ catabolic process `GO:0019677`	biological process
NMN(-) `CHEBI:14649`	small molecule
NAD(1-) `CHEBI:57540`	small molecule
hydron `CHEBI:15378`	small molecule
SMN1 Scer `SGD:S000001245`	protein
hydrogenphosphate `CHEBI:43474`	small molecule
peroxisome `GO:0005777`	cellular component
extracellular region `GO:0005576`	cellular component
vacuole `GO:0005773`	cellular component
magnesium(2+) `CHEBI:18420`	cofactor
zinc(2+) `CHEBI:29105`	cofactor
AMP + H2O -> adenosine + phosphate `gomodel:AMP-DEPHOSPHORYLATION-RXN`	molecular activity
NADH pyrophosphatase activity `gomodel:NADPYROPHOSPHAT-RXN`	molecular activity

Mechanistic edges

Mechanistic edges and their cited evidence
Subject	Predicate and description	Object	Evidence
AMP + H2O -> adenosine + phosphate `gomodel:AMP-DEPHOSPHORYLATION-RXN`	has_output	adenosine `CHEBI:16335`	gomodel:YeastPathways_PERIPLASMA-NAD-DEGRADATION Source assertion: The model asserts gomodel:AMP-DEPHOSPHORYLATION-RXN RO:0002234 gomodel:CHEBI_16335_AMP-DEPHOSPHORYLATION-RXN. Source location `./YeastPathways_PERIPLASMA-NAD-DEGRADATION.json#/facts/0; endpoint types: /individuals/0/type; /individuals/5/type`
NADH pyrophosphatase activity `gomodel:NADPYROPHOSPHAT-RXN`	has_output	adenosine 5'-monophosphate(2-) `CHEBI:456215`	gomodel:YeastPathways_PERIPLASMA-NAD-DEGRADATION Source assertion: The model asserts gomodel:NADPYROPHOSPHAT-RXN RO:0002234 gomodel:CHEBI_456215_NADPYROPHOSPHAT-RXN. Source location `./YeastPathways_PERIPLASMA-NAD-DEGRADATION.json#/facts/2; endpoint types: /individuals/9/type; /individuals/7/type`
AMP + H2O -> adenosine + phosphate `gomodel:AMP-DEPHOSPHORYLATION-RXN`	has_input	water `CHEBI:15377`	gomodel:YeastPathways_PERIPLASMA-NAD-DEGRADATION Source assertion: The model asserts gomodel:AMP-DEPHOSPHORYLATION-RXN RO:0002233 gomodel:CHEBI_15377_AMP-DEPHOSPHORYLATION-RXN. Source location `./YeastPathways_PERIPLASMA-NAD-DEGRADATION.json#/facts/3; endpoint types: /individuals/0/type; /individuals/2/type`
NPY1 Scer `SGD:S000003035`	enables	NADH pyrophosphatase activity `gomodel:NADPYROPHOSPHAT-RXN`	gomodel:YeastPathways_PERIPLASMA-NAD-DEGRADATION Source assertion: The model asserts gomodel:NADPYROPHOSPHAT-RXN RO:0002333 gomodel:YGL067W-MONOMER_NADPYROPHOSPHAT-RXN_controller. Source location `./YeastPathways_PERIPLASMA-NAD-DEGRADATION.json#/facts/4; endpoint types: /individuals/9/type; /individuals/10/type`
NADH pyrophosphatase activity `gomodel:NADPYROPHOSPHAT-RXN`	part_of	NAD+ catabolic process `GO:0019677`	gomodel:YeastPathways_PERIPLASMA-NAD-DEGRADATION Source assertion: The model asserts gomodel:NADPYROPHOSPHAT-RXN BFO:0000050 gomodel:YeastPathways_PERIPLASMA-NAD-DEGRADATION/YeastPathways_PERIPLASMA-NAD-DEGRADATION. Source location `./YeastPathways_PERIPLASMA-NAD-DEGRADATION.json#/facts/5; endpoint types: /individuals/9/type; /individuals/25/type`
NADH pyrophosphatase activity `gomodel:NADPYROPHOSPHAT-RXN`	has_output	NMN(-) `CHEBI:14649`	gomodel:YeastPathways_PERIPLASMA-NAD-DEGRADATION Source assertion: The model asserts gomodel:NADPYROPHOSPHAT-RXN RO:0002234 gomodel:CHEBI_14649_NADPYROPHOSPHAT-RXN. Source location `./YeastPathways_PERIPLASMA-NAD-DEGRADATION.json#/facts/6; endpoint types: /individuals/9/type; /individuals/1/type`
AMP + H2O -> adenosine + phosphate `gomodel:AMP-DEPHOSPHORYLATION-RXN`	part_of	NAD+ catabolic process `GO:0019677`	gomodel:YeastPathways_PERIPLASMA-NAD-DEGRADATION Source assertion: The model asserts gomodel:AMP-DEPHOSPHORYLATION-RXN BFO:0000050 gomodel:YeastPathways_PERIPLASMA-NAD-DEGRADATION/YeastPathways_PERIPLASMA-NAD-DEGRADATION. Source location `./YeastPathways_PERIPLASMA-NAD-DEGRADATION.json#/facts/7; endpoint types: /individuals/0/type; /individuals/25/type`
NADH pyrophosphatase activity `gomodel:NADPYROPHOSPHAT-RXN`	has_input	NAD(1-) `CHEBI:57540`	gomodel:YeastPathways_PERIPLASMA-NAD-DEGRADATION Source assertion: The model asserts gomodel:NADPYROPHOSPHAT-RXN RO:0002233 gomodel:CHEBI_57540_NADPYROPHOSPHAT-RXN. Source location `./YeastPathways_PERIPLASMA-NAD-DEGRADATION.json#/facts/8; endpoint types: /individuals/9/type; /individuals/8/type`
NADH pyrophosphatase activity `gomodel:NADPYROPHOSPHAT-RXN`	has_output	hydron `CHEBI:15378`	gomodel:YeastPathways_PERIPLASMA-NAD-DEGRADATION Source assertion: The model asserts gomodel:NADPYROPHOSPHAT-RXN RO:0002234 gomodel:CHEBI_15378_NADPYROPHOSPHAT-RXN. Source location `./YeastPathways_PERIPLASMA-NAD-DEGRADATION.json#/facts/9; endpoint types: /individuals/9/type; /individuals/4/type`
SMN1 Scer `SGD:S000001245`	enables	AMP + H2O -> adenosine + phosphate `gomodel:AMP-DEPHOSPHORYLATION-RXN`	gomodel:YeastPathways_PERIPLASMA-NAD-DEGRADATION Source assertion: The model asserts gomodel:AMP-DEPHOSPHORYLATION-RXN RO:0002333 gomodel:YeastPathways_PERIPLASMA-NAD-DEGRADATION/6a4c244800003007. Source location `./YeastPathways_PERIPLASMA-NAD-DEGRADATION.json#/facts/10; endpoint types: /individuals/0/type; /individuals/26/type`
AMP + H2O -> adenosine + phosphate `gomodel:AMP-DEPHOSPHORYLATION-RXN`	has_input	adenosine 5'-monophosphate(2-) `CHEBI:456215`	gomodel:YeastPathways_PERIPLASMA-NAD-DEGRADATION Source assertion: The model asserts gomodel:AMP-DEPHOSPHORYLATION-RXN RO:0002233 gomodel:CHEBI_456215_NADPYROPHOSPHAT-RXN. Source location `./YeastPathways_PERIPLASMA-NAD-DEGRADATION.json#/facts/12; endpoint types: /individuals/0/type; /individuals/7/type`
NADH pyrophosphatase activity `gomodel:NADPYROPHOSPHAT-RXN`	has_input	water `CHEBI:15377`	gomodel:YeastPathways_PERIPLASMA-NAD-DEGRADATION Source assertion: The model asserts gomodel:NADPYROPHOSPHAT-RXN RO:0002233 gomodel:CHEBI_15377_NADPYROPHOSPHAT-RXN. Source location `./YeastPathways_PERIPLASMA-NAD-DEGRADATION.json#/facts/13; endpoint types: /individuals/9/type; /individuals/3/type`
AMP + H2O -> adenosine + phosphate `gomodel:AMP-DEPHOSPHORYLATION-RXN`	has_output	hydrogenphosphate `CHEBI:43474`	gomodel:YeastPathways_PERIPLASMA-NAD-DEGRADATION Source assertion: The model asserts gomodel:AMP-DEPHOSPHORYLATION-RXN RO:0002234 gomodel:CHEBI_43474_AMP-DEPHOSPHORYLATION-RXN. Source location `./YeastPathways_PERIPLASMA-NAD-DEGRADATION.json#/facts/14; endpoint types: /individuals/0/type; /individuals/6/type`
NPY1 Scer `SGD:S000003035`	located_in Physical protein location from reviewed UniProt. ECO:0000269 (PubMed:11361135)	peroxisome `GO:0005777`	UniProtKB:P53164 Source assertion: UniProtKB:P53164 annotates location Peroxisome (SL-0204). 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/2140/comments/1/subcellularLocations/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d` UniProtKB:P53164 Source assertion: UniProtKB:P53164 has the exact SGD cross-reference SGD:S000003035. 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/2140/uniProtKBCrossReferences/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
SMN1 Scer `SGD:S000001245`	located_in Physical protein location from reviewed UniProt. ECO:0000269 (PubMed:35123996)	extracellular region `GO:0005576`	UniProtKB:P38887 Source assertion: UniProtKB:P38887 annotates location Secreted (SL-0243). 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/1493/comments/1/subcellularLocations/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d` UniProtKB:P38887 Source assertion: UniProtKB:P38887 has the exact SGD cross-reference SGD:S000001245. 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/1493/uniProtKBCrossReferences/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
SMN1 Scer `SGD:S000001245`	located_in Physical protein location from reviewed UniProt. ECO:0000269 (PubMed:14562095)	vacuole `GO:0005773`	UniProtKB:P38887 Source assertion: UniProtKB:P38887 annotates location Vacuole (SL-0272). 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/1493/comments/1/subcellularLocations/1; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d` UniProtKB:P38887 Source assertion: UniProtKB:P38887 has the exact SGD cross-reference SGD:S000001245. 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/1493/uniProtKBCrossReferences/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
NPY1 Scer `SGD:S000003035`	has_cofactor UniProtKB reviewed (Swiss-Prot) annotation. UniProt evidence: ECO:0000250 (UniProtKB:Q9DCN1) Binds 3 Mg(2+) ions per subunit. UniProt note evidence: ECO:0000250 (UniProtKB:Q9DCN1)	magnesium(2+) `CHEBI:18420`	UniProtKB:P53164 Source assertion: UniProtKB:P53164 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/2140/comments/0/cofactors/0; /results/2140/comments/0/note` UniProtKB:P53164 Source assertion: UniProtKB:P53164 has the exact SGD cross-reference SGD:S000003035. 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/2140/uniProtKBCrossReferences/0`
NPY1 Scer `SGD:S000003035`	has_cofactor UniProtKB reviewed (Swiss-Prot) annotation. UniProt evidence: ECO:0000250 (UniProtKB:Q9DCN1) Binds 1 zinc ion per subunit. UniProt note evidence: ECO:0000250 (UniProtKB:Q9DCN1)	zinc(2+) `CHEBI:29105`	UniProtKB:P53164 Source assertion: UniProtKB:P53164 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/2140/comments/1/cofactors/0; /results/2140/comments/1/note` UniProtKB:P53164 Source assertion: UniProtKB:P53164 has the exact SGD cross-reference SGD:S000003035. 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/2140/uniProtKBCrossReferences/0`
SMN1 Scer `SGD:S000001245`	has_cofactor UniProtKB reviewed (Swiss-Prot) annotation. UniProt evidence: ECO:0000250 (UniProtKB:P21589)	zinc(2+) `CHEBI:29105`	UniProtKB:P38887 Source assertion: UniProtKB:P38887 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/1493/comments/0/cofactors/0` UniProtKB:P38887 Source assertion: UniProtKB:P38887 has the exact SGD cross-reference SGD:S000001245. 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/1493/uniProtKBCrossReferences/0`

References

gomodel:YeastPathways_PERIPLASMA-NAD-DEGRADATION GO-CAM periplasmic NAD degradation model YeastPathways_PERIPLASMA-NAD-DEGRADATION (source version: Pinned Noctua JSON archive; model date 2026-07-14; member ./YeastPathways_PERIPLASMA-NAD-DEGRADATION.json)
UniProtKB:P53164 Reviewed UniProtKB P53164 location annotations (source version: UniProt release 2026_03)
UniProtKB:P38887 Reviewed UniProtKB P38887 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 3 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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