adenosine nucleotides degradation II

MetaCyc:SALVADEHYPOX-PWY

The complete native five-step route converts AMP through adenosine, inosine, hypoxanthine and xanthine to urate. This E. coli-focused representation preserves all five native reactions, alternative nucleotidases and phosphorylases, supported assemblies and source-specific regulation. The terminal NAD-linked XdhABC assignment remains putative/inferred despite genetic support for xanthine consumption. Formal Rhea chemical species are retained, including neutral uric acid for its urate-labelled product. Periplasmic and intracellular alternatives do not imply an unrepresented transporter. MG1655 native annotations, K-12 reviewed proteins and historical W3110 experiments remain distinct. The META PWY-5691 connection is an opaque downstream interface, not evidence that MG1655 carries its three oxidative reactions. Current eight-step PathBank SMP0002103 remains a different, held definition. Recombinant YfiH/PgeF activities are separate qualified in-vitro claims, with the later weak-PNP and failed-growth-rescue limits retained. Historical Add induction reported for E. coli B remains strain-specific. Independent MG1655 experiments measured adenine-induced add transcription (17.61-fold under the cited M9 glucose conditions), without establishing direct PurR regulation; the unidentified UshA inhibitor and condition-dependent UmpG oligomer receive no invented identities. XdhA Mo-MPT annotation and phenotype-based MCD inference remain distinct.

Pathway type
purine nucleotide degradation
Organism scope

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Pathway network

78 nodes · 102 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.

Pathway network: adenosine nucleotides degradation II 78 nodes · 102 asserted directed edges. Every arrow links to its evidence table row; nodes link to their component details. Isolated declared components are retained. CHEBI:456215 — consumes → RHEA:29376; Evidence: RHEA:29376consumes CHEBI:15377 — consumes → RHEA:29376; Evidence: RHEA:29376consumes RHEA:29376 — produces → CHEBI:16335; Evidence: RHEA:29376produces RHEA:29376 — produces → CHEBI:43474; Evidence: RHEA:29376produces RHEA:29376 — part_of → MetaCyc:SALVADEHYPOX-PWY; Evidence: MetaCyc:SALVADEHYPOX-PWYpart of CHEBI:16335 — consumes → RHEA:24409; Evidence: RHEA:24409consumes CHEBI:15377 — consumes → RHEA:24409; Evidence: RHEA:24409consumes CHEBI:15378 — consumes → RHEA:24409; Evidence: RHEA:24409consumes RHEA:24409 — produces → CHEBI:17596; Evidence: RHEA:24409produces RHEA:24409 — produces → CHEBI:28938; Evidence: RHEA:24409produces RHEA:24409 — part_of → MetaCyc:SALVADEHYPOX-PWY; Evidence: MetaCyc:SALVADEHYPOX-PWYpart of CHEBI:17596 — consumes → RHEA:27647; Evidence: RHEA:27647consumes CHEBI:43474 — consumes → RHEA:27647; Evidence: RHEA:27647consumes RHEA:27647 — produces → CHEBI:57720; Evidence: RHEA:27647produces RHEA:27647 — produces → CHEBI:17368; Evidence: RHEA:27647produces RHEA:27647 — part_of → MetaCyc:SALVADEHYPOX-PWY; The native reaction record permits reversibility; the pathway layout selects L2R degradation. This directional Rhea node preserves that selected orientation, not irreversibility.; Evidence: MetaCyc:SALVADEHYPOX-PWYpart of CHEBI:17368 — consumes → RHEA:24671; Evidence: RHEA:24671consumes CHEBI:57540 — consumes → RHEA:24671; Evidence: RHEA:24671consumes CHEBI:15377 — consumes → RHEA:24671; Evidence: RHEA:24671consumes RHEA:24671 — produces → CHEBI:17712; Evidence: RHEA:24671produces RHEA:24671 — produces → CHEBI:57945; Evidence: RHEA:24671produces RHEA:24671 — produces → CHEBI:15378; Evidence: RHEA:24671produces RHEA:24671 — part_of → MetaCyc:SALVADEHYPOX-PWY; Evidence: MetaCyc:SALVADEHYPOX-PWYpart of CHEBI:17712 — consumes → RHEA:16670; Evidence: RHEA:16670consumes CHEBI:57540 — consumes → RHEA:16670; Evidence: RHEA:16670consumes CHEBI:15377 — consumes → RHEA:16670; Evidence: RHEA:16670consumes RHEA:16670 — produces → CHEBI:17775; Evidence: RHEA:16670produces RHEA:16670 — produces → CHEBI:57945; Evidence: RHEA:16670produces RHEA:16670 — produces → CHEBI:15378; Evidence: RHEA:16670produces RHEA:16670 — part_of → MetaCyc:SALVADEHYPOX-PWY; The native reaction record permits reversibility; the pathway layout selects L2R degradation. This directional Rhea node preserves that selected orientation, not irreversibility.; Evidence: MetaCyc:SALVADEHYPOX-PWYpart of RHEA:29376 — provides_input_for → RHEA:24409; Material continuity in the defined pathway. This is not an added membrane-transport reaction or a claim that every alternative enzyme shares a compartment.; Evidence: MetaCyc:SALVADEHYPOX-PWYprovides input for RHEA:24409 — provides_input_for → RHEA:27647; Material continuity in the defined pathway. This is not an added membrane-transport reaction or a claim that every alternative enzyme shares a compartment.; Evidence: MetaCyc:SALVADEHYPOX-PWYprovides input for RHEA:27647 — provides_input_for → RHEA:24671; Material continuity in the defined pathway. This is not an added membrane-transport reaction or a claim that every alternative enzyme shares a compartment.; Evidence: MetaCyc:SALVADEHYPOX-PWYprovides input for RHEA:24671 — provides_input_for → RHEA:16670; Material continuity in the defined pathway. This is not an added membrane-transport reaction or a claim that every alternative enzyme shares a compartment.; Evidence: MetaCyc:SALVADEHYPOX-PWYprovides input for RHEA:16670 — provides_input_for → MetaCyc:PWY-5691; Opaque, source-scoped META urate-conversion interface. The ECOLI definition omits this link; this edge does not assign the oxidative downstream pathway to MG1655.; Evidence: MetaCyc:SALVADEHYPOX-PWY, EcoCyc:URATEprovides input for UniProtKB:P00634 — part_of → EcoCyc:ALKAPHOSPHA-CPLX; Native assembly, not a mixed phosphatase heteromer.; Evidence: EcoCyc:ALKAPHOSPHA-CPLX, UniProtKB:P00634part of UniProtKB:P0AE22 — part_of → EcoCyc:APHA-CPLX; Native assembly, not a mixed phosphatase heteromer.; Evidence: EcoCyc:APHA-CPLX, UniProtKB:P0AE22part of UniProtKB:P0ABP8 — part_of → EcoCyc:DEOD-CPLX; Native assembly, not a mixed phosphatase heteromer.; Evidence: EcoCyc:DEOD-CPLX, UniProtKB:P0ABP8part of UniProtKB:P45563 — part_of → EcoCyc:XANTHOSINEPHOSPHORY-CPLX; Native assembly representation; XapA also has reported trimer coexistence, and this hexamer is not every preparation.; Evidence: EcoCyc:XANTHOSINEPHOSPHORY-CPLX, UniProtKB:P45563part of UniProtKB:P0C037 — part_of → EcoCyc:CPLX0-8619; Native assembly, not a mixed phosphatase heteromer.; Evidence: EcoCyc:CPLX0-8619, UniProtKB:P0C037part of UniProtKB:Q46799 — part_of → EcoCyc:CPLX0-761; Putative complex composition; no exact native coefficient asserted.; Evidence: EcoCyc:CPLX0-761, UniProtKB:Q46799part of UniProtKB:Q46800 — part_of → EcoCyc:CPLX0-761; Putative complex composition; no exact native coefficient asserted.; Evidence: EcoCyc:CPLX0-761, UniProtKB:Q46800part of UniProtKB:Q46801 — part_of → EcoCyc:CPLX0-761; Putative complex composition; no exact native coefficient asserted.; Evidence: EcoCyc:CPLX0-761, UniProtKB:Q46801part of EcoCyc:ALKAPHOSPHA-CPLX — catalyzes → RHEA:29376; Periplasmic PhoA alternative; not an assembly with UshA or AphA.; Evidence: EcoCyc:AMP-DEPHOSPHORYLATION-RXNcatalyzes UniProtKB:P07024 — catalyzes → RHEA:29376; Source-qualified nucleotidase alternative. Periplasmic and intracellular possibilities are not joined by an invented transporter.; Evidence: EcoCyc:USHA-MONOMERcatalyzes UniProtKB:P0AF24 — catalyzes → RHEA:29376; Source-qualified nucleotidase alternative. Periplasmic and intracellular possibilities are not joined by an invented transporter.; Evidence: EcoCyc:EG10634-MONOMERcatalyzes UniProtKB:P0A840 — catalyzes → RHEA:29376; Source-qualified nucleotidase alternative. Periplasmic and intracellular possibilities are not joined by an invented transporter.; Evidence: EcoCyc:EG11817-MONOMERcatalyzes EcoCyc:APHA-CPLX — catalyzes → RHEA:29376; Periplasmic broad-specificity AphA homotetramer alternative; neither a mixed phosphatase complex nor an assertion of uniquely dominant AMP flux.; Evidence: UniProtKB:P0AE22, EcoCyc:APHA-CPLXcatalyzes UniProtKB:P22333 — catalyzes → RHEA:24409; Evidence: UniProtKB:P22333catalyzes EcoCyc:DEOD-CPLX — catalyzes → RHEA:27647; Alternative inosine phosphorylase; pathway direction does not deny reversibility.; Evidence: EcoCyc:DEOD-CPLXcatalyzes EcoCyc:XANTHOSINEPHOSPHORY-CPLX — catalyzes → RHEA:27647; Alternative inosine phosphorylase; pathway direction does not deny reversibility.; Evidence: EcoCyc:XANTHOSINEPHOSPHORY-CPLXcatalyzes EcoCyc:CPLX0-8619 — catalyzes → RHEA:27647; Alternative inosine phosphorylase; pathway direction does not deny reversibility.; Evidence: EcoCyc:CPLX0-8619catalyzes EcoCyc:CPLX0-761 — enables → RHEA:24671; Putative/inferred NAD-linked XdhABC activity. Genetic evidence supports involvement in xanthine consumption; exact electron-acceptor preference and purified cofactor occupancy remain unmeasured here.; Evidence: EcoCyc:CPLX0-761, PMID:10986234enables EcoCyc:CPLX0-761 — enables → RHEA:16670; Putative/inferred NAD-linked XdhABC activity. Genetic evidence supports involvement in xanthine consumption; exact electron-acceptor preference and purified cofactor occupancy remain unmeasured here.; Evidence: EcoCyc:CPLX0-761, PMID:41070194enables UniProtKB:P00634 — has_cofactor → CHEBI:18420; Binds 1 Mg(2+) ion.; Evidence: UniProtKB:P00634has cofactor UniProtKB:P00634 — has_cofactor → CHEBI:29105; Binds 2 Zn(2+) ions.; Evidence: UniProtKB:P00634has cofactor UniProtKB:P07024 — has_cofactor → CHEBI:29105; Binds 2 Zn(2+) ions per subunit.; Evidence: UniProtKB:P07024has cofactor UniProtKB:P0AE22 — has_cofactor → CHEBI:18420; Binds 1 Mg(2+) ion per subunit.; Evidence: UniProtKB:P0AE22has cofactor UniProtKB:P22333 — has_cofactor → CHEBI:29105; Binds 1 zinc ion per subunit.; Evidence: UniProtKB:P22333has cofactor UniProtKB:P0A840 — has_cofactor → CHEBI:29035; Binds 1 divalent metal cation per subunit. Highest nucleotidase activity with Mn(2+), followed by Co(2+), Ni(2+) and Mg(2+). Highest exopolyphosphatase activity with Mg(2+), followed by Co(2+) and Zn(2+). Only its nucleotidase metal series is represented; Zn support for the separate exopolyphosphatase activity is not transferred to AMP hydrolysis.; Evidence: UniProtKB:P0A840has cofactor UniProtKB:P0A840 — has_cofactor → CHEBI:48828; Binds 1 divalent metal cation per subunit. Highest nucleotidase activity with Mn(2+), followed by Co(2+), Ni(2+) and Mg(2+). Highest exopolyphosphatase activity with Mg(2+), followed by Co(2+) and Zn(2+). Only its nucleotidase metal series is represented; Zn support for the separate exopolyphosphatase activity is not transferred to AMP hydrolysis.; Evidence: UniProtKB:P0A840has cofactor UniProtKB:P0A840 — has_cofactor → CHEBI:49786; Binds 1 divalent metal cation per subunit. Highest nucleotidase activity with Mn(2+), followed by Co(2+), Ni(2+) and Mg(2+). Highest exopolyphosphatase activity with Mg(2+), followed by Co(2+) and Zn(2+). Only its nucleotidase metal series is represented; Zn support for the separate exopolyphosphatase activity is not transferred to AMP hydrolysis.; Evidence: UniProtKB:P0A840has cofactor UniProtKB:P0A840 — has_cofactor → CHEBI:18420; Binds 1 divalent metal cation per subunit. Highest nucleotidase activity with Mn(2+), followed by Co(2+), Ni(2+) and Mg(2+). Highest exopolyphosphatase activity with Mg(2+), followed by Co(2+) and Zn(2+). Only its nucleotidase metal series is represented; Zn support for the separate exopolyphosphatase activity is not transferred to AMP hydrolysis.; Evidence: UniProtKB:P0A840has cofactor UniProtKB:P0AF24 — has_cofactor → CHEBI:18420; Magnesium. Can also use other divalent metal cations as manganese, cobalt or zinc.; Evidence: UniProtKB:P0AF24has cofactor UniProtKB:P0AF24 — has_cofactor → CHEBI:29035; Magnesium. Can also use other divalent metal cations as manganese, cobalt or zinc.; Evidence: UniProtKB:P0AF24has cofactor UniProtKB:P0AF24 — has_cofactor → CHEBI:48828; Magnesium. Can also use other divalent metal cations as manganese, cobalt or zinc.; Evidence: UniProtKB:P0AF24has cofactor UniProtKB:P0AF24 — has_cofactor → CHEBI:29105; Magnesium. Can also use other divalent metal cations as manganese, cobalt or zinc.; Evidence: UniProtKB:P0AF24has cofactor UniProtKB:Q46799 — has_cofactor → CHEBI:71302; Binds 1 Mo-molybdopterin (Mo-MPT) cofactor per subunit. This is an inferred XdhABC-subunit annotation, not measured purified occupancy. XdhA Mo-MPT and phenotype-based MCD proposals remain distinct. The 2009 MCD proposal is a competing phenotype-based interpretation, not an additional concurrent cofactor assignment.; Evidence: UniProtKB:Q46799, PMID:19542235has cofactor UniProtKB:Q46800 — has_cofactor → CHEBI:57692; This is an inferred XdhABC-subunit annotation, not measured purified occupancy. XdhA Mo-MPT and phenotype-based MCD proposals remain distinct.; Evidence: UniProtKB:Q46800has cofactor UniProtKB:Q46801 — has_cofactor → CHEBI:190135; Binds 2 [2Fe-2S] clusters. This is an inferred XdhABC-subunit annotation, not measured purified occupancy. XdhA Mo-MPT and phenotype-based MCD proposals remain distinct.; Evidence: UniProtKB:Q46801has cofactor UniProtKB:P00634 — located_in → GO:0042597; Protein-location annotation; it does not locate all alternative pathway reactions in one compartment or supply a transporter.; Evidence: UniProtKB:P00634located in UniProtKB:P07024 — located_in → GO:0042597; Protein-location annotation; it does not locate all alternative pathway reactions in one compartment or supply a transporter.; Evidence: UniProtKB:P07024located in UniProtKB:P0AE22 — located_in → GO:0042597; Protein-location annotation; it does not locate all alternative pathway reactions in one compartment or supply a transporter.; Evidence: UniProtKB:P0AE22located in UniProtKB:P0A840 — located_in → GO:0005737; Protein-location annotation; it does not locate all alternative pathway reactions in one compartment or supply a transporter.; Evidence: UniProtKB:P0A840located in UniProtKB:P33644 — located_in → GO:0005737; Protein-location annotation; it does not locate all alternative pathway reactions in one compartment or supply a transporter.; Evidence: UniProtKB:P33644located in CHEBI:16236 — activates → UniProtKB:P0AE22; Source-annotated assay effect; no unreported dose, pH or intracellular concentration is assigned. Chelator/reagent nodes preserve the named chemical identity without assuming a measured protonation state.; Evidence: UniProtKB:P0AE22activates CHEBI:4735 — inhibits → UniProtKB:P0AE22; Source-annotated assay effect; no unreported dose, pH or intracellular concentration is assigned. Chelator/reagent nodes preserve the named chemical identity without assuming a measured protonation state.; Evidence: UniProtKB:P0AE22inhibits CHEBI:30740 — inhibits → UniProtKB:P0AE22; Source-annotated assay effect; no unreported dose, pH or intracellular concentration is assigned. Chelator/reagent nodes preserve the named chemical identity without assuming a measured protonation state.; Evidence: UniProtKB:P0AE22inhibits CHEBI:44975 — inhibits → UniProtKB:P0AE22; Source-annotated assay effect; no unreported dose, pH or intracellular concentration is assigned. Chelator/reagent nodes preserve the named chemical identity without assuming a measured protonation state.; Evidence: UniProtKB:P0AE22inhibits CHEBI:46837 — inhibits → UniProtKB:P0AE22; Source-annotated assay effect; no unreported dose, pH or intracellular concentration is assigned. Chelator/reagent nodes preserve the named chemical identity without assuming a measured protonation state.; Evidence: UniProtKB:P0AE22inhibits CHEBI:33838 — inhibits → UniProtKB:P0AE22; Source-annotated assay effect; no unreported dose, pH or intracellular concentration is assigned. Chelator/reagent nodes preserve the named chemical identity without assuming a measured protonation state.; Evidence: UniProtKB:P0AE22inhibits CHEBI:43474 — inhibits → UniProtKB:P0AE22; Source-annotated assay effect; no unreported dose, pH or intracellular concentration is assigned. Chelator/reagent nodes preserve the named chemical identity without assuming a measured protonation state.; Evidence: UniProtKB:P0AE22inhibits CHEBI:29108 — inhibits → UniProtKB:P0AE22; Source-annotated assay effect; no unreported dose, pH or intracellular concentration is assigned. Chelator/reagent nodes preserve the named chemical identity without assuming a measured protonation state.; Evidence: UniProtKB:P0AE22inhibits CHEBI:16213 — inhibits → UniProtKB:P22333; Inhibitor annotation from the reviewed protein; its cited full primary methods were not inspected.; Evidence: UniProtKB:P22333inhibits CHEBI:28420 — inhibits → UniProtKB:P22333; Inhibitor annotation from the reviewed protein; its cited full primary methods were not inspected.; Evidence: UniProtKB:P22333inhibits CHEBI:33206 — inhibits → UniProtKB:P45563; Assay inhibition; the annotation abbreviates the sulfonic reagent p-CMB, which is not used to merge it with the benzoic reagent.; Evidence: UniProtKB:P45563inhibits CHEBI:18320 — activates → UniProtKB:P45563; object molecular state: XapA after inactivation by p-chloromercuriphenylsulfonic acid; subsequent dithiothreitol incubation restores activity.; Evidence UniProtKB:P45563: Dithiothreitol incubation restores XapA activity after inactivation by the chloromercuriphenylsulfonic reagent. This is conditional recovery, not general activation of untreated enzyme. ($.comments[2] (ACTIVITY REGULATION)); Activity restoration only after the source-specified chemical inactivation.; Evidence: UniProtKB:P45563activates CHEBI:17326 — inhibits → UniProtKB:P0A840; Source-scoped class-level inhibition; no invented exact nucleotide dose or universal effect across every triphosphate.; Evidence: UniProtKB:P0A840inhibits CHEBI:29036 — inhibits → EcoCyc:DEOD-CPLX; Reviewed native assay annotation. Phosphate negative cooperativity is retained separately as substrate-binding behavior, not equated with inhibition.; Evidence: EcoCyc:DEOD-CPLXinhibits CHEBI:29105 — inhibits → EcoCyc:DEOD-CPLX; Reviewed native assay annotation. Phosphate negative cooperativity is retained separately as substrate-binding behavior, not equated with inhibition.; Evidence: EcoCyc:DEOD-CPLXinhibits UniProtKB:P33644 — catalyzes → RHEA:24409; subject experimental construct: Recombinant K-12 P33644/YfiH sequence in pPSG-IBA105, expressed in BL21(DE3), StrepTrap- and size-exclusion-purified; exact tag terminus and cleavage status are unspecified in the inspected methods.; Evidence PMID:31978345: The 2020 YfiH construct used synthesized K-12 UniProt P33644 sequence in pPSG-IBA105, expressed in BL21(DE3), purified by StrepTrap and size exclusion. Exact YfiH tag terminus and cleavage status are not specified in the inspected methods. (PMC6978800 full HTML #sec4.4.1 and #sec4.4.4); Recombinant in-vitro alternative. No native cellular flux, Cu/Zn requirement or catalytic-triad mechanism is inferred.; Evidence: PMID:31978345, UniProtKB:P33644catalyzes UniProtKB:P33644 — catalyzes → RHEA:27647; subject experimental construct: Recombinant K-12 P33644/YfiH sequence in pPSG-IBA105, expressed in BL21(DE3), StrepTrap- and size-exclusion-purified; exact tag terminus and cleavage status are unspecified in the inspected methods.; Evidence PMID:31978345: The 2020 YfiH construct used synthesized K-12 UniProt P33644 sequence in pPSG-IBA105, expressed in BL21(DE3), purified by StrepTrap and size exclusion. Exact YfiH tag terminus and cleavage status are not specified in the inspected methods. (PMC6978800 full HTML #sec4.4.1 and #sec4.4.4); Recombinant in-vitro alternative. No native cellular flux, Cu/Zn requirement or catalytic-triad mechanism is inferred.; Evidence: PMID:31978345, UniProtKB:P33644catalyzes UniProtKB:P33644 — catalyzes → RHEA:27647; subject experimental construct: Recombinant PgeF expressed in BL21(lambdaDE3) lacking PgeF and purified by Ni2+-NTA; exact tag end/removal is not assigned because supplemental construct tables were not inspected.; Evidence PMID:40632566: The 2025 PgeF proteins were expressed in BL21(λDE3) lacking PgeF and purified by Ni2+-NTA. Supplemental construct details were not inspected; do not invent a tag end, tag removal, or exact wild-type assembly for these assays. (PMC12280929 full HTML #s13, #s18, #s20); Weak in-vitro PNP: 2.5 micromolar protein, 1 microgram substrate/100 microlitres PBS, 16 h at 37 C; no detected activity at 5 nM and no deoD-mutant growth rescue on inosine. Ni-NTA purification does not make nickel a cofactor.; Evidence: PMID:40632566catalyzes UniProtKB:P23841 — part_of → EcoCyc:CPLX0-7681; Native ligand-bound regulatory state; no exact subunit or ligand occupancy is assigned.; Evidence: EcoCyc:CPLX0-7681, EcoCyc:EG11146-MONOMERpart of CHEBI:18107 — part_of → EcoCyc:CPLX0-7681; Native ligand-bound regulatory state; no exact subunit or ligand occupancy is assigned.; Evidence: EcoCyc:CPLX0-7681, EcoCyc:XANTHOSINEpart of EcoCyc:CPLX0-7681 — activates → Entrez:946878; Positive transcriptional regulation projected through native promoter/TU/gene membership. Free XapR is not substituted for its xanthosine-bound state.; Evidence: EcoCyc:CPLX0-7681, EcoCyc:TU301, EcoCyc:TU0-45226, Entrez:946878activates CHEBI:28997 — activates → Entrez:946878; Expression-level induction by deoxyinosine, weaker than xanthosine; no direct binding to XapR or catalytic allostery is inferred.; Evidence: UniProtKB:P45563activates CHEBI:59640 — activates → Entrez:945283; Inferred expression induction, not direct activation or ligand binding to UmpH. The chemical node retains the source's nonspecific N-acetylglucosamine label.; Evidence: UniProtKB:P0AF24, Entrez:945283activates CHEBI:17596 — activates → Entrez:945654; Native source-level induction; historical full methods were not inspected. The generic deoxyribonucleoside class does not assert that every member was tested.; Evidence: EcoCyc:DEOD-CPLX, Entrez:945654activates CHEBI:16750 — activates → Entrez:945654; Native source-level induction; historical full methods were not inspected. The generic deoxyribonucleoside class does not assert that every member was tested.; Evidence: EcoCyc:DEOD-CPLX, Entrez:945654activates CHEBI:18274 — activates → Entrez:945654; Native source-level induction; historical full methods were not inspected. The generic deoxyribonucleoside class does not assert that every member was tested.; Evidence: EcoCyc:DEOD-CPLX, Entrez:945654activates CHEBI:16708 — activates → Entrez:945851; Measured transcript-level induction in wild-type E. coli K-12 MG1655: 17.61-fold after adenine supplementation (100 micrograms/mL) in M9 with 2 g/L glucose, at 37 C with agitation and sampled at mid-log phase. This is gene-expression context, not direct activation of Add protein or evidence of direct PurR regulation.; Evidence: PMID:21572102, Entrez:945851activates adenosine 5'-monophosphate(2-); CHEBI:456215; Declared type: small_molecule small molecule adenosine 5'-monophosphate(2-) water; CHEBI:15377; Declared type: small_molecule small molecule water adenosine; CHEBI:16335; Declared type: small_molecule small molecule adenosine hydrogenphosphate; CHEBI:43474; Declared type: small_molecule small molecule hydrogenphosphate hydron; CHEBI:15378; Declared type: small_molecule small molecule hydron inosine; CHEBI:17596; Declared type: small_molecule small molecule inosine ammonium; CHEBI:28938; Declared type: small_molecule small molecule ammonium alpha-D-ribose 1-phosphate(2-); CHEBI:57720; Declared type: small_molecule small molecule alpha-D-ribose 1-phosphate(2-) hypoxanthine; CHEBI:17368; Declared type: small_molecule small molecule hypoxanthine NAD(1-); CHEBI:57540; Declared type: small_molecule small molecule NAD(1-) 9H-xanthine; CHEBI:17712; Declared type: small_molecule small molecule 9H-xanthine NADH(2-); CHEBI:57945; Declared type: small_molecule small molecule NADH(2-) 7,9-dihydro-1H-purine-2,6,8(3H)-trione; CHEBI:17775; Declared type: small_molecule small molecule 7,9-dihydro-1H-purine- 2,6,8(3H)-trione Alkaline phosphatase; UniProtKB:P00634; Declared type: protein protein Alkaline phosphatase Protein UshA; UniProtKB:P07024; Declared type: protein protein Protein UshA Purine nucleoside phosphorylase DeoD-type; UniProtKB:P0ABP8; Declared type: protein protein Purine nucleoside phosphorylase DeoD-type Class B acid phosphatase; UniProtKB:P0AE22; Declared type: protein protein Class B acid phosphatase Adenosine deaminase; UniProtKB:P22333; Declared type: protein protein Adenosine deaminase 5'/3'-nucleotidase SurE; UniProtKB:P0A840; Declared type: protein protein 5'/3'-nucleotidase SurE Ribonucleotide monophosphatase NagD; UniProtKB:P0AF24; Declared type: protein protein Ribonucleotide monophosphatase NagD Purine nucleoside phosphorylase 2; UniProtKB:P45563; Declared type: protein protein Purine nucleoside phosphorylase 2 Pyrimidine/purine nucleoside phosphorylase; UniProtKB:P0C037; Declared type: protein protein Pyrimidine/purine nucleoside phosphorylase Peptidoglycan editing factor PgeF; UniProtKB:P33644; Declared type: protein protein Peptidoglycan editing factor PgeF Putative xanthine dehydrogenase molybdenum-binding subunit XdhA; UniProtKB:Q46799; Declared type: protein protein Putative xanthine dehydrogenase molybdenum- binding subunit XdhA Putative xanthine dehydrogenase FAD-binding subunit XdhB; UniProtKB:Q46800; Declared type: protein protein Putative xanthine dehydrogenase FAD-binding subunit XdhB Putative xanthine dehydrogenase iron-sulfur-binding subunit XdhC; UniProtKB:Q46801; Declared type: protein protein Putative xanthine dehydrogenase iron-sulfur- binding subunit XdhC alkaline phosphatase; EcoCyc:ALKAPHOSPHA-CPLX; Declared type: complex complex alkaline phosphatase acid phosphatase / phosphotransferase; EcoCyc:APHA-CPLX; Declared type: complex complex acid phosphatase / phosphotransferase purine nucleoside phosphorylase; EcoCyc:DEOD-CPLX; Declared type: complex complex purine nucleoside phosphorylase xanthosine phosphorylase; EcoCyc:XANTHOSINEPHOSPHORY-CPLX; Declared type: complex complex xanthosine phosphorylase nucleoside phosphorylase PpnP; EcoCyc:CPLX0-8619; Declared type: complex complex nucleoside phosphorylase PpnP putative xanthine dehydrogenase; EcoCyc:CPLX0-761; Declared type: complex complex putative xanthine dehydrogenase magnesium(2+); CHEBI:18420; Declared type: cofactor cofactor magnesium(2+) zinc(2+); CHEBI:29105; Declared type: cofactor cofactor zinc(2+) manganese(2+); CHEBI:29035; Declared type: cofactor cofactor manganese(2+) cobalt(2+); CHEBI:48828; Declared type: cofactor cofactor cobalt(2+) nickel(2+); CHEBI:49786; Declared type: cofactor cofactor nickel(2+) Mo(VI)O2(OH)-molybdopterin cofactor(4-); CHEBI:71302; Declared type: cofactor cofactor Mo(VI)O2(OH)-molybdopterin cofactor(4-) FAD(3-); CHEBI:57692; Declared type: cofactor cofactor FAD(3-) di-mu-sulfido-diiron; CHEBI:190135; Declared type: cofactor cofactor di-mu-sulfido-diiron periplasmic space; GO:0042597; Declared type: cellular_component cellular component periplasmic space cytoplasm; GO:0005737; Declared type: cellular_component cellular component cytoplasm ethanol; CHEBI:16236; Declared type: small_molecule small molecule ethanol ethylenediaminetetraacetic acid; CHEBI:4735; Declared type: small_molecule small molecule ethylenediaminetetraacetic acid ethylene glycol bis(2-aminoethyl)tetraacetic acid; CHEBI:30740; Declared type: small_molecule small molecule ethylene glycol bis(2-aminoethyl)tetraacetic acid 1,10-phenanthroline; CHEBI:44975; Declared type: small_molecule small molecule 1,10-phenanthroline dipicolinic acid; CHEBI:46837; Declared type: small_molecule small molecule dipicolinic acid nucleoside; CHEBI:33838; Declared type: chemical_entity chemical entity nucleoside calcium(2+); CHEBI:29108; Declared type: small_molecule small molecule calcium(2+) coformycin; CHEBI:16213; Declared type: small_molecule small molecule coformycin p-chloromercuribenzoic acid; CHEBI:28420; Declared type: small_molecule small molecule p-chloromercuribenzoic acid p-chloromercuribenzenesulfonic acid; CHEBI:33206; Declared type: small_molecule small molecule p- chloromercuribenzenesulfonic acid 1,4-dithiothreitol; CHEBI:18320; Declared type: small_molecule small molecule 1,4-dithiothreitol nucleoside 5'-triphoshate; CHEBI:17326; Declared type: chemical_entity chemical entity nucleoside 5'-triphoshate copper(2+); CHEBI:29036; Declared type: small_molecule small molecule copper(2+) xapA; Entrez:946878; Declared type: gene gene xapA umpH; Entrez:945283; Declared type: gene gene umpH deoD; Entrez:945654; Declared type: gene gene deoD HTH-type transcriptional regulator XapR; UniProtKB:P23841; Declared type: protein protein HTH-type transcriptional regulator XapR XapR-xanthosine DNA-binding transcriptional activator; EcoCyc:CPLX0-7681; Declared type: complex complex XapR-xanthosine DNA-binding transcriptional activator xanthosine; CHEBI:18107; Declared type: small_molecule small molecule xanthosine 2'-deoxyinosine; CHEBI:28997; Declared type: small_molecule small molecule 2'-deoxyinosine N-acetylglucosamine; CHEBI:59640; Declared type: chemical_entity chemical entity N-acetylglucosamine guanosine; CHEBI:16750; Declared type: small_molecule small molecule guanosine 2'-deoxyribonucleoside; CHEBI:18274; Declared type: chemical_entity chemical entity 2'-deoxyribonucleoside adenine; CHEBI:16708; Declared type: small_molecule small molecule adenine add; Entrez:945851; Declared type: gene gene add urate conversion to allantoin I; MetaCyc:PWY-5691; Declared type: pathway pathway urate conversion to allantoin I AMP + H2O => adenosine + phosphate; RHEA:29376; Declared type: reaction/activity; Source reaction direction: left_to_right reaction / activity AMP + H2O => adenosine + phosphate adenosine + H2O + H(+) => inosine + NH4(+); RHEA:24409; Declared type: reaction/activity; Source reaction direction: left_to_right reaction / activity adenosine + H2O + H(+) => inosine + NH4(+) inosine + phosphate => alpha-D-ribose 1-phosphate + hypoxanthine; RHEA:27647; Declared type: reaction/activity; Source reaction direction: left_to_right reaction / activity inosine + phosphate => alpha-D-ribose 1-phosphate + hypoxanthine hypoxanthine + NAD(+) + H2O => xanthine + NADH + H(+); RHEA:24671; Declared type: reaction/activity; Source reaction direction: left_to_right reaction / activity hypoxanthine + NAD(+) + H2O => xanthine + NADH + H(+) xanthine + NAD(+) + H2O => urate + NADH + H(+); RHEA:16670; Declared type: reaction/activity; Source reaction direction: left_to_right reaction / activity xanthine + NAD(+) + H2O => urate + NADH + H(+) adenosine nucleotides degradation II; MetaCyc:SALVADEHYPOX-PWY; Declared type: pathway pathway adenosine nucleotides degradation II Purine nucleoside phosphorylase 2; UniProtKB:P45563; Declared type: protein; molecular state: XapA after inactivation by p-chloromercuriphenylsulfonic acid; subsequent dithiothreitol incubation restores activity.; Evidence UniProtKB:P45563: Dithiothreitol incubation restores XapA activity after inactivation by the chloromercuriphenylsulfonic reagent. This is conditional recovery, not general activation of untreated enzyme. ($.comments[2] (ACTIVITY REGULATION)) molecular state Purine nucleoside phosphorylase 2 [molecular state: XapA after inactivation by p- chloromercuriphenylsulfonic acid; subsequent dithiothreitol incubation…] Peptidoglycan editing factor PgeF; UniProtKB:P33644; Declared type: protein; experimental construct: Recombinant K-12 P33644/YfiH sequence in pPSG-IBA105, expressed in BL21(DE3), StrepTrap- and size-exclusion-purified; exact tag terminus and cleavage status are unspecified in the inspected methods.; Evidence PMID:31978345: The 2020 YfiH construct used synthesized K-12 UniProt P33644 sequence in pPSG-IBA105, expressed in BL21(DE3), purified by StrepTrap and size exclusion. Exact YfiH tag terminus and cleavage status are not specified in the inspected methods. (PMC6978800 full HTML #sec4.4.1 and #sec4.4.4) experimental construct Peptidoglycan editing factor PgeF [experimental construct: Recombinant K-12 P33644/YfiH sequence in pPSG-IBA105, expressed in BL21(DE3), StrepTrap- and size-…] Peptidoglycan editing factor PgeF; UniProtKB:P33644; Declared type: protein; experimental construct: Recombinant K-12 P33644/YfiH sequence in pPSG-IBA105, expressed in BL21(DE3), StrepTrap- and size-exclusion-purified; exact tag terminus and cleavage status are unspecified in the inspected methods.; Evidence PMID:31978345: The 2020 YfiH construct used synthesized K-12 UniProt P33644 sequence in pPSG-IBA105, expressed in BL21(DE3), purified by StrepTrap and size exclusion. Exact YfiH tag terminus and cleavage status are not specified in the inspected methods. (PMC6978800 full HTML #sec4.4.1 and #sec4.4.4) experimental construct Peptidoglycan editing factor PgeF [experimental construct: Recombinant K-12 P33644/YfiH sequence in pPSG-IBA105, expressed in BL21(DE3), StrepTrap- and size-…] Peptidoglycan editing factor PgeF; UniProtKB:P33644; Declared type: protein; experimental construct: Recombinant PgeF expressed in BL21(lambdaDE3) lacking PgeF and purified by Ni2+-NTA; exact tag end/removal is not assigned because supplemental construct tables were not inspected.; Evidence PMID:40632566: The 2025 PgeF proteins were expressed in BL21(λDE3) lacking PgeF and purified by Ni2+-NTA. Supplemental construct details were not inspected; do not invent a tag end, tag removal, or exact wild-type assembly for these assays. (PMC12280929 full HTML #s13, #s18, #s20) experimental construct Peptidoglycan editing factor PgeF [experimental construct: Recombinant PgeF expressed in BL21(lambdaDE3) lacking PgeF and purified by Ni2+-NTA; exact tag…]

Components and activities

Declared biological components and source reaction directions
NodeKind or roleSource direction
Escherichia coli K-12
NCBITaxon:83333		taxon
Escherichia coli str. K-12 substr. MG1655
NCBITaxon:511145		taxon
adenosine 5'-monophosphate(2-)
CHEBI:456215		small molecule
water
CHEBI:15377		small molecule
adenosine
CHEBI:16335		small molecule
hydrogenphosphate
CHEBI:43474		small molecule
hydron
CHEBI:15378		small molecule
inosine
CHEBI:17596		small molecule
ammonium
CHEBI:28938		small molecule
alpha-D-ribose 1-phosphate(2-)
CHEBI:57720		small molecule
hypoxanthine
CHEBI:17368		small molecule
NAD(1-)
CHEBI:57540		small molecule
9H-xanthine
CHEBI:17712		small molecule
NADH(2-)
CHEBI:57945		small molecule
7,9-dihydro-1H-purine-2,6,8(3H)-trione
CHEBI:17775		small molecule
Alkaline phosphatase
UniProtKB:P00634		protein
Protein UshA
UniProtKB:P07024		protein
Purine nucleoside phosphorylase DeoD-type
UniProtKB:P0ABP8		protein
Class B acid phosphatase
UniProtKB:P0AE22		protein
Adenosine deaminase
UniProtKB:P22333		protein
5'/3'-nucleotidase SurE
UniProtKB:P0A840		protein
Ribonucleotide monophosphatase NagD
UniProtKB:P0AF24		protein
Purine nucleoside phosphorylase 2
UniProtKB:P45563		protein
Pyrimidine/purine nucleoside phosphorylase
UniProtKB:P0C037		protein
Peptidoglycan editing factor PgeF
UniProtKB:P33644		protein
Putative xanthine dehydrogenase molybdenum-binding subunit XdhA
UniProtKB:Q46799		protein
Putative xanthine dehydrogenase FAD-binding subunit XdhB
UniProtKB:Q46800		protein
Putative xanthine dehydrogenase iron-sulfur-binding subunit XdhC
UniProtKB:Q46801		protein
alkaline phosphatase
EcoCyc:ALKAPHOSPHA-CPLX		complex
acid phosphatase / phosphotransferase
EcoCyc:APHA-CPLX		complex
purine nucleoside phosphorylase
EcoCyc:DEOD-CPLX		complex
xanthosine phosphorylase
EcoCyc:XANTHOSINEPHOSPHORY-CPLX		complex
nucleoside phosphorylase PpnP
EcoCyc:CPLX0-8619		complex
putative xanthine dehydrogenase
EcoCyc:CPLX0-761		complex
magnesium(2+)
CHEBI:18420		cofactor
zinc(2+)
CHEBI:29105		cofactor
manganese(2+)
CHEBI:29035		cofactor
cobalt(2+)
CHEBI:48828		cofactor
nickel(2+)
CHEBI:49786		cofactor
Mo(VI)O2(OH)-molybdopterin cofactor(4-)
CHEBI:71302		cofactor
FAD(3-)
CHEBI:57692		cofactor
di-mu-sulfido-diiron
CHEBI:190135		cofactor
periplasmic space
GO:0042597		cellular component
cytoplasm
GO:0005737		cellular component
ethanol
CHEBI:16236		small molecule
ethylenediaminetetraacetic acid
CHEBI:4735		small molecule
ethylene glycol bis(2-aminoethyl)tetraacetic acid
CHEBI:30740		small molecule
1,10-phenanthroline
CHEBI:44975		small molecule
dipicolinic acid
CHEBI:46837		small molecule
nucleoside
CHEBI:33838		chemical entity
calcium(2+)
CHEBI:29108		small molecule
coformycin
CHEBI:16213		small molecule
p-chloromercuribenzoic acid
CHEBI:28420		small molecule
p-chloromercuribenzenesulfonic acid
CHEBI:33206		small molecule
1,4-dithiothreitol
CHEBI:18320		small molecule
nucleoside 5'-triphoshate
CHEBI:17326		chemical entity
copper(2+)
CHEBI:29036		small molecule
xapA
Entrez:946878		gene
umpH
Entrez:945283		gene
deoD
Entrez:945654		gene
HTH-type transcriptional regulator XapR
UniProtKB:P23841		protein
XapR-xanthosine DNA-binding transcriptional activator
EcoCyc:CPLX0-7681		complex
xanthosine
CHEBI:18107		small molecule
2'-deoxyinosine
CHEBI:28997		small molecule
N-acetylglucosamine
CHEBI:59640		chemical entity
guanosine
CHEBI:16750		small molecule
2'-deoxyribonucleoside
CHEBI:18274		chemical entity
adenine
CHEBI:16708		small molecule
add
Entrez:945851		gene
urate conversion to allantoin I
MetaCyc:PWY-5691		pathway
AMP + H2O => adenosine + phosphate
RHEA:29376		reactionleft to right
adenosine + H2O + H(+) => inosine + NH4(+)
RHEA:24409		reactionleft to right
inosine + phosphate => alpha-D-ribose 1-phosphate + hypoxanthine
RHEA:27647		reactionleft to right
hypoxanthine + NAD(+) + H2O => xanthine + NADH + H(+)
RHEA:24671		reactionleft to right
xanthine + NAD(+) + H2O => urate + NADH + H(+)
RHEA:16670		reactionleft to right

Mechanistic edges

Mechanistic edges and their cited evidence
SubjectPredicate and descriptionObjectEvidence
adenosine 5'-monophosphate(2-)
CHEBI:456215		consumes

AMP + H2O => adenosine + phosphate
RHEA:29376
  • RHEA:29376

    Source assertion: RHEA:29376 explicitly lists CHEBI:456215 as a substrate with coefficient 1; its linked Rhea formula and charge agree with the bound ChEBI 255 identity.

    Source locationrhea.rdf.gz; rh:29376 rh:substrates <http://rdf.rhea-db.org/29375_L>; <http://rdf.rhea-db.org/29375_L> rh:contains1 <http://rdf.rhea-db.org/Participant_29375_compound_2590>; <http://rdf.rhea-db.org/Participant_29375_compound_2590> rh:compound <http://rdf.rhea-db.org/Compound_2590> / rh:chebi
water
CHEBI:15377		consumes

AMP + H2O => adenosine + phosphate
RHEA:29376
  • RHEA:29376

    Source assertion: RHEA:29376 explicitly lists CHEBI:15377 as a substrate with coefficient 1; its linked Rhea formula and charge agree with the bound ChEBI 255 identity.

    Source locationrhea.rdf.gz; rh:29376 rh:substrates <http://rdf.rhea-db.org/29375_L>; <http://rdf.rhea-db.org/29375_L> rh:contains1 <http://rdf.rhea-db.org/Participant_29375_compound_1283>; <http://rdf.rhea-db.org/Participant_29375_compound_1283> rh:compound <http://rdf.rhea-db.org/Compound_1283> / rh:chebi
AMP + H2O => adenosine + phosphate
RHEA:29376		produces

adenosine
CHEBI:16335
  • RHEA:29376

    Source assertion: RHEA:29376 explicitly lists CHEBI:16335 as a product with coefficient 1; its linked Rhea formula and charge agree with the bound ChEBI 255 identity.

    Source locationrhea.rdf.gz; rh:29376 rh:products <http://rdf.rhea-db.org/29375_R>; <http://rdf.rhea-db.org/29375_R> rh:contains1 <http://rdf.rhea-db.org/Participant_29375_compound_2547>; <http://rdf.rhea-db.org/Participant_29375_compound_2547> rh:compound <http://rdf.rhea-db.org/Compound_2547> / rh:chebi
AMP + H2O => adenosine + phosphate
RHEA:29376		produces

hydrogenphosphate
CHEBI:43474
  • RHEA:29376

    Source assertion: RHEA:29376 explicitly lists CHEBI:43474 as a product with coefficient 1; its linked Rhea formula and charge agree with the bound ChEBI 255 identity.

    Source locationrhea.rdf.gz; rh:29376 rh:products <http://rdf.rhea-db.org/29375_R>; <http://rdf.rhea-db.org/29375_R> rh:contains1 <http://rdf.rhea-db.org/Participant_29375_compound_5518>; <http://rdf.rhea-db.org/Participant_29375_compound_5518> rh:compound <http://rdf.rhea-db.org/Compound_5518> / rh:chebi
AMP + H2O => adenosine + phosphate
RHEA:29376		part_of

MetaCyc:SALVADEHYPOX-PWY
  • MetaCyc:SALVADEHYPOX-PWY

    Source assertion: META 27.0 lists AMP-DEPHOSPHORYLATION-RXN among the complete five reactions of SALVADEHYPOX-PWY; its L2R layout matches this directional Rhea chemistry.

    Source locationptools-xml/Pathway[@frameid="SALVADEHYPOX-PWY"]/reaction-list/Reaction[@frameid="AMP-DEPHOSPHORYLATION-RXN"]; reaction-layout[Reaction/@frameid="AMP-DEPHOSPHORYLATION-RXN"]
adenosine
CHEBI:16335		consumes

adenosine + H2O + H(+) => inosine + NH4(+)
RHEA:24409
  • RHEA:24409

    Source assertion: RHEA:24409 explicitly lists CHEBI:16335 as a substrate with coefficient 1; its linked Rhea formula and charge agree with the bound ChEBI 255 identity.

    Source locationrhea.rdf.gz; rh:24409 rh:substrates <http://rdf.rhea-db.org/24408_L>; <http://rdf.rhea-db.org/24408_L> rh:contains1 <http://rdf.rhea-db.org/Participant_24408_compound_2547>; <http://rdf.rhea-db.org/Participant_24408_compound_2547> rh:compound <http://rdf.rhea-db.org/Compound_2547> / rh:chebi
water
CHEBI:15377		consumes

adenosine + H2O + H(+) => inosine + NH4(+)
RHEA:24409
  • RHEA:24409

    Source assertion: RHEA:24409 explicitly lists CHEBI:15377 as a substrate with coefficient 1; its linked Rhea formula and charge agree with the bound ChEBI 255 identity.

    Source locationrhea.rdf.gz; rh:24409 rh:substrates <http://rdf.rhea-db.org/24408_L>; <http://rdf.rhea-db.org/24408_L> rh:contains1 <http://rdf.rhea-db.org/Participant_24408_compound_1283>; <http://rdf.rhea-db.org/Participant_24408_compound_1283> rh:compound <http://rdf.rhea-db.org/Compound_1283> / rh:chebi
hydron
CHEBI:15378		consumes

adenosine + H2O + H(+) => inosine + NH4(+)
RHEA:24409
  • RHEA:24409

    Source assertion: RHEA:24409 explicitly lists CHEBI:15378 as a substrate with coefficient 1; its linked Rhea formula and charge agree with the bound ChEBI 255 identity.

    Source locationrhea.rdf.gz; rh:24409 rh:substrates <http://rdf.rhea-db.org/24408_L>; <http://rdf.rhea-db.org/24408_L> rh:contains1 <http://rdf.rhea-db.org/Participant_24408_compound_3249>; <http://rdf.rhea-db.org/Participant_24408_compound_3249> rh:compound <http://rdf.rhea-db.org/Compound_3249> / rh:chebi
adenosine + H2O + H(+) => inosine + NH4(+)
RHEA:24409		produces

inosine
CHEBI:17596
  • RHEA:24409

    Source assertion: RHEA:24409 explicitly lists CHEBI:17596 as a product with coefficient 1; its linked Rhea formula and charge agree with the bound ChEBI 255 identity.

    Source locationrhea.rdf.gz; rh:24409 rh:products <http://rdf.rhea-db.org/24408_R>; <http://rdf.rhea-db.org/24408_R> rh:contains1 <http://rdf.rhea-db.org/Participant_24408_compound_1231>; <http://rdf.rhea-db.org/Participant_24408_compound_1231> rh:compound <http://rdf.rhea-db.org/Compound_1231> / rh:chebi
adenosine + H2O + H(+) => inosine + NH4(+)
RHEA:24409		produces

ammonium
CHEBI:28938
  • RHEA:24409

    Source assertion: RHEA:24409 explicitly lists CHEBI:28938 as a product with coefficient 1; its linked Rhea formula and charge agree with the bound ChEBI 255 identity.

    Source locationrhea.rdf.gz; rh:24409 rh:products <http://rdf.rhea-db.org/24408_R>; <http://rdf.rhea-db.org/24408_R> rh:contains1 <http://rdf.rhea-db.org/Participant_24408_compound_1012>; <http://rdf.rhea-db.org/Participant_24408_compound_1012> rh:compound <http://rdf.rhea-db.org/Compound_1012> / rh:chebi
adenosine + H2O + H(+) => inosine + NH4(+)
RHEA:24409		part_of

MetaCyc:SALVADEHYPOX-PWY
  • MetaCyc:SALVADEHYPOX-PWY

    Source assertion: META 27.0 lists ADENODEAMIN-RXN among the complete five reactions of SALVADEHYPOX-PWY; its L2R layout matches this directional Rhea chemistry.

    Source locationptools-xml/Pathway[@frameid="SALVADEHYPOX-PWY"]/reaction-list/Reaction[@frameid="ADENODEAMIN-RXN"]; reaction-layout[Reaction/@frameid="ADENODEAMIN-RXN"]
inosine
CHEBI:17596		consumes

inosine + phosphate => alpha-D-ribose 1-phosphate + hypoxanthine
RHEA:27647
  • RHEA:27647

    Source assertion: RHEA:27647 explicitly lists CHEBI:17596 as a substrate with coefficient 1; its linked Rhea formula and charge agree with the bound ChEBI 255 identity.

    Source locationrhea.rdf.gz; rh:27647 rh:substrates <http://rdf.rhea-db.org/27646_L>; <http://rdf.rhea-db.org/27646_L> rh:contains1 <http://rdf.rhea-db.org/Participant_27646_compound_1231>; <http://rdf.rhea-db.org/Participant_27646_compound_1231> rh:compound <http://rdf.rhea-db.org/Compound_1231> / rh:chebi
hydrogenphosphate
CHEBI:43474		consumes

inosine + phosphate => alpha-D-ribose 1-phosphate + hypoxanthine
RHEA:27647
  • RHEA:27647

    Source assertion: RHEA:27647 explicitly lists CHEBI:43474 as a substrate with coefficient 1; its linked Rhea formula and charge agree with the bound ChEBI 255 identity.

    Source locationrhea.rdf.gz; rh:27647 rh:substrates <http://rdf.rhea-db.org/27646_L>; <http://rdf.rhea-db.org/27646_L> rh:contains1 <http://rdf.rhea-db.org/Participant_27646_compound_5518>; <http://rdf.rhea-db.org/Participant_27646_compound_5518> rh:compound <http://rdf.rhea-db.org/Compound_5518> / rh:chebi
inosine + phosphate => alpha-D-ribose 1-phosphate + hypoxanthine
RHEA:27647		produces

alpha-D-ribose 1-phosphate(2-)
CHEBI:57720
  • RHEA:27647

    Source assertion: RHEA:27647 explicitly lists CHEBI:57720 as a product with coefficient 1; its linked Rhea formula and charge agree with the bound ChEBI 255 identity.

    Source locationrhea.rdf.gz; rh:27647 rh:products <http://rdf.rhea-db.org/27646_R>; <http://rdf.rhea-db.org/27646_R> rh:contains1 <http://rdf.rhea-db.org/Participant_27646_compound_2276>; <http://rdf.rhea-db.org/Participant_27646_compound_2276> rh:compound <http://rdf.rhea-db.org/Compound_2276> / rh:chebi
inosine + phosphate => alpha-D-ribose 1-phosphate + hypoxanthine
RHEA:27647		produces

hypoxanthine
CHEBI:17368
  • RHEA:27647

    Source assertion: RHEA:27647 explicitly lists CHEBI:17368 as a product with coefficient 1; its linked Rhea formula and charge agree with the bound ChEBI 255 identity.

    Source locationrhea.rdf.gz; rh:27647 rh:products <http://rdf.rhea-db.org/27646_R>; <http://rdf.rhea-db.org/27646_R> rh:contains1 <http://rdf.rhea-db.org/Participant_27646_compound_3881>; <http://rdf.rhea-db.org/Participant_27646_compound_3881> rh:compound <http://rdf.rhea-db.org/Compound_3881> / rh:chebi
inosine + phosphate => alpha-D-ribose 1-phosphate + hypoxanthine
RHEA:27647		part_of

The native reaction record permits reversibility; the pathway layout selects L2R degradation. This directional Rhea node preserves that selected orientation, not irreversibility.

MetaCyc:SALVADEHYPOX-PWY
  • MetaCyc:SALVADEHYPOX-PWY

    Source assertion: META 27.0 lists INOPHOSPHOR-RXN among the complete five reactions of SALVADEHYPOX-PWY; its L2R layout matches this directional Rhea chemistry.

    Source locationptools-xml/Pathway[@frameid="SALVADEHYPOX-PWY"]/reaction-list/Reaction[@frameid="INOPHOSPHOR-RXN"]; reaction-layout[Reaction/@frameid="INOPHOSPHOR-RXN"]
hypoxanthine
CHEBI:17368		consumes

hypoxanthine + NAD(+) + H2O => xanthine + NADH + H(+)
RHEA:24671
  • RHEA:24671

    Source assertion: RHEA:24671 explicitly lists CHEBI:17368 as a substrate with coefficient 1; its linked Rhea formula and charge agree with the bound ChEBI 255 identity.

    Source locationrhea.rdf.gz; rh:24671 rh:substrates <http://rdf.rhea-db.org/24670_L>; <http://rdf.rhea-db.org/24670_L> rh:contains1 <http://rdf.rhea-db.org/Participant_24670_compound_3881>; <http://rdf.rhea-db.org/Participant_24670_compound_3881> rh:compound <http://rdf.rhea-db.org/Compound_3881> / rh:chebi
NAD(1-)
CHEBI:57540		consumes

hypoxanthine + NAD(+) + H2O => xanthine + NADH + H(+)
RHEA:24671
  • RHEA:24671

    Source assertion: RHEA:24671 explicitly lists CHEBI:57540 as a substrate with coefficient 1; its linked Rhea formula and charge agree with the bound ChEBI 255 identity.

    Source locationrhea.rdf.gz; rh:24671 rh:substrates <http://rdf.rhea-db.org/24670_L>; <http://rdf.rhea-db.org/24670_L> rh:contains1 <http://rdf.rhea-db.org/Participant_24670_compound_3484>; <http://rdf.rhea-db.org/Participant_24670_compound_3484> rh:compound <http://rdf.rhea-db.org/Compound_3484> / rh:chebi
water
CHEBI:15377		consumes

hypoxanthine + NAD(+) + H2O => xanthine + NADH + H(+)
RHEA:24671
  • RHEA:24671

    Source assertion: RHEA:24671 explicitly lists CHEBI:15377 as a substrate with coefficient 1; its linked Rhea formula and charge agree with the bound ChEBI 255 identity.

    Source locationrhea.rdf.gz; rh:24671 rh:substrates <http://rdf.rhea-db.org/24670_L>; <http://rdf.rhea-db.org/24670_L> rh:contains1 <http://rdf.rhea-db.org/Participant_24670_compound_1283>; <http://rdf.rhea-db.org/Participant_24670_compound_1283> rh:compound <http://rdf.rhea-db.org/Compound_1283> / rh:chebi
hypoxanthine + NAD(+) + H2O => xanthine + NADH + H(+)
RHEA:24671		produces

9H-xanthine
CHEBI:17712
  • RHEA:24671

    Source assertion: RHEA:24671 explicitly lists CHEBI:17712 as a product with coefficient 1; its linked Rhea formula and charge agree with the bound ChEBI 255 identity.

    Source locationrhea.rdf.gz; rh:24671 rh:products <http://rdf.rhea-db.org/24670_R>; <http://rdf.rhea-db.org/24670_R> rh:contains1 <http://rdf.rhea-db.org/Participant_24670_compound_3237>; <http://rdf.rhea-db.org/Participant_24670_compound_3237> rh:compound <http://rdf.rhea-db.org/Compound_3237> / rh:chebi
hypoxanthine + NAD(+) + H2O => xanthine + NADH + H(+)
RHEA:24671		produces

NADH(2-)
CHEBI:57945
  • RHEA:24671

    Source assertion: RHEA:24671 explicitly lists CHEBI:57945 as a product with coefficient 1; its linked Rhea formula and charge agree with the bound ChEBI 255 identity.

    Source locationrhea.rdf.gz; rh:24671 rh:products <http://rdf.rhea-db.org/24670_R>; <http://rdf.rhea-db.org/24670_R> rh:contains1 <http://rdf.rhea-db.org/Participant_24670_compound_1650>; <http://rdf.rhea-db.org/Participant_24670_compound_1650> rh:compound <http://rdf.rhea-db.org/Compound_1650> / rh:chebi
hypoxanthine + NAD(+) + H2O => xanthine + NADH + H(+)
RHEA:24671		produces

hydron
CHEBI:15378
  • RHEA:24671

    Source assertion: RHEA:24671 explicitly lists CHEBI:15378 as a product with coefficient 1; its linked Rhea formula and charge agree with the bound ChEBI 255 identity.

    Source locationrhea.rdf.gz; rh:24671 rh:products <http://rdf.rhea-db.org/24670_R>; <http://rdf.rhea-db.org/24670_R> rh:contains1 <http://rdf.rhea-db.org/Participant_24670_compound_3249>; <http://rdf.rhea-db.org/Participant_24670_compound_3249> rh:compound <http://rdf.rhea-db.org/Compound_3249> / rh:chebi
hypoxanthine + NAD(+) + H2O => xanthine + NADH + H(+)
RHEA:24671		part_of

MetaCyc:SALVADEHYPOX-PWY
  • MetaCyc:SALVADEHYPOX-PWY

    Source assertion: META 27.0 lists RXN-7682 among the complete five reactions of SALVADEHYPOX-PWY; its L2R layout matches this directional Rhea chemistry.

    Source locationptools-xml/Pathway[@frameid="SALVADEHYPOX-PWY"]/reaction-list/Reaction[@frameid="RXN-7682"]; reaction-layout[Reaction/@frameid="RXN-7682"]
9H-xanthine
CHEBI:17712		consumes

xanthine + NAD(+) + H2O => urate + NADH + H(+)
RHEA:16670
  • RHEA:16670

    Source assertion: RHEA:16670 explicitly lists CHEBI:17712 as a substrate with coefficient 1; its linked Rhea formula and charge agree with the bound ChEBI 255 identity.

    Source locationrhea.rdf.gz; rh:16670 rh:substrates <http://rdf.rhea-db.org/16669_L>; <http://rdf.rhea-db.org/16669_L> rh:contains1 <http://rdf.rhea-db.org/Participant_16669_compound_3237>; <http://rdf.rhea-db.org/Participant_16669_compound_3237> rh:compound <http://rdf.rhea-db.org/Compound_3237> / rh:chebi
NAD(1-)
CHEBI:57540		consumes

xanthine + NAD(+) + H2O => urate + NADH + H(+)
RHEA:16670
  • RHEA:16670

    Source assertion: RHEA:16670 explicitly lists CHEBI:57540 as a substrate with coefficient 1; its linked Rhea formula and charge agree with the bound ChEBI 255 identity.

    Source locationrhea.rdf.gz; rh:16670 rh:substrates <http://rdf.rhea-db.org/16669_L>; <http://rdf.rhea-db.org/16669_L> rh:contains1 <http://rdf.rhea-db.org/Participant_16669_compound_3484>; <http://rdf.rhea-db.org/Participant_16669_compound_3484> rh:compound <http://rdf.rhea-db.org/Compound_3484> / rh:chebi
water
CHEBI:15377		consumes

xanthine + NAD(+) + H2O => urate + NADH + H(+)
RHEA:16670
  • RHEA:16670

    Source assertion: RHEA:16670 explicitly lists CHEBI:15377 as a substrate with coefficient 1; its linked Rhea formula and charge agree with the bound ChEBI 255 identity.

    Source locationrhea.rdf.gz; rh:16670 rh:substrates <http://rdf.rhea-db.org/16669_L>; <http://rdf.rhea-db.org/16669_L> rh:contains1 <http://rdf.rhea-db.org/Participant_16669_compound_1283>; <http://rdf.rhea-db.org/Participant_16669_compound_1283> rh:compound <http://rdf.rhea-db.org/Compound_1283> / rh:chebi
xanthine + NAD(+) + H2O => urate + NADH + H(+)
RHEA:16670		produces

7,9-dihydro-1H-purine-2,6,8(3H)-trione
CHEBI:17775
  • RHEA:16670

    Source assertion: RHEA:16670 explicitly lists CHEBI:17775 as a product with coefficient 1; its linked Rhea formula and charge agree with the bound ChEBI 255 identity.

    Source locationrhea.rdf.gz; rh:16670 rh:products <http://rdf.rhea-db.org/16669_R>; <http://rdf.rhea-db.org/16669_R> rh:contains1 <http://rdf.rhea-db.org/Participant_16669_compound_6691>; <http://rdf.rhea-db.org/Participant_16669_compound_6691> rh:compound <http://rdf.rhea-db.org/Compound_6691> / rh:chebi
xanthine + NAD(+) + H2O => urate + NADH + H(+)
RHEA:16670		produces

NADH(2-)
CHEBI:57945
  • RHEA:16670

    Source assertion: RHEA:16670 explicitly lists CHEBI:57945 as a product with coefficient 1; its linked Rhea formula and charge agree with the bound ChEBI 255 identity.

    Source locationrhea.rdf.gz; rh:16670 rh:products <http://rdf.rhea-db.org/16669_R>; <http://rdf.rhea-db.org/16669_R> rh:contains1 <http://rdf.rhea-db.org/Participant_16669_compound_1650>; <http://rdf.rhea-db.org/Participant_16669_compound_1650> rh:compound <http://rdf.rhea-db.org/Compound_1650> / rh:chebi
xanthine + NAD(+) + H2O => urate + NADH + H(+)
RHEA:16670		produces

hydron
CHEBI:15378
  • RHEA:16670

    Source assertion: RHEA:16670 explicitly lists CHEBI:15378 as a product with coefficient 1; its linked Rhea formula and charge agree with the bound ChEBI 255 identity.

    Source locationrhea.rdf.gz; rh:16670 rh:products <http://rdf.rhea-db.org/16669_R>; <http://rdf.rhea-db.org/16669_R> rh:contains1 <http://rdf.rhea-db.org/Participant_16669_compound_3249>; <http://rdf.rhea-db.org/Participant_16669_compound_3249> rh:compound <http://rdf.rhea-db.org/Compound_3249> / rh:chebi
xanthine + NAD(+) + H2O => urate + NADH + H(+)
RHEA:16670		part_of

The native reaction record permits reversibility; the pathway layout selects L2R degradation. This directional Rhea node preserves that selected orientation, not irreversibility.

MetaCyc:SALVADEHYPOX-PWY
  • MetaCyc:SALVADEHYPOX-PWY

    Source assertion: META 27.0 lists RXN0-901 among the complete five reactions of SALVADEHYPOX-PWY; its L2R layout matches this directional Rhea chemistry.

    Source locationptools-xml/Pathway[@frameid="SALVADEHYPOX-PWY"]/reaction-list/Reaction[@frameid="RXN0-901"]; reaction-layout[Reaction/@frameid="RXN0-901"]
AMP + H2O => adenosine + phosphate
RHEA:29376		provides_input_for

Material continuity in the defined pathway. This is not an added membrane-transport reaction or a claim that every alternative enzyme shares a compartment.

adenosine + H2O + H(+) => inosine + NH4(+)
RHEA:24409
  • MetaCyc:SALVADEHYPOX-PWY

    Source assertion: The native predecessor relation orders AMP-DEPHOSPHORYLATION-RXN before ADENODEAMIN-RXN; the pathway layouts share the intervening named metabolite.

    Source locationptools-xml/Pathway/reaction-ordering/Reaction[@frameid="ADENODEAMIN-RXN"] with predecessor-reactions/Reaction[@frameid="AMP-DEPHOSPHORYLATION-RXN"]
adenosine + H2O + H(+) => inosine + NH4(+)
RHEA:24409		provides_input_for

Material continuity in the defined pathway. This is not an added membrane-transport reaction or a claim that every alternative enzyme shares a compartment.

inosine + phosphate => alpha-D-ribose 1-phosphate + hypoxanthine
RHEA:27647
  • MetaCyc:SALVADEHYPOX-PWY

    Source assertion: The native predecessor relation orders ADENODEAMIN-RXN before INOPHOSPHOR-RXN; the pathway layouts share the intervening named metabolite.

    Source locationptools-xml/Pathway/reaction-ordering/Reaction[@frameid="INOPHOSPHOR-RXN"] with predecessor-reactions/Reaction[@frameid="ADENODEAMIN-RXN"]
inosine + phosphate => alpha-D-ribose 1-phosphate + hypoxanthine
RHEA:27647		provides_input_for

Material continuity in the defined pathway. This is not an added membrane-transport reaction or a claim that every alternative enzyme shares a compartment.

hypoxanthine + NAD(+) + H2O => xanthine + NADH + H(+)
RHEA:24671
  • MetaCyc:SALVADEHYPOX-PWY

    Source assertion: The native predecessor relation orders INOPHOSPHOR-RXN before RXN-7682; the pathway layouts share the intervening named metabolite.

    Source locationptools-xml/Pathway/reaction-ordering/Reaction[@frameid="RXN-7682"] with predecessor-reactions/Reaction[@frameid="INOPHOSPHOR-RXN"]
hypoxanthine + NAD(+) + H2O => xanthine + NADH + H(+)
RHEA:24671		provides_input_for

Material continuity in the defined pathway. This is not an added membrane-transport reaction or a claim that every alternative enzyme shares a compartment.

xanthine + NAD(+) + H2O => urate + NADH + H(+)
RHEA:16670
  • MetaCyc:SALVADEHYPOX-PWY

    Source assertion: The native predecessor relation orders RXN-7682 before RXN0-901; the pathway layouts share the intervening named metabolite.

    Source locationptools-xml/Pathway/reaction-ordering/Reaction[@frameid="RXN0-901"] with predecessor-reactions/Reaction[@frameid="RXN-7682"]
xanthine + NAD(+) + H2O => urate + NADH + H(+)
RHEA:16670		provides_input_for

Opaque, source-scoped META urate-conversion interface. The ECOLI definition omits this link; this edge does not assign the oxidative downstream pathway to MG1655.

urate conversion to allantoin I
MetaCyc:PWY-5691
  • MetaCyc:SALVADEHYPOX-PWY

    Source assertion: META 27.0 links pathway output URATE to PWY-5691. The link is a downstream pathway interface, not membership of its three reactions.

    Source locationptools-xml/Pathway/pathway-link[Compound/@frameid="URATE"]/link-target/Pathway[@frameid="PWY-5691"]
  • EcoCyc:URATE

    Source assertion: The native URATE compound links ChEBI 17775, the formal neutral species used for the Rhea urate-labelled product. This mapping does not add an E. coli downstream urate pathway.

    Source locationptools-xml/Compound[@frameid="URATE"]/dblink[dblink-db="CHEBI"]/dblink-oid
Alkaline phosphatase
UniProtKB:P00634		part_of

Native assembly, not a mixed phosphatase heteromer.

alkaline phosphatase
EcoCyc:ALKAPHOSPHA-CPLX
  • EcoCyc:ALKAPHOSPHA-CPLX

    Source assertion: The native ECOLI assembly contains 2 copies of ALKAPHOSPHA-MONOMER.

    Source locationptools-xml/Protein[@frameid="ALKAPHOSPHA-CPLX"]/component[Protein/@frameid="ALKAPHOSPHA-MONOMER"]/coefficient
  • UniProtKB:P00634

    Source assertion: The issuing reviewed protein entry has an explicit BioCyc cross-reference to EcoCyc:ALKAPHOSPHA-MONOMER.

    Source location$.uniProtKBCrossReferences[database="BioCyc",id="EcoCyc:ALKAPHOSPHA-MONOMER"]
Class B acid phosphatase
UniProtKB:P0AE22		part_of

Native assembly, not a mixed phosphatase heteromer.

acid phosphatase / phosphotransferase
EcoCyc:APHA-CPLX
  • EcoCyc:APHA-CPLX

    Source assertion: The native ECOLI assembly contains 4 copies of APHA-MONOMER.

    Source locationptools-xml/Protein[@frameid="APHA-CPLX"]/component[Protein/@frameid="APHA-MONOMER"]/coefficient
  • UniProtKB:P0AE22

    Source assertion: The issuing reviewed protein entry has an explicit BioCyc cross-reference to EcoCyc:APHA-MONOMER.

    Source location$.uniProtKBCrossReferences[database="BioCyc",id="EcoCyc:APHA-MONOMER"]
Purine nucleoside phosphorylase DeoD-type
UniProtKB:P0ABP8		part_of

Native assembly, not a mixed phosphatase heteromer.

purine nucleoside phosphorylase
EcoCyc:DEOD-CPLX
  • EcoCyc:DEOD-CPLX

    Source assertion: The native ECOLI assembly contains 6 copies of DEOD-MONOMER.

    Source locationptools-xml/Protein[@frameid="DEOD-CPLX"]/component[Protein/@frameid="DEOD-MONOMER"]/coefficient
  • UniProtKB:P0ABP8

    Source assertion: The issuing reviewed protein entry has an explicit BioCyc cross-reference to EcoCyc:DEOD-MONOMER.

    Source location$.uniProtKBCrossReferences[database="BioCyc",id="EcoCyc:DEOD-MONOMER"]
Purine nucleoside phosphorylase 2
UniProtKB:P45563		part_of

Native assembly representation; XapA also has reported trimer coexistence, and this hexamer is not every preparation.

xanthosine phosphorylase
EcoCyc:XANTHOSINEPHOSPHORY-CPLX
  • EcoCyc:XANTHOSINEPHOSPHORY-CPLX

    Source assertion: The native ECOLI assembly contains 6 copies of XANTHOSINEPHOSPHORY-MONOMER.

    Source locationptools-xml/Protein[@frameid="XANTHOSINEPHOSPHORY-CPLX"]/component[Protein/@frameid="XANTHOSINEPHOSPHORY-MONOMER"]/coefficient
  • UniProtKB:P45563

    Source assertion: The issuing reviewed protein entry has an explicit BioCyc cross-reference to EcoCyc:XANTHOSINEPHOSPHORY-MONOMER.

    Source location$.uniProtKBCrossReferences[database="BioCyc",id="EcoCyc:XANTHOSINEPHOSPHORY-MONOMER"]
Pyrimidine/purine nucleoside phosphorylase
UniProtKB:P0C037		part_of

Native assembly, not a mixed phosphatase heteromer.

nucleoside phosphorylase PpnP
EcoCyc:CPLX0-8619
  • EcoCyc:CPLX0-8619

    Source assertion: The native ECOLI assembly contains 2 copies of EG12159-MONOMER.

    Source locationptools-xml/Protein[@frameid="CPLX0-8619"]/component[Protein/@frameid="EG12159-MONOMER"]/coefficient
  • UniProtKB:P0C037

    Source assertion: The issuing reviewed protein entry has an explicit BioCyc cross-reference to EcoCyc:EG12159-MONOMER.

    Source location$.uniProtKBCrossReferences[database="BioCyc",id="EcoCyc:EG12159-MONOMER"]
Putative xanthine dehydrogenase molybdenum-binding subunit XdhA
UniProtKB:Q46799		part_of

Putative complex composition; no exact native coefficient asserted.

putative xanthine dehydrogenase
EcoCyc:CPLX0-761
  • EcoCyc:CPLX0-761

    Source assertion: The native putative xanthine dehydrogenase includes G7485-MONOMER without an explicit component coefficient; this does not establish measured stoichiometry.

    Source locationptools-xml/Protein[@frameid="CPLX0-761"]/component[Protein/@frameid="G7485-MONOMER"]
  • UniProtKB:Q46799

    Source assertion: The reviewed protein maps to native EcoCyc:G7485-MONOMER; the heterotrimer annotation is inferred, not a purified assembly measurement.

    Source location$.uniProtKBCrossReferences; $.comments[commentType="SUBUNIT"]
Putative xanthine dehydrogenase FAD-binding subunit XdhB
UniProtKB:Q46800		part_of

Putative complex composition; no exact native coefficient asserted.

putative xanthine dehydrogenase
EcoCyc:CPLX0-761
  • EcoCyc:CPLX0-761

    Source assertion: The native putative xanthine dehydrogenase includes G7486-MONOMER without an explicit component coefficient; this does not establish measured stoichiometry.

    Source locationptools-xml/Protein[@frameid="CPLX0-761"]/component[Protein/@frameid="G7486-MONOMER"]
  • UniProtKB:Q46800

    Source assertion: The reviewed protein maps to native EcoCyc:G7486-MONOMER; the heterotrimer annotation is inferred, not a purified assembly measurement.

    Source location$.uniProtKBCrossReferences; $.comments[commentType="SUBUNIT"]
Putative xanthine dehydrogenase iron-sulfur-binding subunit XdhC
UniProtKB:Q46801		part_of

Putative complex composition; no exact native coefficient asserted.

putative xanthine dehydrogenase
EcoCyc:CPLX0-761
  • EcoCyc:CPLX0-761

    Source assertion: The native putative xanthine dehydrogenase includes G7487-MONOMER without an explicit component coefficient; this does not establish measured stoichiometry.

    Source locationptools-xml/Protein[@frameid="CPLX0-761"]/component[Protein/@frameid="G7487-MONOMER"]
  • UniProtKB:Q46801

    Source assertion: The reviewed protein maps to native EcoCyc:G7487-MONOMER; the heterotrimer annotation is inferred, not a purified assembly measurement.

    Source location$.uniProtKBCrossReferences; $.comments[commentType="SUBUNIT"]
alkaline phosphatase
EcoCyc:ALKAPHOSPHA-CPLX		catalyzes

Periplasmic PhoA alternative; not an assembly with UshA or AphA.

AMP + H2O => adenosine + phosphate
RHEA:29376
  • EcoCyc:AMP-DEPHOSPHORYLATION-RXN

    Source assertion: ENZRXN0-7738 explicitly assigns ALKAPHOSPHA-CPLX to AMP-DEPHOSPHORYLATION-RXN in ECOLI 27.0.

    Source locationptools-xml/Reaction/enzymatic-reaction/Enzymatic-Reaction[@frameid="ENZRXN0-7738"]
Protein UshA
UniProtKB:P07024		catalyzes

Source-qualified nucleotidase alternative. Periplasmic and intracellular possibilities are not joined by an invented transporter.

AMP + H2O => adenosine + phosphate
RHEA:29376
  • EcoCyc:USHA-MONOMER

    Source assertion: Native UshA is a broad 5-prime ribonucleotidase; ushA aphA double knockout blocks purine-nucleotide carbon utilization. AMP hydrolysis is retained as the annotated alternative, not proof of dominant intracellular flux.

    Source locationptools-xml/Protein[@frameid="USHA-MONOMER"]/comment
Ribonucleotide monophosphatase NagD
UniProtKB:P0AF24		catalyzes

Source-qualified nucleotidase alternative. Periplasmic and intracellular possibilities are not joined by an invented transporter.

AMP + H2O => adenosine + phosphate
RHEA:29376
  • EcoCyc:EG10634-MONOMER

    Source assertion: The native UmpH comment explicitly lists AMP among its effective phosphatase substrates. This broad-specificity alternative does not establish its dominant physiological substrate.

    Source locationptools-xml/Protein[@frameid="EG10634-MONOMER"]/comment
5'/3'-nucleotidase SurE
UniProtKB:P0A840		catalyzes

Source-qualified nucleotidase alternative. Periplasmic and intracellular possibilities are not joined by an invented transporter.

AMP + H2O => adenosine + phosphate
RHEA:29376
  • EcoCyc:EG11817-MONOMER

    Source assertion: The native UmpG comment explicitly lists 5-prime AMP among high-affinity substrates, with divalent-metal-dependent phosphatase activity. No exact oligomer stoichiometry is assigned.

    Source locationptools-xml/Protein[@frameid="EG11817-MONOMER"]/comment
acid phosphatase / phosphotransferase
EcoCyc:APHA-CPLX		catalyzes

Periplasmic broad-specificity AphA homotetramer alternative; neither a mixed phosphatase complex nor an assertion of uniquely dominant AMP flux.

AMP + H2O => adenosine + phosphate
RHEA:29376
  • UniProtKB:P0AE22

    Source assertion: Reviewed AphA dephosphorylates 3-prime and 5-prime nucleotides, including the AMP substrate class. This is a broad-specificity alternative, without a claim of uniquely dominant physiological AMP flux.

    Source location$.comments[0] (FUNCTION)
  • EcoCyc:APHA-CPLX

    Source assertion: APHA-CPLX catalyzes the generic nucleoside 5-prime-monophosphate phosphatase reaction 5-NUCLEOTID-RXN via ENZRXN0-7768.

    Source locationptools-xml/Protein/catalyzes/Enzymatic-Reaction[@frameid="ENZRXN0-7768"]/reaction
Adenosine deaminase
UniProtKB:P22333		catalyzes

adenosine + H2O + H(+) => inosine + NH4(+)
RHEA:24409
  • UniProtKB:P22333

    Source assertion: The reviewed Add entry assigns adenosine hydrolytic deamination to RHEA:24408 and cites experimental and HAMAP inference annotations.

    Source location$.comments[commentType="CATALYTIC ACTIVITY"]/reaction[reactionCrossReferences/id="RHEA:24408"]
purine nucleoside phosphorylase
EcoCyc:DEOD-CPLX		catalyzes

Alternative inosine phosphorylase; pathway direction does not deny reversibility.

inosine + phosphate => alpha-D-ribose 1-phosphate + hypoxanthine
RHEA:27647
  • EcoCyc:DEOD-CPLX

    Source assertion: Native INOPHOSPHOR-ENZRXN assigns this assembly to INOPHOSPHOR-RXN, inosine phosphorolysis. The reversible reaction is oriented toward hypoxanthine in this degradation route.

    Source locationptools-xml/Protein/catalyzes/Enzymatic-Reaction[@frameid="INOPHOSPHOR-ENZRXN"]/reaction
xanthosine phosphorylase
EcoCyc:XANTHOSINEPHOSPHORY-CPLX		catalyzes

Alternative inosine phosphorylase; pathway direction does not deny reversibility.

inosine + phosphate => alpha-D-ribose 1-phosphate + hypoxanthine
RHEA:27647
  • EcoCyc:XANTHOSINEPHOSPHORY-CPLX

    Source assertion: Native ENZRXN0-7335 assigns this assembly to INOPHOSPHOR-RXN, inosine phosphorolysis. The reversible reaction is oriented toward hypoxanthine in this degradation route.

    Source locationptools-xml/Protein/catalyzes/Enzymatic-Reaction[@frameid="ENZRXN0-7335"]/reaction
nucleoside phosphorylase PpnP
EcoCyc:CPLX0-8619		catalyzes

Alternative inosine phosphorylase; pathway direction does not deny reversibility.

inosine + phosphate => alpha-D-ribose 1-phosphate + hypoxanthine
RHEA:27647
  • EcoCyc:CPLX0-8619

    Source assertion: Native ENZRXN0-8336 assigns this assembly to INOPHOSPHOR-RXN, inosine phosphorolysis. The reversible reaction is oriented toward hypoxanthine in this degradation route.

    Source locationptools-xml/Protein/catalyzes/Enzymatic-Reaction[@frameid="ENZRXN0-8336"]/reaction
putative xanthine dehydrogenase
EcoCyc:CPLX0-761		enables

Putative/inferred NAD-linked XdhABC activity. Genetic evidence supports involvement in xanthine consumption; exact electron-acceptor preference and purified cofactor occupancy remain unmeasured here.

hypoxanthine + NAD(+) + H2O => xanthine + NADH + H(+)
RHEA:24671
  • EcoCyc:CPLX0-761

    Source assertion: ECOLI 27.0 assigns the putative XdhABC complex to RXN-7682 via ENZRXN0-1061. This native NAD-linked annotation is not a direct purified-enzyme demonstration of NAD preference.

    Source locationptools-xml/Protein[@frameid="CPLX0-761"]/catalyzes/Enzymatic-Reaction[@frameid="ENZRXN0-1061"]
  • PMID:10986234

    Source assertion: In W3110 derivatives, xdhA genetics and radiolabel experiments support purine interconversion; the authors could not directly assay XDH/XO. The heterotrimer and NAD preference are not experimentally established by this work.

    Source locationPMC110974 full HTML #sec14, #sec20
putative xanthine dehydrogenase
EcoCyc:CPLX0-761		enables

Putative/inferred NAD-linked XdhABC activity. Genetic evidence supports involvement in xanthine consumption; exact electron-acceptor preference and purified cofactor occupancy remain unmeasured here.

xanthine + NAD(+) + H2O => urate + NADH + H(+)
RHEA:16670
  • EcoCyc:CPLX0-761

    Source assertion: ECOLI 27.0 assigns the putative XdhABC complex to RXN0-901 via ENZRXN0-1062. This native NAD-linked annotation is not a direct purified-enzyme demonstration of NAD preference.

    Source locationptools-xml/Protein[@frameid="CPLX0-761"]/catalyzes/Enzymatic-Reaction[@frameid="ENZRXN0-1062"]
  • PMID:41070194

    Source assertion: In anaerobic MG1655 M9 glucose cultures, deletion of xdhA abolished xanthine consumption; deletion of xdhD allowed consumption with urate accumulation. This supports XdhA-linked oxidation, without measuring purified XdhABC NAD preference.

    Source locationPMC12507026 full HTML #s8 Fig4b-c and #s14
Alkaline phosphatase
UniProtKB:P00634		has_cofactor

Binds 1 Mg(2+) ion.

magnesium(2+)
CHEBI:18420
  • UniProtKB:P00634

    Source assertion: Reviewed annotation. UniProtKB:P00634 has the annotated cofactor Mg(2+). Binds 1 Mg(2+) ion.

    Source locationJSON Pointer /comments/1; cofactor identity /comments/1/cofactors/0/cofactorCrossReference/id
Alkaline phosphatase
UniProtKB:P00634		has_cofactor

Binds 2 Zn(2+) ions.

zinc(2+)
CHEBI:29105
  • UniProtKB:P00634

    Source assertion: Reviewed annotation. UniProtKB:P00634 has the annotated cofactor Zn(2+). Binds 2 Zn(2+) ions.

    Source locationJSON Pointer /comments/2; cofactor identity /comments/2/cofactors/0/cofactorCrossReference/id
Protein UshA
UniProtKB:P07024		has_cofactor

Binds 2 Zn(2+) ions per subunit.

zinc(2+)
CHEBI:29105
  • UniProtKB:P07024

    Source assertion: Reviewed annotation. UniProtKB:P07024 has the annotated cofactor Zn(2+). Binds 2 Zn(2+) ions per subunit.

    Source locationJSON Pointer /comments/3; cofactor identity /comments/3/cofactors/0/cofactorCrossReference/id
Class B acid phosphatase
UniProtKB:P0AE22		has_cofactor

Binds 1 Mg(2+) ion per subunit.

magnesium(2+)
CHEBI:18420
  • UniProtKB:P0AE22

    Source assertion: Reviewed annotation. UniProtKB:P0AE22 has the annotated cofactor Mg(2+). Binds 1 Mg(2+) ion per subunit.

    Source locationJSON Pointer /comments/2; cofactor identity /comments/2/cofactors/0/cofactorCrossReference/id
Adenosine deaminase
UniProtKB:P22333		has_cofactor

Binds 1 zinc ion per subunit.

zinc(2+)
CHEBI:29105
  • UniProtKB:P22333

    Source assertion: Source inference ECO:0000255. UniProtKB:P22333 has the annotated cofactor Zn(2+). Binds 1 zinc ion per subunit.

    Source locationJSON Pointer /comments/3; cofactor identity /comments/3/cofactors/0/cofactorCrossReference/id
5'/3'-nucleotidase SurE
UniProtKB:P0A840		has_cofactor

Binds 1 divalent metal cation per subunit. Highest nucleotidase activity with Mn(2+), followed by Co(2+), Ni(2+) and Mg(2+). Highest exopolyphosphatase activity with Mg(2+), followed by Co(2+) and Zn(2+). Only its nucleotidase metal series is represented; Zn support for the separate exopolyphosphatase activity is not transferred to AMP hydrolysis.

manganese(2+)
CHEBI:29035
  • UniProtKB:P0A840

    Source assertion: Reviewed annotation. UniProtKB:P0A840 has the annotated cofactor Mn(2+). Binds 1 divalent metal cation per subunit. Highest nucleotidase activity with Mn(2+), followed by Co(2+), Ni(2+) and Mg(2+). Highest exopolyphosphatase activity with Mg(2+), followed by Co(2+) and Zn(2+).

    Source locationJSON Pointer /comments/9; cofactor identity /comments/9/cofactors/0/cofactorCrossReference/id
5'/3'-nucleotidase SurE
UniProtKB:P0A840		has_cofactor

Binds 1 divalent metal cation per subunit. Highest nucleotidase activity with Mn(2+), followed by Co(2+), Ni(2+) and Mg(2+). Highest exopolyphosphatase activity with Mg(2+), followed by Co(2+) and Zn(2+). Only its nucleotidase metal series is represented; Zn support for the separate exopolyphosphatase activity is not transferred to AMP hydrolysis.

cobalt(2+)
CHEBI:48828
  • UniProtKB:P0A840

    Source assertion: Reviewed annotation. UniProtKB:P0A840 has the annotated cofactor Co(2+). Binds 1 divalent metal cation per subunit. Highest nucleotidase activity with Mn(2+), followed by Co(2+), Ni(2+) and Mg(2+). Highest exopolyphosphatase activity with Mg(2+), followed by Co(2+) and Zn(2+).

    Source locationJSON Pointer /comments/9; cofactor identity /comments/9/cofactors/1/cofactorCrossReference/id
5'/3'-nucleotidase SurE
UniProtKB:P0A840		has_cofactor

Binds 1 divalent metal cation per subunit. Highest nucleotidase activity with Mn(2+), followed by Co(2+), Ni(2+) and Mg(2+). Highest exopolyphosphatase activity with Mg(2+), followed by Co(2+) and Zn(2+). Only its nucleotidase metal series is represented; Zn support for the separate exopolyphosphatase activity is not transferred to AMP hydrolysis.

nickel(2+)
CHEBI:49786
  • UniProtKB:P0A840

    Source assertion: Reviewed annotation. UniProtKB:P0A840 has the annotated cofactor Ni(2+). Binds 1 divalent metal cation per subunit. Highest nucleotidase activity with Mn(2+), followed by Co(2+), Ni(2+) and Mg(2+). Highest exopolyphosphatase activity with Mg(2+), followed by Co(2+) and Zn(2+).

    Source locationJSON Pointer /comments/9; cofactor identity /comments/9/cofactors/2/cofactorCrossReference/id
5'/3'-nucleotidase SurE
UniProtKB:P0A840		has_cofactor

Binds 1 divalent metal cation per subunit. Highest nucleotidase activity with Mn(2+), followed by Co(2+), Ni(2+) and Mg(2+). Highest exopolyphosphatase activity with Mg(2+), followed by Co(2+) and Zn(2+). Only its nucleotidase metal series is represented; Zn support for the separate exopolyphosphatase activity is not transferred to AMP hydrolysis.

magnesium(2+)
CHEBI:18420
  • UniProtKB:P0A840

    Source assertion: Reviewed annotation. UniProtKB:P0A840 has the annotated cofactor Mg(2+). Binds 1 divalent metal cation per subunit. Highest nucleotidase activity with Mn(2+), followed by Co(2+), Ni(2+) and Mg(2+). Highest exopolyphosphatase activity with Mg(2+), followed by Co(2+) and Zn(2+).

    Source locationJSON Pointer /comments/9; cofactor identity /comments/9/cofactors/3/cofactorCrossReference/id
Ribonucleotide monophosphatase NagD
UniProtKB:P0AF24		has_cofactor

Magnesium. Can also use other divalent metal cations as manganese, cobalt or zinc.

magnesium(2+)
CHEBI:18420
  • UniProtKB:P0AF24

    Source assertion: Reviewed annotation. UniProtKB:P0AF24 has the annotated cofactor Mg(2+). Magnesium. Can also use other divalent metal cations as manganese, cobalt or zinc.

    Source locationJSON Pointer /comments/2; cofactor identity /comments/2/cofactors/0/cofactorCrossReference/id
Ribonucleotide monophosphatase NagD
UniProtKB:P0AF24		has_cofactor

Magnesium. Can also use other divalent metal cations as manganese, cobalt or zinc.

manganese(2+)
CHEBI:29035
  • UniProtKB:P0AF24

    Source assertion: Reviewed annotation. UniProtKB:P0AF24 has the annotated cofactor Mn(2+). Magnesium. Can also use other divalent metal cations as manganese, cobalt or zinc.

    Source locationJSON Pointer /comments/2; cofactor identity /comments/2/cofactors/1/cofactorCrossReference/id
Ribonucleotide monophosphatase NagD
UniProtKB:P0AF24		has_cofactor

Magnesium. Can also use other divalent metal cations as manganese, cobalt or zinc.

cobalt(2+)
CHEBI:48828
  • UniProtKB:P0AF24

    Source assertion: Reviewed annotation. UniProtKB:P0AF24 has the annotated cofactor Co(2+). Magnesium. Can also use other divalent metal cations as manganese, cobalt or zinc.

    Source locationJSON Pointer /comments/2; cofactor identity /comments/2/cofactors/2/cofactorCrossReference/id
Ribonucleotide monophosphatase NagD
UniProtKB:P0AF24		has_cofactor

Magnesium. Can also use other divalent metal cations as manganese, cobalt or zinc.

zinc(2+)
CHEBI:29105
  • UniProtKB:P0AF24

    Source assertion: Reviewed annotation. UniProtKB:P0AF24 has the annotated cofactor Zn(2+). Magnesium. Can also use other divalent metal cations as manganese, cobalt or zinc.

    Source locationJSON Pointer /comments/2; cofactor identity /comments/2/cofactors/3/cofactorCrossReference/id
Putative xanthine dehydrogenase molybdenum-binding subunit XdhA
UniProtKB:Q46799		has_cofactor

Binds 1 Mo-molybdopterin (Mo-MPT) cofactor per subunit. This is an inferred XdhABC-subunit annotation, not measured purified occupancy. XdhA Mo-MPT and phenotype-based MCD proposals remain distinct. The 2009 MCD proposal is a competing phenotype-based interpretation, not an additional concurrent cofactor assignment.

Mo(VI)O2(OH)-molybdopterin cofactor(4-)
CHEBI:71302
  • UniProtKB:Q46799

    Source assertion: Source inference ECO:0000250. UniProtKB:Q46799 has the annotated cofactor Mo-molybdopterin. Binds 1 Mo-molybdopterin (Mo-MPT) cofactor per subunit.

    Source locationJSON Pointer /comments/3; cofactor identity /comments/3/cofactors/0/cofactorCrossReference/id
  • PMID:19542235

    Source assertion: The 2009 study inferred MCD use by XdhABC/XdhD from adenine-sensitive growth phenotypes of mocA, xdhA and xdhD mutants. Purified MocA/YagTSR experiments do not directly measure the cofactor bound to XdhABC.

    Source locationPMC2755913 full HTML #sec7, #sec18, #sec23
Putative xanthine dehydrogenase FAD-binding subunit XdhB
UniProtKB:Q46800		has_cofactor

This is an inferred XdhABC-subunit annotation, not measured purified occupancy. XdhA Mo-MPT and phenotype-based MCD proposals remain distinct.

FAD(3-)
CHEBI:57692
  • UniProtKB:Q46800

    Source assertion: Source inference ECO:0000250. UniProtKB:Q46800 has the annotated cofactor FAD.

    Source locationJSON Pointer /comments/3; cofactor identity /comments/3/cofactors/0/cofactorCrossReference/id
Putative xanthine dehydrogenase iron-sulfur-binding subunit XdhC
UniProtKB:Q46801		has_cofactor

Binds 2 [2Fe-2S] clusters. This is an inferred XdhABC-subunit annotation, not measured purified occupancy. XdhA Mo-MPT and phenotype-based MCD proposals remain distinct.

di-mu-sulfido-diiron
CHEBI:190135
  • UniProtKB:Q46801

    Source assertion: Source inference ECO:0000250. UniProtKB:Q46801 has the annotated cofactor [2Fe-2S] cluster. Binds 2 [2Fe-2S] clusters.

    Source locationJSON Pointer /comments/1; cofactor identity /comments/1/cofactors/0/cofactorCrossReference/id
Alkaline phosphatase
UniProtKB:P00634		located_in

Protein-location annotation; it does not locate all alternative pathway reactions in one compartment or supply a transporter.

periplasmic space
GO:0042597
  • UniProtKB:P00634

    Source assertion: The reviewed entry annotates Periplasm.

    Source location$.comments[5] (SUBCELLULAR LOCATION)
Protein UshA
UniProtKB:P07024		located_in

Protein-location annotation; it does not locate all alternative pathway reactions in one compartment or supply a transporter.

periplasmic space
GO:0042597
  • UniProtKB:P07024

    Source assertion: The reviewed entry annotates Periplasm. Exported from the cell, except a small proportion that is internally localized

    Source location$.comments[6] (SUBCELLULAR LOCATION)
Class B acid phosphatase
UniProtKB:P0AE22		located_in

Protein-location annotation; it does not locate all alternative pathway reactions in one compartment or supply a transporter.

periplasmic space
GO:0042597
  • UniProtKB:P0AE22

    Source assertion: The reviewed entry annotates Periplasm.

    Source location$.comments[6] (SUBCELLULAR LOCATION)
5'/3'-nucleotidase SurE
UniProtKB:P0A840		located_in

Protein-location annotation; it does not locate all alternative pathway reactions in one compartment or supply a transporter.

cytoplasm
GO:0005737
  • UniProtKB:P0A840

    Source assertion: The reviewed entry annotates Cytoplasm.

    Source location$.comments[13] (SUBCELLULAR LOCATION)
Peptidoglycan editing factor PgeF
UniProtKB:P33644		located_in

Protein-location annotation; it does not locate all alternative pathway reactions in one compartment or supply a transporter.

cytoplasm
GO:0005737
  • UniProtKB:P33644

    Source assertion: The reviewed entry annotates Cytoplasm. Was originally thought to be periplasmic, but the presence of the N-terminal region in the structure indicates that PgeF does not possess a signal peptide and therefore is a cytoplasmic protein (PubMed:28612943, PubMed:35164571). It was subsequently confirmed that it is located in the cytoplasm (PubMed:40632566)

    Source location$.comments[10] (SUBCELLULAR LOCATION)
ethanol
CHEBI:16236		activates

Source-annotated assay effect; no unreported dose, pH or intracellular concentration is assigned. Chelator/reagent nodes preserve the named chemical identity without assuming a measured protonation state.

Class B acid phosphatase
UniProtKB:P0AE22
  • UniProtKB:P0AE22

    Source assertion: Reviewed activity-regulation annotation states that ethanol activates AphA; this is enzyme-assay modulation, not transcriptional regulation.

    Source location$.comments[3] (ACTIVITY REGULATION)
ethylenediaminetetraacetic acid
CHEBI:4735		inhibits

Source-annotated assay effect; no unreported dose, pH or intracellular concentration is assigned. Chelator/reagent nodes preserve the named chemical identity without assuming a measured protonation state.

Class B acid phosphatase
UniProtKB:P0AE22
  • UniProtKB:P0AE22

    Source assertion: Reviewed activity-regulation annotation states that EDTA strongly inhibits AphA; this is enzyme-assay modulation, not transcriptional regulation.

    Source location$.comments[3] (ACTIVITY REGULATION)
ethylene glycol bis(2-aminoethyl)tetraacetic acid
CHEBI:30740		inhibits

Source-annotated assay effect; no unreported dose, pH or intracellular concentration is assigned. Chelator/reagent nodes preserve the named chemical identity without assuming a measured protonation state.

Class B acid phosphatase
UniProtKB:P0AE22
  • UniProtKB:P0AE22

    Source assertion: Reviewed activity-regulation annotation states that EGTA inhibits AphA; this is enzyme-assay modulation, not transcriptional regulation.

    Source location$.comments[3] (ACTIVITY REGULATION)
1,10-phenanthroline
CHEBI:44975		inhibits

Source-annotated assay effect; no unreported dose, pH or intracellular concentration is assigned. Chelator/reagent nodes preserve the named chemical identity without assuming a measured protonation state.

Class B acid phosphatase
UniProtKB:P0AE22
  • UniProtKB:P0AE22

    Source assertion: Reviewed activity-regulation annotation states that 1,10-phenanthroline inhibits AphA; this is enzyme-assay modulation, not transcriptional regulation.

    Source location$.comments[3] (ACTIVITY REGULATION)
dipicolinic acid
CHEBI:46837		inhibits

Source-annotated assay effect; no unreported dose, pH or intracellular concentration is assigned. Chelator/reagent nodes preserve the named chemical identity without assuming a measured protonation state.

Class B acid phosphatase
UniProtKB:P0AE22
  • UniProtKB:P0AE22

    Source assertion: Reviewed activity-regulation annotation states that dipicolinic acid inhibits AphA; this is enzyme-assay modulation, not transcriptional regulation.

    Source location$.comments[3] (ACTIVITY REGULATION)
nucleoside
CHEBI:33838		inhibits

Source-annotated assay effect; no unreported dose, pH or intracellular concentration is assigned. Chelator/reagent nodes preserve the named chemical identity without assuming a measured protonation state.

Class B acid phosphatase
UniProtKB:P0AE22
  • UniProtKB:P0AE22

    Source assertion: Reviewed activity-regulation annotation states that nucleosides inhibit AphA; this is enzyme-assay modulation, not transcriptional regulation.

    Source location$.comments[3] (ACTIVITY REGULATION)
hydrogenphosphate
CHEBI:43474		inhibits

Source-annotated assay effect; no unreported dose, pH or intracellular concentration is assigned. Chelator/reagent nodes preserve the named chemical identity without assuming a measured protonation state.

Class B acid phosphatase
UniProtKB:P0AE22
  • UniProtKB:P0AE22

    Source assertion: Reviewed activity-regulation annotation states that inorganic phosphate inhibits AphA; this is enzyme-assay modulation, not transcriptional regulation.

    Source location$.comments[3] (ACTIVITY REGULATION)
calcium(2+)
CHEBI:29108		inhibits

Source-annotated assay effect; no unreported dose, pH or intracellular concentration is assigned. Chelator/reagent nodes preserve the named chemical identity without assuming a measured protonation state.

Class B acid phosphatase
UniProtKB:P0AE22
  • UniProtKB:P0AE22

    Source assertion: Reviewed activity-regulation annotation states that calcium(2+) inhibits AphA; this is enzyme-assay modulation, not transcriptional regulation.

    Source location$.comments[3] (ACTIVITY REGULATION)
coformycin
CHEBI:16213		inhibits

Inhibitor annotation from the reviewed protein; its cited full primary methods were not inspected.

Adenosine deaminase
UniProtKB:P22333
  • UniProtKB:P22333

    Source assertion: Reviewed Add activity is inhibited by coformycin (ECO:0000269, cited PMID357905). The original retrieved paper metadata has no abstract, so detailed assay conditions are not claimed.

    Source location$.comments[4] (ACTIVITY REGULATION)
p-chloromercuribenzoic acid
CHEBI:28420		inhibits

Inhibitor annotation from the reviewed protein; its cited full primary methods were not inspected.

Adenosine deaminase
UniProtKB:P22333
  • UniProtKB:P22333

    Source assertion: Reviewed Add activity is inhibited by p-chloromercuribenzoate (ECO:0000269, cited PMID357905). The original retrieved paper metadata has no abstract, so detailed assay conditions are not claimed.

    Source location$.comments[4] (ACTIVITY REGULATION)
p-chloromercuribenzenesulfonic acid
CHEBI:33206		inhibits

Assay inhibition; the annotation abbreviates the sulfonic reagent p-CMB, which is not used to merge it with the benzoic reagent.

Purine nucleoside phosphorylase 2
UniProtKB:P45563
  • UniProtKB:P45563

    Source assertion: Reviewed XapA is rapidly inactivated by p-chloromercuriphenylsulfonic acid; this is the sulfonic reagent, distinct from Add's chloromercuribenzoate.

    Source location$.comments[2] (ACTIVITY REGULATION)
1,4-dithiothreitol
CHEBI:18320		activates

Activity restoration only after the source-specified chemical inactivation.

Purine nucleoside phosphorylase 2
UniProtKB:P45563

molecular state: XapA after inactivation by p-chloromercuriphenylsulfonic acid; subsequent dithiothreitol incubation restores activity.

Qualification evidence
  • UniProtKB:P45563

    Source assertion: Dithiothreitol incubation restores XapA activity after inactivation by the chloromercuriphenylsulfonic reagent. This is conditional recovery, not general activation of untreated enzyme.

    Source location$.comments[2] (ACTIVITY REGULATION)
  • UniProtKB:P45563

    Source assertion: Dithiothreitol incubation restores XapA activity after inactivation by the chloromercuriphenylsulfonic reagent. This is conditional recovery, not general activation of untreated enzyme.

    Source location$.comments[2] (ACTIVITY REGULATION)
nucleoside 5'-triphoshate
CHEBI:17326		inhibits

Source-scoped class-level inhibition; no invented exact nucleotide dose or universal effect across every triphosphate.

5'/3'-nucleotidase SurE
UniProtKB:P0A840
  • UniProtKB:P0A840

    Source assertion: SurE is inhibited by various tested ribo- or deoxyribonucleoside 5-prime-triphosphates but is insensitive to nucleoside diphosphates. The class node does not mean every member was tested.

    Source location$.comments[10] (ACTIVITY REGULATION)
copper(2+)
CHEBI:29036		inhibits

Reviewed native assay annotation. Phosphate negative cooperativity is retained separately as substrate-binding behavior, not equated with inhibition.

purine nucleoside phosphorylase
EcoCyc:DEOD-CPLX
  • EcoCyc:DEOD-CPLX

    Source assertion: The native DeoD comment reports inhibition by Cu(2+). It also records conflicting reports for nickel and sulfate; those disputed effects are not asserted here.

    Source locationptools-xml/Protein[@frameid="DEOD-CPLX"]/comment
zinc(2+)
CHEBI:29105		inhibits

Reviewed native assay annotation. Phosphate negative cooperativity is retained separately as substrate-binding behavior, not equated with inhibition.

purine nucleoside phosphorylase
EcoCyc:DEOD-CPLX
  • EcoCyc:DEOD-CPLX

    Source assertion: The native DeoD comment reports inhibition by Zn(2+). It also records conflicting reports for nickel and sulfate; those disputed effects are not asserted here.

    Source locationptools-xml/Protein[@frameid="DEOD-CPLX"]/comment
Peptidoglycan editing factor PgeF
UniProtKB:P33644

experimental construct: Recombinant K-12 P33644/YfiH sequence in pPSG-IBA105, expressed in BL21(DE3), StrepTrap- and size-exclusion-purified; exact tag terminus and cleavage status are unspecified in the inspected methods.

Qualification evidence
  • PMID:31978345

    Source assertion: The 2020 YfiH construct used synthesized K-12 UniProt P33644 sequence in pPSG-IBA105, expressed in BL21(DE3), purified by StrepTrap and size exclusion. Exact YfiH tag terminus and cleavage status are not specified in the inspected methods.

    Source locationPMC6978800 full HTML #sec4.4.1 and #sec4.4.4
catalyzes

Recombinant in-vitro alternative. No native cellular flux, Cu/Zn requirement or catalytic-triad mechanism is inferred.

adenosine + H2O + H(+) => inosine + NH4(+)
RHEA:24409
  • PMID:31978345

    Source assertion: The 2020 study reports adenosine deamination by recombinant affinity-purified YfiH/PgeF in vitro. The result does not demonstrate its contribution to physiological purine flux in E. coli.

    Source locationPMC6978800 full HTML #sec2.3 Fig3 and #sec4.4.10
  • UniProtKB:P33644

    Source assertion: Reviewed P33644 records RHEA:24408 adenosine deamination, with experimental evidence citing PMID31978345.

    Source location$.comments[5]
Peptidoglycan editing factor PgeF
UniProtKB:P33644

experimental construct: Recombinant K-12 P33644/YfiH sequence in pPSG-IBA105, expressed in BL21(DE3), StrepTrap- and size-exclusion-purified; exact tag terminus and cleavage status are unspecified in the inspected methods.

Qualification evidence
  • PMID:31978345

    Source assertion: The 2020 YfiH construct used synthesized K-12 UniProt P33644 sequence in pPSG-IBA105, expressed in BL21(DE3), purified by StrepTrap and size exclusion. Exact YfiH tag terminus and cleavage status are not specified in the inspected methods.

    Source locationPMC6978800 full HTML #sec4.4.1 and #sec4.4.4
catalyzes

Recombinant in-vitro alternative. No native cellular flux, Cu/Zn requirement or catalytic-triad mechanism is inferred.

inosine + phosphate => alpha-D-ribose 1-phosphate + hypoxanthine
RHEA:27647
  • PMID:31978345

    Source assertion: The 2020 study reports inosine phosphorolysis by recombinant affinity-purified YfiH/PgeF in vitro. The result does not demonstrate its contribution to physiological purine flux in E. coli.

    Source locationPMC6978800 full HTML #sec2.3 Fig3 and #sec4.4.10
  • UniProtKB:P33644

    Source assertion: Reviewed P33644 records RHEA:27646 inosine phosphorolysis, with experimental evidence citing PMID31978345.

    Source location$.comments[3]
Peptidoglycan editing factor PgeF
UniProtKB:P33644

experimental construct: Recombinant PgeF expressed in BL21(lambdaDE3) lacking PgeF and purified by Ni2+-NTA; exact tag end/removal is not assigned because supplemental construct tables were not inspected.

Qualification evidence
  • PMID:40632566

    Source assertion: The 2025 PgeF proteins were expressed in BL21(λDE3) lacking PgeF and purified by Ni2+-NTA. Supplemental construct details were not inspected; do not invent a tag end, tag removal, or exact wild-type assembly for these assays.

    Source locationPMC12280929 full HTML #s13, #s18, #s20
catalyzes

Weak in-vitro PNP: 2.5 micromolar protein, 1 microgram substrate/100 microlitres PBS, 16 h at 37 C; no detected activity at 5 nM and no deoD-mutant growth rescue on inosine. Ni-NTA purification does not make nickel a cofactor.

inosine + phosphate => alpha-D-ribose 1-phosphate + hypoxanthine
RHEA:27647
  • PMID:40632566

    Source assertion: Recombinant PgeF/YfiH phosphorolyzes inosine in vitro. The 2025 study detected weak activity at 2.5 μM protein, none at 5 nM, and no rescue of a deoD mutant on inosine as sole carbon source.

    Source locationPMC12280929 full HTML #s6, #s11, #s20
HTH-type transcriptional regulator XapR
UniProtKB:P23841		part_of

Native ligand-bound regulatory state; no exact subunit or ligand occupancy is assigned.

XapR-xanthosine DNA-binding transcriptional activator
EcoCyc:CPLX0-7681
  • EcoCyc:CPLX0-7681

    Source assertion: EcoCyc CPLX0-7681 is the XapR–xanthosine transcriptional activator, with direct components EG11146-MONOMER and XANTHOSINE. Neither component has a stoichiometric coefficient in the native record.

    Source locationptools-xml/Protein[@frameid="CPLX0-7681"]/component
  • EcoCyc:EG11146-MONOMER

    Source assertion: The native XapR monomer has a direct UNIPROT P23841 dblink. The native state separately contains XANTHOSINE.

    Source locationptools-xml/Protein/dblink[dblink-db="UNIPROT"]/dblink-oid
xanthosine
CHEBI:18107		part_of

Native ligand-bound regulatory state; no exact subunit or ligand occupancy is assigned.

XapR-xanthosine DNA-binding transcriptional activator
EcoCyc:CPLX0-7681
  • EcoCyc:CPLX0-7681

    Source assertion: EcoCyc CPLX0-7681 is the XapR–xanthosine transcriptional activator, with direct components EG11146-MONOMER and XANTHOSINE. Neither component has a stoichiometric coefficient in the native record.

    Source locationptools-xml/Protein[@frameid="CPLX0-7681"]/component
  • EcoCyc:XANTHOSINE

    Source assertion: The issuing ECOLI XANTHOSINE compound has a direct ChEBI 18107 unification cross-reference.

    Source locationptools-xml/Compound[@frameid="XANTHOSINE"]/dblink[dblink-db="CHEBI"]/dblink-oid
XapR-xanthosine DNA-binding transcriptional activator
EcoCyc:CPLX0-7681		activates

Positive transcriptional regulation projected through native promoter/TU/gene membership. Free XapR is not substituted for its xanthosine-bound state.

xapA
Entrez:946878
  • EcoCyc:CPLX0-7681

    Source assertion: Native positive regulation targets xapAp and xapAp2. This gene-level edge projects their transcription-unit membership to xapA, not catalytic activation of XapA enzyme.

    Source locationptools-xml/Protein/regulates/Regulation[@frameid="REG0-5106"]; Regulation[@frameid="REG0-15010"]
  • EcoCyc:TU301

    Source assertion: The native xapAB transcription unit contains promoter PM501 and gene G85 (xapA).

    Source locationptools-xml/Transcription-Unit/component
  • EcoCyc:TU0-45226

    Source assertion: The second native transcription unit contains promoter PM0-46524 and gene G85 (xapA).

    Source locationptools-xml/Transcription-Unit/component
  • Entrez:946878

    Source assertion: The issuing Gene record resolves MG1655 xapA, locus b2407, with UniProt P45563 and EcoCyc G85 cross-references.

    Source locationEntrezgene-Set/Entrezgene/Entrezgene_gene/Gene-ref; Entrezgene_source; Entrezgene_unique-keys; Entrezgene-Set/Entrezgene/Entrezgene_locus/Gene-commentary/Gene-commentary_products/Gene-commentary/Gene-commentary_source/Other-source/Other-source_src/Dbtag[Dbtag_db="UniProtKB/Swiss-Prot"]/Dbtag_tag/Object-id/Object-id_str
2'-deoxyinosine
CHEBI:28997		activates

Expression-level induction by deoxyinosine, weaker than xanthosine; no direct binding to XapR or catalytic allostery is inferred.

xapA
Entrez:946878
  • UniProtKB:P45563

    Source assertion: Reviewed XapA expression is induced by xanthosine and to a lesser extent deoxyinosine; full expression requires the XapR-xanthosine activator.

    Source location$.comments[7] (INDUCTION)
N-acetylglucosamine
CHEBI:59640		activates

Inferred expression induction, not direct activation or ligand binding to UmpH. The chemical node retains the source's nonspecific N-acetylglucosamine label.

umpH
Entrez:945283
  • UniProtKB:P0AF24

    Source assertion: Reviewed UmpH/NagD is annotated as induced by N-acetylglucosamine (ECO:0000305). This is an inferred expression-induction annotation, not direct catalytic activation.

    Source location$.comments[5] (INDUCTION; ECO:0000305)
  • Entrez:945283

    Source assertion: The issuing Gene record identifies MG1655 umpH (b0675), with P0AF24 and EcoCyc EG10634 cross-references.

    Source locationEntrezgene-Set/Entrezgene/Entrezgene_gene/Gene-ref; Entrezgene_source; Entrezgene_unique-keys; Entrezgene-Set/Entrezgene/Entrezgene_locus/Gene-commentary/Gene-commentary_products/Gene-commentary/Gene-commentary_source/Other-source/Other-source_src/Dbtag[Dbtag_db="UniProtKB/Swiss-Prot"]/Dbtag_tag/Object-id/Object-id_str
inosine
CHEBI:17596		activates

Native source-level induction; historical full methods were not inspected. The generic deoxyribonucleoside class does not assert that every member was tested.

deoD
Entrez:945654
  • EcoCyc:DEOD-CPLX

    Source assertion: The native comment reports induction of DeoD expression by growth with inosine. This is expression regulation, not a direct allosteric activity effect.

    Source locationptools-xml/Protein[@frameid="DEOD-CPLX"]/comment
  • Entrez:945654

    Source assertion: The issuing Gene record identifies MG1655 deoD (b4384), with P0ABP8 and EcoCyc EG10222 cross-references.

    Source locationEntrezgene-Set/Entrezgene/Entrezgene_gene/Gene-ref; Entrezgene_source; Entrezgene_unique-keys; Entrezgene-Set/Entrezgene/Entrezgene_locus/Gene-commentary/Gene-commentary_products/Gene-commentary/Gene-commentary_source/Other-source/Other-source_src/Dbtag[Dbtag_db="UniProtKB/Swiss-Prot"]/Dbtag_tag/Object-id/Object-id_str
guanosine
CHEBI:16750		activates

Native source-level induction; historical full methods were not inspected. The generic deoxyribonucleoside class does not assert that every member was tested.

deoD
Entrez:945654
  • EcoCyc:DEOD-CPLX

    Source assertion: The native comment reports induction of DeoD expression by growth with guanosine. This is expression regulation, not a direct allosteric activity effect.

    Source locationptools-xml/Protein[@frameid="DEOD-CPLX"]/comment
  • Entrez:945654

    Source assertion: The issuing Gene record identifies MG1655 deoD (b4384), with P0ABP8 and EcoCyc EG10222 cross-references.

    Source locationEntrezgene-Set/Entrezgene/Entrezgene_gene/Gene-ref; Entrezgene_source; Entrezgene_unique-keys; Entrezgene-Set/Entrezgene/Entrezgene_locus/Gene-commentary/Gene-commentary_products/Gene-commentary/Gene-commentary_source/Other-source/Other-source_src/Dbtag[Dbtag_db="UniProtKB/Swiss-Prot"]/Dbtag_tag/Object-id/Object-id_str
2'-deoxyribonucleoside
CHEBI:18274		activates

Native source-level induction; historical full methods were not inspected. The generic deoxyribonucleoside class does not assert that every member was tested.

deoD
Entrez:945654
  • EcoCyc:DEOD-CPLX

    Source assertion: The native comment reports induction of DeoD expression by growth with purine and pyrimidine deoxyribonucleosides. This is expression regulation, not a direct allosteric activity effect.

    Source locationptools-xml/Protein[@frameid="DEOD-CPLX"]/comment
  • Entrez:945654

    Source assertion: The issuing Gene record identifies MG1655 deoD (b4384), with P0ABP8 and EcoCyc EG10222 cross-references.

    Source locationEntrezgene-Set/Entrezgene/Entrezgene_gene/Gene-ref; Entrezgene_source; Entrezgene_unique-keys; Entrezgene-Set/Entrezgene/Entrezgene_locus/Gene-commentary/Gene-commentary_products/Gene-commentary/Gene-commentary_source/Other-source/Other-source_src/Dbtag[Dbtag_db="UniProtKB/Swiss-Prot"]/Dbtag_tag/Object-id/Object-id_str
adenine
CHEBI:16708		activates

Measured transcript-level induction in wild-type E. coli K-12 MG1655: 17.61-fold after adenine supplementation (100 micrograms/mL) in M9 with 2 g/L glucose, at 37 C with agitation and sampled at mid-log phase. This is gene-expression context, not direct activation of Add protein or evidence of direct PurR regulation.

add
Entrez:945851
  • PMID:21572102

    Source assertion: In wild-type E. coli K-12 MG1655 grown to mid-log phase at 37 C in M9 with 2 g/L glucose, 100 micrograms/mL adenine increased add transcript 17.61-fold. The study explicitly excludes add from direct PurR regulation.

    Source locationPMC3159470 full HTML #sec3 (strain and culture); #sec9 (wild-type transcript response); #sec13 (direct PurR boundary)
  • Entrez:945851

    Source assertion: The issuing Gene original identifies MG1655 add, locus b1623, taxon511145, and directly links its protein product to UniProtKB P22333.

    Source locationEntrezgene-Set/Entrezgene/Entrezgene_gene/Gene-ref; Entrezgene-Set/Entrezgene/Entrezgene_source/BioSource/BioSource_org/Org-ref/Org-ref_db/Dbtag[Dbtag_db="taxon"]/Dbtag_tag/Object-id/Object-id_id; Entrezgene-Set/Entrezgene/Entrezgene_locus/Gene-commentary/Gene-commentary_products/Gene-commentary/Gene-commentary_source/Other-source/Other-source_src/Dbtag[Dbtag_db="UniProtKB/Swiss-Prot"]/Dbtag_tag/Object-id/Object-id_str

References

Curation history