pyrimidine deoxyribonucleosides degradation

MetaCyc:PWY-7181

The complete three-reaction MetaCyc route annotated for Escherichia coli K-12 MG1655 deaminates 2'-deoxycytidine to 2'-deoxyuridine through the zinc-containing Cdd homodimer, then cleaves 2'-deoxyuridine to uracil and 2-deoxy-alpha-D-ribose 1-phosphate through the DeoA homodimer. A parallel DeoA branch cleaves thymidine to thymine and the same sugar phosphate. The graph selects degradation-directed chemistry for both reversible phosphorolyses. This native boundary ends at the free bases and sugar phosphate; nucleoside uptake, subsequent sugar or ring degradation, and nucleotide salvage are separate processes. Primary enzyme assays and K-12 mutant studies support the functions, while the MG1655 scope follows native database annotation; mutant thymidylate-salvage phenotypes do not quantify wild-type pathway flux.

Pathway type

pyrimidine deoxyribonucleoside catabolism

Organism scope

Escherichia coli str. K-12 substr. MG1655 NCBITaxon:511145

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Pathway network

20 nodes · 25 asserted directed edges

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Chemical / cofactor
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Cell / process context
Pathway
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Dashed arrow: membership, location or cofactor relation

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Components and activities

Declared biological components and source reaction directions
Node	Kind or role	Source direction
Escherichia coli str. K-12 substr. MG1655 `NCBITaxon:511145`	taxon
2'-deoxycytidine `CHEBI:15698`	small molecule
water `CHEBI:15377`	small molecule
hydron `CHEBI:15378`	small molecule
2'-deoxyuridine `CHEBI:16450`	small molecule
ammonium `CHEBI:28938`	small molecule
hydrogenphosphate `CHEBI:43474`	small molecule
2-deoxy-alpha-D-ribose 1-phosphate(2-) `CHEBI:57259`	small molecule
uracil `CHEBI:17568`	small molecule
thymidine `CHEBI:17748`	small molecule
thymine `CHEBI:17821`	small molecule
zinc(2+) `CHEBI:29105`	cofactor
cytosol `GO:0005829`	cellular component
Cytidine deaminase `UniProtKB:P0ABF6`	protein
Thymidine phosphorylase `UniProtKB:P07650`	protein
cytidine/deoxycytidine deaminase `MetaCyc:CYTIDEAM-CPLX`	complex
thymidine phosphorylase / uracil phosphorylase `MetaCyc:DEOA-CPLX`	complex
2'-deoxycytidine + H2O + H(+) => 2'-deoxyuridine + NH4(+) `RHEA:13434`	molecular activity	left to right
2'-deoxyuridine + phosphate => 2-deoxy-alpha-D-ribose 1-phosphate + uracil `RHEA:22825`	molecular activity	left to right
thymidine + phosphate => 2-deoxy-alpha-D-ribose 1-phosphate + thymine `RHEA:16038`	molecular activity	left to right

Mechanistic edges

Mechanistic edges and their cited evidence
Subject	Predicate and description	Object	Evidence
2'-deoxycytidine `CHEBI:15698`	consumes	2'-deoxycytidine + H2O + H(+) => 2'-deoxyuridine + NH4(+) `RHEA:13434`	RHEA:13434 Source assertion: Rhea RHEA:13434 assigns CHEBI:15698 to substrates with coefficient 1; the compound resolves to this exact ChEBI species. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/13434']/rh:substrates; rdf:Description[@rdf:about='http://rdf.rhea-db.org/13433_L']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_13433_compound_5580']; rh:compound/rh:chebi`
water `CHEBI:15377`	consumes	2'-deoxycytidine + H2O + H(+) => 2'-deoxyuridine + NH4(+) `RHEA:13434`	RHEA:13434 Source assertion: Rhea RHEA:13434 assigns CHEBI:15377 to substrates with coefficient 1; the compound resolves to this exact ChEBI species. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/13434']/rh:substrates; rdf:Description[@rdf:about='http://rdf.rhea-db.org/13433_L']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_13433_compound_1283']; rh:compound/rh:chebi`
hydron `CHEBI:15378`	consumes	2'-deoxycytidine + H2O + H(+) => 2'-deoxyuridine + NH4(+) `RHEA:13434`	RHEA:13434 Source assertion: Rhea RHEA:13434 assigns CHEBI:15378 to substrates with coefficient 1; the compound resolves to this exact ChEBI species. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/13434']/rh:substrates; rdf:Description[@rdf:about='http://rdf.rhea-db.org/13433_L']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_13433_compound_3249']; rh:compound/rh:chebi`
2'-deoxycytidine + H2O + H(+) => 2'-deoxyuridine + NH4(+) `RHEA:13434`	produces	2'-deoxyuridine `CHEBI:16450`	RHEA:13434 Source assertion: Rhea RHEA:13434 assigns CHEBI:16450 to products with coefficient 1; the compound resolves to this exact ChEBI species. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/13434']/rh:products; rdf:Description[@rdf:about='http://rdf.rhea-db.org/13433_R']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_13433_compound_5154']; rh:compound/rh:chebi`
2'-deoxycytidine + H2O + H(+) => 2'-deoxyuridine + NH4(+) `RHEA:13434`	produces	ammonium `CHEBI:28938`	RHEA:13434 Source assertion: Rhea RHEA:13434 assigns CHEBI:28938 to products with coefficient 1; the compound resolves to this exact ChEBI species. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/13434']/rh:products; rdf:Description[@rdf:about='http://rdf.rhea-db.org/13433_R']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_13433_compound_1012']; rh:compound/rh:chebi`
2'-deoxyuridine `CHEBI:16450`	consumes	2'-deoxyuridine + phosphate => 2-deoxy-alpha-D-ribose 1-phosphate + uracil `RHEA:22825`	RHEA:22825 Source assertion: Rhea RHEA:22825 assigns CHEBI:16450 to substrates with coefficient 1; the compound resolves to this exact ChEBI species. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/22825']/rh:substrates; rdf:Description[@rdf:about='http://rdf.rhea-db.org/22824_L']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_22824_compound_5154']; rh:compound/rh:chebi`
hydrogenphosphate `CHEBI:43474`	consumes	2'-deoxyuridine + phosphate => 2-deoxy-alpha-D-ribose 1-phosphate + uracil `RHEA:22825`	RHEA:22825 Source assertion: Rhea RHEA:22825 assigns CHEBI:43474 to substrates with coefficient 1; the compound resolves to this exact ChEBI species. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/22825']/rh:substrates; rdf:Description[@rdf:about='http://rdf.rhea-db.org/22824_L']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_22824_compound_5518']; rh:compound/rh:chebi`
2'-deoxyuridine + phosphate => 2-deoxy-alpha-D-ribose 1-phosphate + uracil `RHEA:22825`	produces	2-deoxy-alpha-D-ribose 1-phosphate(2-) `CHEBI:57259`	RHEA:22825 Source assertion: Rhea RHEA:22825 assigns CHEBI:57259 to products with coefficient 1; the compound resolves to this exact ChEBI species. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/22825']/rh:products; rdf:Description[@rdf:about='http://rdf.rhea-db.org/22824_R']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_22824_compound_3098']; rh:compound/rh:chebi`
2'-deoxyuridine + phosphate => 2-deoxy-alpha-D-ribose 1-phosphate + uracil `RHEA:22825`	produces	uracil `CHEBI:17568`	RHEA:22825 Source assertion: Rhea RHEA:22825 assigns CHEBI:17568 to products with coefficient 1; the compound resolves to this exact ChEBI species. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/22825']/rh:products; rdf:Description[@rdf:about='http://rdf.rhea-db.org/22824_R']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_22824_compound_4063']; rh:compound/rh:chebi`
thymidine `CHEBI:17748`	consumes	thymidine + phosphate => 2-deoxy-alpha-D-ribose 1-phosphate + thymine `RHEA:16038`	RHEA:16038 Source assertion: Rhea RHEA:16038 assigns CHEBI:17748 to substrates with coefficient 1; the compound resolves to this exact ChEBI species. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/16038']/rh:substrates; rdf:Description[@rdf:about='http://rdf.rhea-db.org/16037_L']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_16037_compound_4636']; rh:compound/rh:chebi`
hydrogenphosphate `CHEBI:43474`	consumes	thymidine + phosphate => 2-deoxy-alpha-D-ribose 1-phosphate + thymine `RHEA:16038`	RHEA:16038 Source assertion: Rhea RHEA:16038 assigns CHEBI:43474 to substrates with coefficient 1; the compound resolves to this exact ChEBI species. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/16038']/rh:substrates; rdf:Description[@rdf:about='http://rdf.rhea-db.org/16037_L']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_16037_compound_5518']; rh:compound/rh:chebi`
thymidine + phosphate => 2-deoxy-alpha-D-ribose 1-phosphate + thymine `RHEA:16038`	produces	2-deoxy-alpha-D-ribose 1-phosphate(2-) `CHEBI:57259`	RHEA:16038 Source assertion: Rhea RHEA:16038 assigns CHEBI:57259 to products with coefficient 1; the compound resolves to this exact ChEBI species. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/16038']/rh:products; rdf:Description[@rdf:about='http://rdf.rhea-db.org/16037_R']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_16037_compound_3098']; rh:compound/rh:chebi`
thymidine + phosphate => 2-deoxy-alpha-D-ribose 1-phosphate + thymine `RHEA:16038`	produces	thymine `CHEBI:17821`	RHEA:16038 Source assertion: Rhea RHEA:16038 assigns CHEBI:17821 to products with coefficient 1; the compound resolves to this exact ChEBI species. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/16038']/rh:products; rdf:Description[@rdf:about='http://rdf.rhea-db.org/16037_R']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_16037_compound_2794']; rh:compound/rh:chebi`
Cytidine deaminase `UniProtKB:P0ABF6`	part_of Homodimer membership; the protein component is not represented as an independently active monomer.	cytidine/deoxycytidine deaminase `MetaCyc:CYTIDEAM-CPLX`	MetaCyc:CYTIDEAM-CPLX Source assertion: The native complex contains two copies of CYTIDEAM-MONOMER. Source location `Protein[@frameid='CYTIDEAM-CPLX']/component/Protein; component/coefficient` MetaCyc:CYTIDEAM-MONOMER Source assertion: The component has an explicit UNIPROT unification cross-reference to P0ABF6. Source location `Protein[@frameid='CYTIDEAM-MONOMER']/dblink[dblink-db='UNIPROT'][dblink-relationship='unification']/dblink-oid` PMID:8289286 Source assertion: The primary abstract describes the E. coli cytidine deaminase alpha2 dimer and active sites formed across its subunit interface. Source location `Primary abstract; full publisher article was not available locally.`
Thymidine phosphorylase `UniProtKB:P07650`	part_of Homodimer membership; the protein component is not represented as an independently active monomer.	thymidine phosphorylase / uracil phosphorylase `MetaCyc:DEOA-CPLX`	MetaCyc:DEOA-CPLX Source assertion: The native complex contains two copies of DEOA-MONOMER. Source location `Protein[@frameid='DEOA-CPLX']/component/Protein; component/coefficient` MetaCyc:DEOA-MONOMER Source assertion: The component has an explicit UNIPROT unification cross-reference to P07650. Source location `Protein[@frameid='DEOA-MONOMER']/dblink[dblink-db='UNIPROT'][dblink-relationship='unification']/dblink-oid` PMID:2199449 Source assertion: The primary abstract reports an E. coli thymidine phosphorylase crystal dimer and the deoA-derived amino-acid sequence. Source location `Primary abstract; full publisher article was not available locally.`
cytidine/deoxycytidine deaminase `MetaCyc:CYTIDEAM-CPLX`	catalyzes Direct biochemical support is from a constitutive E. coli mutant, and genetic support is from K-12 mutant derivatives; the native complex annotation supplies MG1655 scope.	2'-deoxycytidine + H2O + H(+) => 2'-deoxyuridine + NH4(+) `RHEA:13434`	MetaCyc:CYTIDEAM-RXN Source assertion: CYTIDEAM-ENZRXN assigns CYTIDEAM-CPLX to deoxycytidine deamination and the reaction has an exact RHEA:13434 unification link. Source location `Reaction[@frameid='CYTIDEAM-RXN']/enzymatic-reaction/Enzymatic-Reaction[@frameid='CYTIDEAM-ENZRXN']/enzyme; dblink[dblink-db='RHEA']` PMID:4202859 Source assertion: Partially purified enzyme from E. coli Y-70-272 deaminates deoxycytidine; the assay identifies deoxyuridine and substrate-specificity measurements include deoxycytidine. Source location `Materials and Methods, pp.797-798; Results, Substrate Specificity and Table VI, p.802.` PMID:17827303 Source assertion: In a K-12 dcd deoA background, cdd mutation strongly increased thymidine dependence; this supports the deoxycytidine-to-deoxyuridine step in that mutant context. Source location `Results, From dCMP to dCyd; Figure 3; Table 1 footnote a.`
thymidine phosphorylase / uracil phosphorylase `MetaCyc:DEOA-CPLX`	catalyzes Degradation direction selected from a reversible phosphorolysis. This is the native DeoA complex, not a separate Udp enzyme.	2'-deoxyuridine + phosphate => 2-deoxy-alpha-D-ribose 1-phosphate + uracil `RHEA:22825`	MetaCyc:URA-PHOSPH-RXN Source assertion: The native URA-PHOSPH-RXN enzymatic-reaction assigns DEOA-CPLX to deoxyuridine phosphorolysis, and its Rhea unification link is the reversible family member 22827. Source location `Reaction[@frameid='URA-PHOSPH-RXN']/enzymatic-reaction; reaction-direction; dblink[dblink-db='RHEA']` RHEA:22825 Source assertion: Rhea master 22824 has bidirectionalReaction 22827 and directionalReaction 22825; 22825 is the left-to-right degradation equation. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/22824']/rh:bidirectionalReaction; rh:directionalReaction; rdf:Description[@rdf:about='http://rdf.rhea-db.org/22825']/rh:substrates; rh:products; rh:equation` PMID:8157589 Source assertion: The primary abstract reports that a deoA mutation spares deoxyuridine from catabolism in E. coli dcd mutants; the work does not quantify this flux in wild-type cells. Source location `Primary abstract, results and final scope statement.`
thymidine phosphorylase / uracil phosphorylase `MetaCyc:DEOA-CPLX`	catalyzes Degradation direction selected from a reversible phosphorolysis. This is the native DeoA complex, not a separate Udp enzyme.	thymidine + phosphate => 2-deoxy-alpha-D-ribose 1-phosphate + thymine `RHEA:16038`	MetaCyc:THYM-PHOSPH-RXN Source assertion: The native THYM-PHOSPH-RXN enzymatic-reaction assigns DEOA-CPLX to thymidine phosphorolysis, and its Rhea unification link is the reversible family member 16040. Source location `Reaction[@frameid='THYM-PHOSPH-RXN']/enzymatic-reaction; reaction-direction; dblink[dblink-db='RHEA']` RHEA:16038 Source assertion: Rhea master 16037 has bidirectionalReaction 16040 and directionalReaction 16038; 16038 is the left-to-right degradation equation. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/16037']/rh:bidirectionalReaction; rh:directionalReaction; rdf:Description[@rdf:about='http://rdf.rhea-db.org/16038']/rh:substrates; rh:products; rh:equation` UniProtKB:P07650 Source assertion: Reviewed P07650 catalytic activity names thymidine plus phosphate yielding sugar phosphate and thymine, with RHEA:16037; the function describes reversible phosphorolysis. Source location `/comments/0 (FUNCTION); /comments/1/reaction (CATALYTIC ACTIVITY).`
Cytidine deaminase `UniProtKB:P0ABF6`	has_cofactor Bound catalytic zinc is distinguished from inhibition by added free zinc in the 1973 assay. No zinc-consumption reaction is asserted.	zinc(2+) `CHEBI:29105`	UniProtKB:P0ABF6 Source assertion: Reviewed P0ABF6 explicitly annotates Zn(2+) CHEBI:29105 as cofactor, supported by three experimental structural publications; the note states one zinc ion. Source location `/comments/3/cofactors/0; /comments/3/note.` PMID:8289286 Source assertion: The E. coli cytidine deaminase structural abstract places zinc in the active-site pocket formed by the dimer. Source location `Primary abstract, zinc-binding pocket and coordination description.`
Cytidine deaminase `UniProtKB:P0ABF6`	located_in Native MG1655 component-location annotation; not inferred from osmotic-shock recovery in a different strain.	cytosol `GO:0005829`	MetaCyc:CYTIDEAM-MONOMER Source assertion: The native component CYTIDEAM-MONOMER, unified with UniProtKB:P0ABF6, is explicitly located in CCO-CYTOSOL. Source location `Protein[@frameid='CYTIDEAM-MONOMER']/location/cco[@frameid='CCO-CYTOSOL']; dblink[dblink-db='UNIPROT']`
Thymidine phosphorylase `UniProtKB:P07650`	located_in Native MG1655 component-location annotation; not inferred from osmotic-shock recovery in a different strain.	cytosol `GO:0005829`	MetaCyc:DEOA-MONOMER Source assertion: The native component DEOA-MONOMER, unified with UniProtKB:P07650, is explicitly located in CCO-CYTOSOL. Source location `Protein[@frameid='DEOA-MONOMER']/location/cco[@frameid='CCO-CYTOSOL']; dblink[dblink-db='UNIPROT']`
2'-deoxycytidine + H2O + H(+) => 2'-deoxyuridine + NH4(+) `RHEA:13434`	part_of	`MetaCyc:PWY-7181`	MetaCyc:PWY-7181 Source assertion: The complete native reaction-list includes CYTIDEAM-RXN; its reaction-layout selects L2R toward degradation products. Source location `Pathway[@frameid='PWY-7181']/reaction-list/Reaction[@frameid='CYTIDEAM-RXN']; reaction-layout[Reaction/@frameid='CYTIDEAM-RXN']/direction` MetaCyc:CYTIDEAM-RXN Source assertion: The native reaction explicitly links PWY-7181 and its exact Rhea family; independent Rhea triples select RHEA:13434. Source location `Reaction[@frameid='CYTIDEAM-RXN']/in-pathway; dblink[dblink-db='RHEA']` RHEA:13434 Source assertion: Rhea family 13433 explicitly assigns 13434 as the left-to-right directional member. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/13433']/rh:directionalReaction; rdf:Description[@rdf:about='http://rdf.rhea-db.org/13434']/rh:substrates; rh:products; rh:equation`
2'-deoxyuridine + phosphate => 2-deoxy-alpha-D-ribose 1-phosphate + uracil `RHEA:22825`	part_of	`MetaCyc:PWY-7181`	MetaCyc:PWY-7181 Source assertion: The complete native reaction-list includes URA-PHOSPH-RXN; its reaction-layout selects L2R toward degradation products. Source location `Pathway[@frameid='PWY-7181']/reaction-list/Reaction[@frameid='URA-PHOSPH-RXN']; reaction-layout[Reaction/@frameid='URA-PHOSPH-RXN']/direction` MetaCyc:URA-PHOSPH-RXN Source assertion: The native reaction explicitly links PWY-7181 and its exact Rhea family; independent Rhea triples select RHEA:22825. Source location `Reaction[@frameid='URA-PHOSPH-RXN']/in-pathway; dblink[dblink-db='RHEA']` RHEA:22825 Source assertion: Rhea family 22824 explicitly assigns 22825 as the left-to-right directional member. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/22824']/rh:directionalReaction; rdf:Description[@rdf:about='http://rdf.rhea-db.org/22825']/rh:substrates; rh:products; rh:equation`
thymidine + phosphate => 2-deoxy-alpha-D-ribose 1-phosphate + thymine `RHEA:16038`	part_of	`MetaCyc:PWY-7181`	MetaCyc:PWY-7181 Source assertion: The complete native reaction-list includes THYM-PHOSPH-RXN; its reaction-layout selects L2R toward degradation products. Source location `Pathway[@frameid='PWY-7181']/reaction-list/Reaction[@frameid='THYM-PHOSPH-RXN']; reaction-layout[Reaction/@frameid='THYM-PHOSPH-RXN']/direction` MetaCyc:THYM-PHOSPH-RXN Source assertion: The native reaction explicitly links PWY-7181 and its exact Rhea family; independent Rhea triples select RHEA:16038. Source location `Reaction[@frameid='THYM-PHOSPH-RXN']/in-pathway; dblink[dblink-db='RHEA']` RHEA:16038 Source assertion: Rhea family 16037 explicitly assigns 16038 as the left-to-right directional member. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/16037']/rh:directionalReaction; rdf:Description[@rdf:about='http://rdf.rhea-db.org/16038']/rh:substrates; rh:products; rh:equation`
2'-deoxycytidine + H2O + H(+) => 2'-deoxyuridine + NH4(+) `RHEA:13434`	provides_input_for Shared-intermediate flow only. The separate thymidine branch is not chained to deoxyuridine phosphorolysis merely because the native layout also lists it as a predecessor.	2'-deoxyuridine + phosphate => 2-deoxy-alpha-D-ribose 1-phosphate + uracil `RHEA:22825`	MetaCyc:PWY-7181 Source assertion: URA-PHOSPH-RXN has CYTIDEAM-RXN as a predecessor; their selected layouts produce and consume DEOXYURIDINE, respectively. Source location `Pathway[@frameid='PWY-7181']/reaction-ordering[Reaction/@frameid='URA-PHOSPH-RXN']/predecessor-reactions/Reaction[@frameid='CYTIDEAM-RXN']; reaction-layout` RHEA:13434 Source assertion: The selected deamination produces CHEBI:16450, the exact deoxyuridine species consumed by RHEA:22825. Source location `rh:products => 13433_R; Participant_13433_compound_5154/rh:compound/rh:chebi` RHEA:22825 Source assertion: The selected phosphorolysis consumes CHEBI:16450, the output of RHEA:13434. Source location `rh:substrates => 22824_L; Participant_22824_compound_5154/rh:compound/rh:chebi`

References

MetaCyc:PWY-7181 MetaCyc pyrimidine deoxyribonucleosides degradation (source version: MetaCyc 22.5 public SGD-hosted native XML)
MetaCyc:CYTIDEAM-RXN MetaCyc native CYTIDEAM-RXN (source version: MetaCyc 22.5 public SGD-hosted native XML)
MetaCyc:URA-PHOSPH-RXN MetaCyc native URA-PHOSPH-RXN (source version: MetaCyc 22.5 public SGD-hosted native XML)
MetaCyc:THYM-PHOSPH-RXN MetaCyc native THYM-PHOSPH-RXN (source version: MetaCyc 22.5 public SGD-hosted native XML)
MetaCyc:CYTIDEAM-CPLX MetaCyc native CYTIDEAM-CPLX (source version: MetaCyc 22.5 public SGD-hosted native XML)
MetaCyc:DEOA-CPLX MetaCyc native DEOA-CPLX (source version: MetaCyc 22.5 public SGD-hosted native XML)
MetaCyc:CYTIDEAM-MONOMER MetaCyc native CYTIDEAM-MONOMER (source version: MetaCyc 22.5 public SGD-hosted native XML)
MetaCyc:DEOA-MONOMER MetaCyc native DEOA-MONOMER (source version: MetaCyc 22.5 public SGD-hosted native XML)
UniProtKB:P0ABF6 Reviewed UniProtKB P0ABF6 (source version: UniProt release 2026_03; response header dated 02-September-2026)
UniProtKB:P07650 Reviewed UniProtKB P07650 (source version: UniProt release 2026_03; response header dated 02-September-2026)
RHEA:13434 Rhea exact directed reaction 13434 (source version: Rhea release 142; complete native RDF gzip)
RHEA:22825 Rhea exact directed reaction 22825 (source version: Rhea release 142; complete native RDF gzip)
RHEA:16038 Rhea exact directed reaction 16038 (source version: Rhea release 142; complete native RDF gzip)
PMID:4202859 The purification and properties of cytidine deaminase from Escherichia coli. (source version: 1973 primary full text, pp.797-803)
PMID:17827303 The Deoxycytidine Pathway for Thymidylate Synthesis in Escherichia coli (source version: 2007 primary full text)
PMID:8157589 De novo synthesis of thymidylate via deoxycytidine in dcd mutants of Escherichia coli. (source version: Primary abstract inspected; full-text acquisition unavailable)
PMID:8289286 Cytidine deaminase. The 2.3 A crystal structure of an enzyme: transition-state analog complex. (source version: Primary abstract inspected; no full-text claim)
PMID:2199449 Three-dimensional structure of thymidine phosphorylase from Escherichia coli at 2.8 A resolution. (source version: Primary abstract inspected; no full-text claim)

Curation history

2026-10-11T00:38:21Z Codex; add-pathway; Curated the full three-reaction PWY-7181 boundary after ignored-inclusive semantic deduplication; verified exact Rhea species/directions, native Cdd and DeoA dimers, source-specific locations and zinc evidence, with primary strain and access limitations retained.
2026-10-11T00:42:17Z codex
- CREATE — Add the native three-reaction pyrimidine deoxyribonucleoside degradation pathway
  Created exact MetaCyc PWY-7181 with deoxycytidine deamination and two phosphorolysis branches, verified Cdd and DeoA assemblies, zinc and qualified cytosol context. The complete native pathway boundary excludes separate transport and downstream sugar catabolism. Preserved biochemical reversibility and strain-specific evidence limits. Author replay verified all reaction sides, elemental and charge balances, identifiers, source locators and local schemas. Evidence and checks are in research/pathway_additions/2026-10-10-next-routes/pyrimidine-curation.md and pyrimidine-validation.json. Independent scientific review and final corpus gates follow before publication.
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2026-10-11T00:44:51Z codex
- EDIT — Resolve independent review findings in pyrimidine evidence provenance
  Removed session-cookie response metadata from the maintained rejected-source receipt while retaining URL, status and scientific body hashes. Added exact master rh:directionalReaction source locators for all three membership bridges. Chemistry, coefficients, assertions and biological scope are unchanged. The author reran actual raw RDF, schema and balance replay successfully; pyrimidine-validation.json retains the original and corrected hashes and issue dispositions. Independent reviewer will re-inspect the changed inputs before saving; full corpus gates and generated products are rerun before publication.
Read this curation session