Pyrimidine Ribonucleosides Degradation

PathBank:SMP0002038

The full seven-step PathBank route for Escherichia coli comprises five biochemical reactions and two NupG proton-coupled imports. Periplasmic CpdB hydrolyzes uridine 2′,3′-cyclic phosphate through 3′-UMP to uridine; imported uridine and cytidine feed cytosolic uridine phosphorolysis, with cytidine first deaminated by the zinc-containing Cdd homodimer. The Udp hexamer releases uracil and alpha-D-ribose 1-phosphate, and DeoB converts the sugar phosphate to D-ribose 5-phosphate. The curated K-12 scope follows reviewed proteins and native annotations; historical mutant assays and recombinant studies do not measure wild-type flux through the entire route. Exact native compartment states are retained for uptake, and inferred dependencies link them to reaction-class chemistry. CpdB metal specificity remains a similarity annotation, while Mn2+ and Co2+ are alternative assay activators of DeoB. The narrower two-reaction MetaCyc:PWY0-1295 core is not asserted to be equivalent to this complete PathBank pathway.

Pathway type

pyrimidine ribonucleoside catabolism

Organism scope

Escherichia coli K-12 NCBITaxon:83333

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Pathway network

38 nodes · 55 asserted directed edges

Arrows show recorded subject → object relationships, not necessarily metabolic flow. Select a node for details or an arrow for evidence. Scroll, zoom or find a node to explore.

Reaction / activity
Chemical / cofactor
Protein / complex
Cell / process context
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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 K-12 `NCBITaxon:83333`	taxon
2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase `UniProtKB:P08331`	protein
Cytidine deaminase `UniProtKB:P0ABF6`	protein
Uridine phosphorylase `UniProtKB:P12758`	protein
Phosphopentomutase `UniProtKB:P0A6K6`	protein
Nucleoside permease NupG `UniProtKB:P0AFF4`	protein
cytidine/deoxycytidine deaminase `MetaCyc:CYTIDEAM-CPLX`	complex
uridine phosphorylase `MetaCyc:URPHOS-CPLX`	complex
periplasmic space `GO:0042597`	cellular component
cytosol `GO:0005829`	cellular component
plasma membrane `GO:0005886`	cellular component
zinc(2+) `CHEBI:29105`	cofactor
divalent metal cation `CHEBI:60240`	cofactor
manganese(2+) `CHEBI:29035`	cofactor
cobalt(2+) `CHEBI:48828`	cofactor
uridine [periplasmic space] `PathBank:SMP0002038/Compound/PW_C000202_Periplasmic_Space`	small molecule
uridine [cytosol] `PathBank:SMP0002038/Compound/PW_C000202_Cytosol`	small molecule
cytidine [periplasmic space] `PathBank:SMP0002038/Compound/PW_C000061_Periplasmic_Space`	small molecule
cytidine [cytosol] `PathBank:SMP0002038/Compound/PW_C000061_Cytosol`	small molecule
hydron [periplasmic space] `PathBank:SMP0002038/Compound/PW_C040034_Periplasmic_Space`	small molecule
hydron [cytosol] `PathBank:SMP0002038/Compound/PW_C040034_Cytosol`	small molecule
2',3'-cyclic UMP(1-) `CHEBI:60873`	small molecule
water `CHEBI:15377`	small molecule
3'-UMP(2-) `CHEBI:60784`	small molecule
hydron `CHEBI:15378`	small molecule
uridine `CHEBI:16704`	small molecule
hydrogenphosphate `CHEBI:43474`	small molecule
cytidine `CHEBI:17562`	small molecule
ammonium `CHEBI:28938`	small molecule
alpha-D-ribose 1-phosphate(2-) `CHEBI:57720`	small molecule
uracil `CHEBI:17568`	small molecule
D-ribofuranose 5-phosphate(2-) `CHEBI:78346`	small molecule
2',3'-cyclophospho-UMP + H2O => 3'-UMP + H(+) `RHEA:27879`	molecular activity	left to right
3'-UMP + H2O => uridine + phosphate `RHEA:27891`	molecular activity	left to right
cytidine + H2O + H(+) => uridine + NH4(+) `RHEA:16070`	molecular activity	left to right
uridine + phosphate => alpha-D-ribose 1-phosphate + uracil `RHEA:24389`	molecular activity	left to right
alpha-D-ribose 1-phosphate => D-ribose 5-phosphate `RHEA:18794`	molecular activity	left to right
uridine(out) + H(+)(out) => uridine(in) + H(+)(in) `RHEA:29953`	molecular activity	right to left
cytidine(out) + H(+)(out) => cytidine(in) + H(+)(in) `RHEA:29985`	molecular activity	right to left

Mechanistic edges

Mechanistic edges and their cited evidence
Subject	Predicate and description	Object	Evidence
2',3'-cyclic UMP(1-) `CHEBI:60873`	consumes	2',3'-cyclophospho-UMP + H2O => 3'-UMP + H(+) `RHEA:27879`	RHEA:27879 Source assertion: Rhea 27879 assigns CHEBI:60873 to substrates with coefficient 1. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/27879']/rh:substrates; rdf:Description[@rdf:about='http://rdf.rhea-db.org/27878_L']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_27878_compound_6281']; rh:compound/rh:chebi`
water `CHEBI:15377`	consumes	2',3'-cyclophospho-UMP + H2O => 3'-UMP + H(+) `RHEA:27879`	RHEA:27879 Source assertion: Rhea 27879 assigns CHEBI:15377 to substrates with coefficient 1. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/27879']/rh:substrates; rdf:Description[@rdf:about='http://rdf.rhea-db.org/27878_L']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_27878_compound_1283']; rh:compound/rh:chebi`
2',3'-cyclophospho-UMP + H2O => 3'-UMP + H(+) `RHEA:27879`	produces	3'-UMP(2-) `CHEBI:60784`	RHEA:27879 Source assertion: Rhea 27879 assigns CHEBI:60784 to products with coefficient 1. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/27879']/rh:products; rdf:Description[@rdf:about='http://rdf.rhea-db.org/27878_R']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_27878_compound_6282']; rh:compound/rh:chebi`
2',3'-cyclophospho-UMP + H2O => 3'-UMP + H(+) `RHEA:27879`	produces	hydron `CHEBI:15378`	RHEA:27879 Source assertion: Rhea 27879 assigns CHEBI:15378 to products with coefficient 1. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/27879']/rh:products; rdf:Description[@rdf:about='http://rdf.rhea-db.org/27878_R']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_27878_compound_3249']; rh:compound/rh:chebi`
3'-UMP(2-) `CHEBI:60784`	consumes	3'-UMP + H2O => uridine + phosphate `RHEA:27891`	RHEA:27891 Source assertion: Rhea 27891 assigns CHEBI:60784 to substrates with coefficient 1. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/27891']/rh:substrates; rdf:Description[@rdf:about='http://rdf.rhea-db.org/27890_L']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_27890_compound_6282']; rh:compound/rh:chebi`
water `CHEBI:15377`	consumes	3'-UMP + H2O => uridine + phosphate `RHEA:27891`	RHEA:27891 Source assertion: Rhea 27891 assigns CHEBI:15377 to substrates with coefficient 1. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/27891']/rh:substrates; rdf:Description[@rdf:about='http://rdf.rhea-db.org/27890_L']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_27890_compound_1283']; rh:compound/rh:chebi`
3'-UMP + H2O => uridine + phosphate `RHEA:27891`	produces	uridine `CHEBI:16704`	RHEA:27891 Source assertion: Rhea 27891 assigns CHEBI:16704 to products with coefficient 1. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/27891']/rh:products; rdf:Description[@rdf:about='http://rdf.rhea-db.org/27890_R']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_27890_compound_4178']; rh:compound/rh:chebi`
3'-UMP + H2O => uridine + phosphate `RHEA:27891`	produces	hydrogenphosphate `CHEBI:43474`	RHEA:27891 Source assertion: Rhea 27891 assigns CHEBI:43474 to products with coefficient 1. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/27891']/rh:products; rdf:Description[@rdf:about='http://rdf.rhea-db.org/27890_R']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_27890_compound_5518']; rh:compound/rh:chebi`
cytidine `CHEBI:17562`	consumes	cytidine + H2O + H(+) => uridine + NH4(+) `RHEA:16070`	RHEA:16070 Source assertion: Rhea 16070 assigns CHEBI:17562 to substrates with coefficient 1. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/16070']/rh:substrates; rdf:Description[@rdf:about='http://rdf.rhea-db.org/16069_L']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_16069_compound_3062']; rh:compound/rh:chebi`
water `CHEBI:15377`	consumes	cytidine + H2O + H(+) => uridine + NH4(+) `RHEA:16070`	RHEA:16070 Source assertion: Rhea 16070 assigns CHEBI:15377 to substrates with coefficient 1. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/16070']/rh:substrates; rdf:Description[@rdf:about='http://rdf.rhea-db.org/16069_L']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_16069_compound_1283']; rh:compound/rh:chebi`
hydron `CHEBI:15378`	consumes	cytidine + H2O + H(+) => uridine + NH4(+) `RHEA:16070`	RHEA:16070 Source assertion: Rhea 16070 assigns CHEBI:15378 to substrates with coefficient 1. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/16070']/rh:substrates; rdf:Description[@rdf:about='http://rdf.rhea-db.org/16069_L']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_16069_compound_3249']; rh:compound/rh:chebi`
cytidine + H2O + H(+) => uridine + NH4(+) `RHEA:16070`	produces	uridine `CHEBI:16704`	RHEA:16070 Source assertion: Rhea 16070 assigns CHEBI:16704 to products with coefficient 1. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/16070']/rh:products; rdf:Description[@rdf:about='http://rdf.rhea-db.org/16069_R']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_16069_compound_4178']; rh:compound/rh:chebi`
cytidine + H2O + H(+) => uridine + NH4(+) `RHEA:16070`	produces	ammonium `CHEBI:28938`	RHEA:16070 Source assertion: Rhea 16070 assigns CHEBI:28938 to products with coefficient 1. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/16070']/rh:products; rdf:Description[@rdf:about='http://rdf.rhea-db.org/16069_R']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_16069_compound_1012']; rh:compound/rh:chebi`
uridine `CHEBI:16704`	consumes	uridine + phosphate => alpha-D-ribose 1-phosphate + uracil `RHEA:24389`	RHEA:24389 Source assertion: Rhea 24389 assigns CHEBI:16704 to substrates with coefficient 1. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/24389']/rh:substrates; rdf:Description[@rdf:about='http://rdf.rhea-db.org/24388_L']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_24388_compound_4178']; rh:compound/rh:chebi`
hydrogenphosphate `CHEBI:43474`	consumes	uridine + phosphate => alpha-D-ribose 1-phosphate + uracil `RHEA:24389`	RHEA:24389 Source assertion: Rhea 24389 assigns CHEBI:43474 to substrates with coefficient 1. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/24389']/rh:substrates; rdf:Description[@rdf:about='http://rdf.rhea-db.org/24388_L']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_24388_compound_5518']; rh:compound/rh:chebi`
uridine + phosphate => alpha-D-ribose 1-phosphate + uracil `RHEA:24389`	produces	alpha-D-ribose 1-phosphate(2-) `CHEBI:57720`	RHEA:24389 Source assertion: Rhea 24389 assigns CHEBI:57720 to products with coefficient 1. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/24389']/rh:products; rdf:Description[@rdf:about='http://rdf.rhea-db.org/24388_R']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_24388_compound_2276']; rh:compound/rh:chebi`
uridine + phosphate => alpha-D-ribose 1-phosphate + uracil `RHEA:24389`	produces	uracil `CHEBI:17568`	RHEA:24389 Source assertion: Rhea 24389 assigns CHEBI:17568 to products with coefficient 1. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/24389']/rh:products; rdf:Description[@rdf:about='http://rdf.rhea-db.org/24388_R']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_24388_compound_4063']; rh:compound/rh:chebi`
alpha-D-ribose 1-phosphate(2-) `CHEBI:57720`	consumes	alpha-D-ribose 1-phosphate => D-ribose 5-phosphate `RHEA:18794`	RHEA:18794 Source assertion: Rhea 18794 assigns CHEBI:57720 to substrates with coefficient 1. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/18794']/rh:substrates; rdf:Description[@rdf:about='http://rdf.rhea-db.org/18793_L']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_18793_compound_2276']; rh:compound/rh:chebi`
alpha-D-ribose 1-phosphate => D-ribose 5-phosphate `RHEA:18794`	produces	D-ribofuranose 5-phosphate(2-) `CHEBI:78346`	RHEA:18794 Source assertion: Rhea 18794 assigns CHEBI:78346 to products with coefficient 1. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/18794']/rh:products; rdf:Description[@rdf:about='http://rdf.rhea-db.org/18793_R']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_18793_compound_9495']; rh:compound/rh:chebi`
uridine [periplasmic space] `PathBank:SMP0002038/Compound/PW_C000202_Periplasmic_Space`	consumes	uridine(out) + H(+)(out) => uridine(in) + H(+)(in) `RHEA:29953`	RHEA:29953 Source assertion: Rhea 29953 assigns CHEBI:16704 to substrates with coefficient 1; the participant is explicitly Out. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/29953']/rh:substrates; rdf:Description[@rdf:about='http://rdf.rhea-db.org/29951_R']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_29951_compound_4178_out']; rh:compound/rh:chebi; rh:location` PathBank:SMP0002038 Source assertion: Native transport 488 assigns this exact Periplasmic_Space physical object to its left side; the entity reference and compartment distinguish it from the corresponding state across the membrane. Source location `bp:Transport[@rdf:ID='Transports/488']/bp:left; bp:SmallMolecule[@rdf:ID='Compound/PW_C000202_Periplasmic_Space']/bp:entityReference; bp:cellularLocation`
hydron [periplasmic space] `PathBank:SMP0002038/Compound/PW_C040034_Periplasmic_Space`	consumes	uridine(out) + H(+)(out) => uridine(in) + H(+)(in) `RHEA:29953`	RHEA:29953 Source assertion: Rhea 29953 assigns CHEBI:15378 to substrates with coefficient 1; the participant is explicitly Out. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/29953']/rh:substrates; rdf:Description[@rdf:about='http://rdf.rhea-db.org/29951_R']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_29951_compound_3249_out']; rh:compound/rh:chebi; rh:location` PathBank:SMP0002038 Source assertion: Native transport 488 assigns this exact Periplasmic_Space physical object to its left side; the entity reference and compartment distinguish it from the corresponding state across the membrane. Source location `bp:Transport[@rdf:ID='Transports/488']/bp:left; bp:SmallMolecule[@rdf:ID='Compound/PW_C040034_Periplasmic_Space']/bp:entityReference; bp:cellularLocation`
uridine(out) + H(+)(out) => uridine(in) + H(+)(in) `RHEA:29953`	produces	uridine [cytosol] `PathBank:SMP0002038/Compound/PW_C000202_Cytosol`	RHEA:29953 Source assertion: Rhea 29953 assigns CHEBI:16704 to products with coefficient 1; the participant is explicitly In. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/29953']/rh:products; rdf:Description[@rdf:about='http://rdf.rhea-db.org/29951_L']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_29951_compound_4178_in']; rh:compound/rh:chebi; rh:location` PathBank:SMP0002038 Source assertion: Native transport 488 assigns this exact Cytosol physical object to its right side; the entity reference and compartment distinguish it from the corresponding state across the membrane. Source location `bp:Transport[@rdf:ID='Transports/488']/bp:right; bp:SmallMolecule[@rdf:ID='Compound/PW_C000202_Cytosol']/bp:entityReference; bp:cellularLocation`
uridine(out) + H(+)(out) => uridine(in) + H(+)(in) `RHEA:29953`	produces	hydron [cytosol] `PathBank:SMP0002038/Compound/PW_C040034_Cytosol`	RHEA:29953 Source assertion: Rhea 29953 assigns CHEBI:15378 to products with coefficient 1; the participant is explicitly In. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/29953']/rh:products; rdf:Description[@rdf:about='http://rdf.rhea-db.org/29951_L']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_29951_compound_3249_in']; rh:compound/rh:chebi; rh:location` PathBank:SMP0002038 Source assertion: Native transport 488 assigns this exact Cytosol physical object to its right side; the entity reference and compartment distinguish it from the corresponding state across the membrane. Source location `bp:Transport[@rdf:ID='Transports/488']/bp:right; bp:SmallMolecule[@rdf:ID='Compound/PW_C040034_Cytosol']/bp:entityReference; bp:cellularLocation`
cytidine [periplasmic space] `PathBank:SMP0002038/Compound/PW_C000061_Periplasmic_Space`	consumes	cytidine(out) + H(+)(out) => cytidine(in) + H(+)(in) `RHEA:29985`	RHEA:29985 Source assertion: Rhea 29985 assigns CHEBI:17562 to substrates with coefficient 1; the participant is explicitly Out. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/29985']/rh:substrates; rdf:Description[@rdf:about='http://rdf.rhea-db.org/29983_R']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_29983_compound_3062_out']; rh:compound/rh:chebi; rh:location` PathBank:SMP0002038 Source assertion: Native transport 489 assigns this exact Periplasmic_Space physical object to its left side; the entity reference and compartment distinguish it from the corresponding state across the membrane. Source location `bp:Transport[@rdf:ID='Transports/489']/bp:left; bp:SmallMolecule[@rdf:ID='Compound/PW_C000061_Periplasmic_Space']/bp:entityReference; bp:cellularLocation`
hydron [periplasmic space] `PathBank:SMP0002038/Compound/PW_C040034_Periplasmic_Space`	consumes	cytidine(out) + H(+)(out) => cytidine(in) + H(+)(in) `RHEA:29985`	RHEA:29985 Source assertion: Rhea 29985 assigns CHEBI:15378 to substrates with coefficient 1; the participant is explicitly Out. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/29985']/rh:substrates; rdf:Description[@rdf:about='http://rdf.rhea-db.org/29983_R']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_29983_compound_3249_out']; rh:compound/rh:chebi; rh:location` PathBank:SMP0002038 Source assertion: Native transport 489 assigns this exact Periplasmic_Space physical object to its left side; the entity reference and compartment distinguish it from the corresponding state across the membrane. Source location `bp:Transport[@rdf:ID='Transports/489']/bp:left; bp:SmallMolecule[@rdf:ID='Compound/PW_C040034_Periplasmic_Space']/bp:entityReference; bp:cellularLocation`
cytidine(out) + H(+)(out) => cytidine(in) + H(+)(in) `RHEA:29985`	produces	cytidine [cytosol] `PathBank:SMP0002038/Compound/PW_C000061_Cytosol`	RHEA:29985 Source assertion: Rhea 29985 assigns CHEBI:17562 to products with coefficient 1; the participant is explicitly In. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/29985']/rh:products; rdf:Description[@rdf:about='http://rdf.rhea-db.org/29983_L']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_29983_compound_3062_in']; rh:compound/rh:chebi; rh:location` PathBank:SMP0002038 Source assertion: Native transport 489 assigns this exact Cytosol physical object to its right side; the entity reference and compartment distinguish it from the corresponding state across the membrane. Source location `bp:Transport[@rdf:ID='Transports/489']/bp:right; bp:SmallMolecule[@rdf:ID='Compound/PW_C000061_Cytosol']/bp:entityReference; bp:cellularLocation`
cytidine(out) + H(+)(out) => cytidine(in) + H(+)(in) `RHEA:29985`	produces	hydron [cytosol] `PathBank:SMP0002038/Compound/PW_C040034_Cytosol`	RHEA:29985 Source assertion: Rhea 29985 assigns CHEBI:15378 to products with coefficient 1; the participant is explicitly In. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/29985']/rh:products; rdf:Description[@rdf:about='http://rdf.rhea-db.org/29983_L']/rh:contains1[@rdf:resource='http://rdf.rhea-db.org/Participant_29983_compound_3249_in']; rh:compound/rh:chebi; rh:location` PathBank:SMP0002038 Source assertion: Native transport 489 assigns this exact Cytosol physical object to its right side; the entity reference and compartment distinguish it from the corresponding state across the membrane. Source location `bp:Transport[@rdf:ID='Transports/489']/bp:right; bp:SmallMolecule[@rdf:ID='Compound/PW_C040034_Cytosol']/bp:entityReference; bp:cellularLocation`
2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase `UniProtKB:P08331`	enables	2',3'-cyclophospho-UMP + H2O => 3'-UMP + H(+) `RHEA:27879`	PathBank:SMP0002038 Source assertion: Native ReactionCatalysis/5858 assigns its protein controller to Reactions/5895; the component or protein reference identifies UniProtKB:P08331. Source location `bp:Catalysis[@rdf:ID='ReactionCatalysis/5858']/bp:controller and bp:controlled; bp:ProteinReference[@rdf:ID='ProteinReference/5948']/bp:xref` RHEA:27879 Source assertion: The explicit Rhea family maps master 27878 to directional member 27879; inspected sides and equation match the selected native chemistry. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/27878']/rh:directionalReaction[@rdf:resource='http://rdf.rhea-db.org/27879']; rdf:Description[@rdf:about='http://rdf.rhea-db.org/27879']/rh:substrates, rh:products, rh:equation` MetaCyc:CPDB-MONOMER Source assertion: Native CpdB annotation links this exact uridine reaction RXN-14091 to CPDB-MONOMER; its UNIPROT unification is P08331. Source location `Protein[@frameid='CPDB-MONOMER']/catalyzes/Enzymatic-Reaction/reaction/Reaction[@frameid='RXN-14091']; dblink[dblink-db='UNIPROT']` PMID:6251162 Source assertion: K-12 cpdB mutants lose most cyclic-UMP and 3′-UMP hydrolysis; the paper explicitly describes the two-step route to uridine. Residual 3′-nucleotidase activity and pyrE-dependent growth selection prevent an exclusivity or wild-type-flux claim. Source location `Printed pp31–32, Methods; Tables1–2; Results and Discussion, first two paragraphs` PMID:27294396 Source assertion: Recombinant BL21 CpdB hydrolyzed cyclic UMP in a coupled phosphate assay. Table1 does not independently establish the uridine-product regiochemistry or K-12 whole-pathway flux. Source location `Methods, Bacterial strains and Enzyme activity assays; Table1 cyclic-UMP row; Results, Enzymatic characterization`
2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase `UniProtKB:P08331`	enables	3'-UMP + H2O => uridine + phosphate `RHEA:27891`	PathBank:SMP0002038 Source assertion: Native ReactionCatalysis/5859 assigns its protein controller to Reactions/5896; the component or protein reference identifies UniProtKB:P08331. Source location `bp:Catalysis[@rdf:ID='ReactionCatalysis/5859']/bp:controller and bp:controlled; bp:ProteinReference[@rdf:ID='ProteinReference/5948']/bp:xref` RHEA:27891 Source assertion: The explicit Rhea family maps master 27890 to directional member 27891; inspected sides and equation match the selected native chemistry. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/27890']/rh:directionalReaction[@rdf:resource='http://rdf.rhea-db.org/27891']; rdf:Description[@rdf:about='http://rdf.rhea-db.org/27891']/rh:substrates, rh:products, rh:equation` MetaCyc:CPDB-MONOMER Source assertion: Native CpdB annotation links this exact uridine reaction RXN-14115 to CPDB-MONOMER; its UNIPROT unification is P08331. Source location `Protein[@frameid='CPDB-MONOMER']/catalyzes/Enzymatic-Reaction/reaction/Reaction[@frameid='RXN-14115']; dblink[dblink-db='UNIPROT']` PMID:6251162 Source assertion: K-12 cpdB mutants lose most cyclic-UMP and 3′-UMP hydrolysis; the paper explicitly describes the two-step route to uridine. Residual 3′-nucleotidase activity and pyrE-dependent growth selection prevent an exclusivity or wild-type-flux claim. Source location `Printed pp31–32, Methods; Tables1–2; Results and Discussion, first two paragraphs`
cytidine/deoxycytidine deaminase `MetaCyc:CYTIDEAM-CPLX`	catalyzes	cytidine + H2O + H(+) => uridine + NH4(+) `RHEA:16070`	PathBank:SMP0002038 Source assertion: Native ReactionCatalysis/5860 assigns its protein complex controller to Reactions/5897; the component or protein reference identifies UniProtKB:P0ABF6. Source location `bp:Catalysis[@rdf:ID='ReactionCatalysis/5860']/bp:controller and bp:controlled; bp:ProteinReference[@rdf:ID='ProteinReference/6175']/bp:xref` RHEA:16070 Source assertion: The explicit Rhea family maps master 16069 to directional member 16070; inspected sides and equation match the selected native chemistry. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/16069']/rh:directionalReaction[@rdf:resource='http://rdf.rhea-db.org/16070']; rdf:Description[@rdf:about='http://rdf.rhea-db.org/16070']/rh:substrates, rh:products, rh:equation` UniProtKB:P0ABF6 Source assertion: The reviewed K-12 entry assigns cytidine deamination and a homodimeric assembly; the exact cytidine reaction, not the deoxy substrate activity, is selected. Source location `comments[1].reaction; SUBUNIT comment; organism.taxonId` PMID:4202859 Source assertion: Purified E. coli cytidine deaminase uses cytidine as substrate; the assay distinguishes cytidine from deoxycytidine. The enzyme came from mutant Y70-272, not a wild-type MG1655 flux experiment. Source location `Printed pp798–799, purification and bacterial strain; TableVI cytidine row`
uridine phosphorylase `MetaCyc:URPHOS-CPLX`	catalyzes	uridine + phosphate => alpha-D-ribose 1-phosphate + uracil `RHEA:24389`	PathBank:SMP0002038 Source assertion: Native ReactionCatalysis/5861 assigns its protein complex controller to Reactions/5898; the component or protein reference identifies UniProtKB:P12758. Source location `bp:Catalysis[@rdf:ID='ReactionCatalysis/5861']/bp:controller and bp:controlled; bp:ProteinReference[@rdf:ID='ProteinReference/10357']/bp:xref` RHEA:24389 Source assertion: The explicit Rhea family maps master 24388 to directional member 24389; inspected sides and equation match the selected native chemistry. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/24388']/rh:directionalReaction[@rdf:resource='http://rdf.rhea-db.org/24389']; rdf:Description[@rdf:about='http://rdf.rhea-db.org/24389']/rh:substrates, rh:products, rh:equation` UniProtKB:P12758 Source assertion: The reviewed K-12 Udp entry assigns uridine phosphorolysis through RHEA:24388 and a homohexamer; weaker deoxynucleoside activities are outside this selected route. Source location `CATALYTIC ACTIVITY and SUBUNIT comments; organism.taxonId` PMID:16751 Source assertion: Purified E. coli uridine phosphorylase showed uridine activity and no cytidine activity. Its historical eight-subunit estimate is not adopted; current hexamer evidence is recorded separately. Source location `Primary abstract, specific activity, substrate specificity and molecular weight sentences`
Phosphopentomutase `UniProtKB:P0A6K6`	enables	alpha-D-ribose 1-phosphate => D-ribose 5-phosphate `RHEA:18794`	PathBank:SMP0002038 Source assertion: Native ReactionCatalysis/5862 assigns its protein controller to Reactions/5899; the component or protein reference identifies UniProtKB:P0A6K6. Source location `bp:Catalysis[@rdf:ID='ReactionCatalysis/5862']/bp:controller and bp:controlled; bp:ProteinReference[@rdf:ID='ProteinReference/6000']/bp:xref` RHEA:18794 Source assertion: The explicit Rhea family maps master 18793 to directional member 18794; inspected sides and equation match the selected native chemistry. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/18793']/rh:directionalReaction[@rdf:resource='http://rdf.rhea-db.org/18794']; rdf:Description[@rdf:about='http://rdf.rhea-db.org/18794']/rh:substrates, rh:products, rh:equation` UniProtKB:P0A6K6 Source assertion: The reviewed K-12 DeoB entry directly annotates alpha-D-ribose1-phosphate to D-ribose5-phosphate, RHEA:18793, with experimental citations1089430 and4992818. Source location `comments[2].reaction and evidences; organism.taxonId` PMID:1089430 Source assertion: The primary abstract reports purified E. coli enzyme as four modified forms of a single45-kDa chain. This supports an enzyme-function assignment without introducing a new complex. Source location `Primary abstract, molecular weight and single polypeptide chain sentences`
Nucleoside permease NupG `UniProtKB:P0AFF4`	enables	uridine(out) + H(+)(out) => uridine(in) + H(+)(in) `RHEA:29953`	PathBank:SMP0002038 Source assertion: Native TransportCatalysis/420 assigns its protein controller to Transports/488; the component or protein reference identifies UniProtKB:P0AFF4. Source location `bp:Catalysis[@rdf:ID='TransportCatalysis/420']/bp:controller and bp:controlled; bp:ProteinReference[@rdf:ID='ProteinReference/7058']/bp:xref` RHEA:29953 Source assertion: The explicit Rhea family maps master 29951 to directional member 29953; inspected sides and equation match the selected native chemistry. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/29951']/rh:directionalReaction[@rdf:resource='http://rdf.rhea-db.org/29953']; rdf:Description[@rdf:about='http://rdf.rhea-db.org/29953']/rh:substrates, rh:products, rh:equation` UniProtKB:P0AFF4 Source assertion: The reviewed K-12 NupG entry assigns this nucleoside/H+ transport family with direct literature support. The native pathway selects import; the master equation is oriented in-to-out. Source location `CATALYTIC ACTIVITY reactionCrossReferences RHEA:29951; FUNCTION comment; organism.taxonId` PMID:15513740 Source assertion: Recombinant NupG transported uridine; competition, oocyte uptake and reconstitution supported broad nucleoside transport energized by proton motive force. This does not quantify native pathway flux or prove an exclusive transporter. Source location `Primary abstract, transport, specificity and reconstitution sentences` PMID:33640454 Source assertion: K12-derived NupG expressed in C43(DE3) bound uridine and cytidine in vitro. These binding and apo-structure measurements support recognition, not direct flux or proton:nucleoside stoichiometry. Source location `Results, Characterization of recombinant NupG, Figure1D/F; Experimental procedures, Protein purification`
Nucleoside permease NupG `UniProtKB:P0AFF4`	enables	cytidine(out) + H(+)(out) => cytidine(in) + H(+)(in) `RHEA:29985`	PathBank:SMP0002038 Source assertion: Native TransportCatalysis/421 assigns its protein controller to Transports/489; the component or protein reference identifies UniProtKB:P0AFF4. Source location `bp:Catalysis[@rdf:ID='TransportCatalysis/421']/bp:controller and bp:controlled; bp:ProteinReference[@rdf:ID='ProteinReference/7058']/bp:xref` RHEA:29985 Source assertion: The explicit Rhea family maps master 29983 to directional member 29985; inspected sides and equation match the selected native chemistry. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/29983']/rh:directionalReaction[@rdf:resource='http://rdf.rhea-db.org/29985']; rdf:Description[@rdf:about='http://rdf.rhea-db.org/29985']/rh:substrates, rh:products, rh:equation` UniProtKB:P0AFF4 Source assertion: The reviewed K-12 NupG entry assigns this nucleoside/H+ transport family with direct literature support. The native pathway selects import; the master equation is oriented in-to-out. Source location `CATALYTIC ACTIVITY reactionCrossReferences RHEA:29983; FUNCTION comment; organism.taxonId` PMID:15513740 Source assertion: Recombinant NupG transported uridine; competition, oocyte uptake and reconstitution supported broad nucleoside transport energized by proton motive force. This does not quantify native pathway flux or prove an exclusive transporter. Source location `Primary abstract, transport, specificity and reconstitution sentences` PMID:33640454 Source assertion: K12-derived NupG expressed in C43(DE3) bound uridine and cytidine in vitro. These binding and apo-structure measurements support recognition, not direct flux or proton:nucleoside stoichiometry. Source location `Results, Characterization of recombinant NupG, Figure1D/F; Experimental procedures, Protein purification`
cytidine/deoxycytidine deaminase `MetaCyc:CYTIDEAM-CPLX`	has_part Native homo-oligomer with 2 copies; membership is distinct from monomer activity.	Cytidine deaminase `UniProtKB:P0ABF6`	PathBank:SMP0002038 Source assertion: Native complex 3973 contains 2 copies of protein 6175, whose protein reference unifies with UniProtKB:P0ABF6. Source location `bp:Complex[@rdf:ID='ProteinComplex/3973']/bp:component and bp:componentStoichiometry; bp:Stoichiometry[@rdf:ID='Protein/6175/Stoichiometry/2.0']; bp:ProteinReference[@rdf:ID='ProteinReference/6175']/bp:xref` UniProtKB:P0ABF6 Source assertion: The current reviewed SUBUNIT annotation independently supports this homo-oligomeric assembly. Source location `SUBUNIT comment`
uridine phosphorylase `MetaCyc:URPHOS-CPLX`	has_part Native homo-oligomer with 6 copies; membership is distinct from monomer activity.	Uridine phosphorylase `UniProtKB:P12758`	PathBank:SMP0002038 Source assertion: Native complex 3974 contains 6 copies of protein 10357, whose protein reference unifies with UniProtKB:P12758. Source location `bp:Complex[@rdf:ID='ProteinComplex/3974']/bp:component and bp:componentStoichiometry; bp:Stoichiometry[@rdf:ID='Protein/10357/Stoichiometry/6.0']; bp:ProteinReference[@rdf:ID='ProteinReference/10357']/bp:xref` UniProtKB:P12758 Source assertion: The current reviewed SUBUNIT annotation independently supports this homo-oligomeric assembly. Source location `SUBUNIT comment` MetaCyc:URPHOS-CPLX Source assertion: Native URPHOS-CPLX contains six URPHOS-MONOMER components. Source location `Protein[@frameid="URPHOS-CPLX"]/component` PMID:12499542 Source assertion: The structural study identifies native uridine phosphorylase as a hexamer assembled by threefold symmetry; this supports the current assignment over the older eight-subunit estimate. Source location `Primary abstract, native hexameric UP assembly sentence`
2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase `UniProtKB:P08331`	has_cofactor	divalent metal cation `CHEBI:60240`	UniProtKB:P08331 Source assertion: The reviewed CpdB entry annotates a divalent-metal cofactor by similarity; no particular physiological metal or binding stoichiometry is asserted. Source location `comments[3] COFACTOR; ECO:0000250`
Phosphopentomutase `UniProtKB:P0A6K6`	has_cofactor	manganese(2+) `CHEBI:29035`	UniProtKB:P0A6K6 Source assertion: Mn2+ activates purified E. coli DeoB; Co2+ is an alternative activator. The two-ion stoichiometry is by similarity and is not asserted by this edge. Source location `comments[3] COFACTOR; PMID4992818 evidence and note`
Phosphopentomutase `UniProtKB:P0A6K6`	has_cofactor	cobalt(2+) `CHEBI:48828`	UniProtKB:P0A6K6 Source assertion: Co2+ and Mn2+ are alternative equally good activators in the cited purified-enzyme assay; they are not asserted to bind simultaneously. Source location `comments[3] COFACTOR; PMID4992818 evidence and note`
Cytidine deaminase `UniProtKB:P0ABF6`	has_cofactor	zinc(2+) `CHEBI:29105`	UniProtKB:P0ABF6 Source assertion: The reviewed Cdd entry assigns zinc as the bound cofactor with experimental structural citations; this does not imply activation by excess free zinc. Source location `COFACTOR comment`
2',3'-cyclophospho-UMP + H2O => 3'-UMP + H(+) `RHEA:27879`	occurs_in	periplasmic space `GO:0042597`	UniProtKB:P08331 Source assertion: CpdB is periplasmic; this localizes its two annotated uridine hydrolyses without assigning a cellular compartment to all copies of the chemical classes. Source location `SUBCELLULAR LOCATION comment; PMID3005231`
3'-UMP + H2O => uridine + phosphate `RHEA:27891`	occurs_in	periplasmic space `GO:0042597`	UniProtKB:P08331 Source assertion: CpdB is periplasmic; this localizes its two annotated uridine hydrolyses without assigning a cellular compartment to all copies of the chemical classes. Source location `SUBCELLULAR LOCATION comment; PMID3005231`
Nucleoside permease NupG `UniProtKB:P0AFF4`	located_in	plasma membrane `GO:0005886`	UniProtKB:P0AFF4 Source assertion: NupG is a multipass cell-inner-membrane transporter with direct experimental evidence. The plasma membrane class describes the bacterial inner membrane. Source location `SUBCELLULAR LOCATION comment`
uridine [periplasmic space] `PathBank:SMP0002038/Compound/PW_C000202_Periplasmic_Space`	located_in	periplasmic space `GO:0042597`	PathBank:SMP0002038 Source assertion: The native physical object has an explicit cellularLocation pointing to this compartment. Source location `bp:SmallMolecule[@rdf:ID="Compound/PW_C000202_Periplasmic_Space"]/bp:cellularLocation; bp:CellularLocationVocabulary/bp:xref` GO:0042597 Source assertion: The native obsolete GO:0005620 cross-reference has explicit IAO:0100001 replacement GO:0042597, also listed as an alternative ID of the current term. Source location `GO:0005620 IAO:0100001; GO:0042597 oio:hasAlternativeId and rdfs:label`
uridine [cytosol] `PathBank:SMP0002038/Compound/PW_C000202_Cytosol`	located_in	cytosol `GO:0005829`	PathBank:SMP0002038 Source assertion: The native physical object has an explicit cellularLocation pointing to this compartment. Source location `bp:SmallMolecule[@rdf:ID="Compound/PW_C000202_Cytosol"]/bp:cellularLocation; bp:CellularLocationVocabulary/bp:xref`
cytidine [periplasmic space] `PathBank:SMP0002038/Compound/PW_C000061_Periplasmic_Space`	located_in	periplasmic space `GO:0042597`	PathBank:SMP0002038 Source assertion: The native physical object has an explicit cellularLocation pointing to this compartment. Source location `bp:SmallMolecule[@rdf:ID="Compound/PW_C000061_Periplasmic_Space"]/bp:cellularLocation; bp:CellularLocationVocabulary/bp:xref` GO:0042597 Source assertion: The native obsolete GO:0005620 cross-reference has explicit IAO:0100001 replacement GO:0042597, also listed as an alternative ID of the current term. Source location `GO:0005620 IAO:0100001; GO:0042597 oio:hasAlternativeId and rdfs:label`
cytidine [cytosol] `PathBank:SMP0002038/Compound/PW_C000061_Cytosol`	located_in	cytosol `GO:0005829`	PathBank:SMP0002038 Source assertion: The native physical object has an explicit cellularLocation pointing to this compartment. Source location `bp:SmallMolecule[@rdf:ID="Compound/PW_C000061_Cytosol"]/bp:cellularLocation; bp:CellularLocationVocabulary/bp:xref`
hydron [periplasmic space] `PathBank:SMP0002038/Compound/PW_C040034_Periplasmic_Space`	located_in	periplasmic space `GO:0042597`	PathBank:SMP0002038 Source assertion: The native physical object has an explicit cellularLocation pointing to this compartment. Source location `bp:SmallMolecule[@rdf:ID="Compound/PW_C040034_Periplasmic_Space"]/bp:cellularLocation; bp:CellularLocationVocabulary/bp:xref` GO:0042597 Source assertion: The native obsolete GO:0005620 cross-reference has explicit IAO:0100001 replacement GO:0042597, also listed as an alternative ID of the current term. Source location `GO:0005620 IAO:0100001; GO:0042597 oio:hasAlternativeId and rdfs:label`
hydron [cytosol] `PathBank:SMP0002038/Compound/PW_C040034_Cytosol`	located_in	cytosol `GO:0005829`	PathBank:SMP0002038 Source assertion: The native physical object has an explicit cellularLocation pointing to this compartment. Source location `bp:SmallMolecule[@rdf:ID="Compound/PW_C040034_Cytosol"]/bp:cellularLocation; bp:CellularLocationVocabulary/bp:xref`
2',3'-cyclophospho-UMP + H2O => 3'-UMP + H(+) `RHEA:27879`	provides_input_for Inferred chemical dependency within the complete source route; alternative uptake and metabolic fates remain possible.	3'-UMP + H2O => uridine + phosphate `RHEA:27891`	PathBank:SMP0002038 Source assertion: Curator inference: 3′-UMP product/substrate connect these native steps. BioPAX pathway membership is explicit; flux, exclusivity and obligatory use of NupG are not measured by the diagram. Source location `bp:Pathway[@rdf:about="http://identifiers.org/smpdb/SMP0002038"]/bp:pathwayComponent; referenced reaction/transport sides and compound entityReference`
3'-UMP + H2O => uridine + phosphate `RHEA:27891`	provides_input_for Inferred chemical dependency within the complete source route; alternative uptake and metabolic fates remain possible.	uridine(out) + H(+)(out) => uridine(in) + H(+)(in) `RHEA:29953`	PathBank:SMP0002038 Source assertion: Curator inference: uridine formed in the periplasm and uridine import connect these native steps. BioPAX pathway membership is explicit; flux, exclusivity and obligatory use of NupG are not measured by the diagram. Source location `bp:Pathway[@rdf:about="http://identifiers.org/smpdb/SMP0002038"]/bp:pathwayComponent; referenced reaction/transport sides and compound entityReference`
uridine(out) + H(+)(out) => uridine(in) + H(+)(in) `RHEA:29953`	provides_input_for Inferred chemical dependency within the complete source route; alternative uptake and metabolic fates remain possible.	uridine + phosphate => alpha-D-ribose 1-phosphate + uracil `RHEA:24389`	PathBank:SMP0002038 Source assertion: Curator inference: cytosolic uridine after import and uridine phosphorolysis connect these native steps. BioPAX pathway membership is explicit; flux, exclusivity and obligatory use of NupG are not measured by the diagram. Source location `bp:Pathway[@rdf:about="http://identifiers.org/smpdb/SMP0002038"]/bp:pathwayComponent; referenced reaction/transport sides and compound entityReference`
cytidine(out) + H(+)(out) => cytidine(in) + H(+)(in) `RHEA:29985`	provides_input_for Inferred chemical dependency within the complete source route; alternative uptake and metabolic fates remain possible.	cytidine + H2O + H(+) => uridine + NH4(+) `RHEA:16070`	PathBank:SMP0002038 Source assertion: Curator inference: cytosolic cytidine after import and cytidine deamination connect these native steps. BioPAX pathway membership is explicit; flux, exclusivity and obligatory use of NupG are not measured by the diagram. Source location `bp:Pathway[@rdf:about="http://identifiers.org/smpdb/SMP0002038"]/bp:pathwayComponent; referenced reaction/transport sides and compound entityReference`
cytidine + H2O + H(+) => uridine + NH4(+) `RHEA:16070`	provides_input_for Inferred chemical dependency within the complete source route; alternative uptake and metabolic fates remain possible.	uridine + phosphate => alpha-D-ribose 1-phosphate + uracil `RHEA:24389`	PathBank:SMP0002038 Source assertion: Curator inference: uridine product/substrate connect these native steps. BioPAX pathway membership is explicit; flux, exclusivity and obligatory use of NupG are not measured by the diagram. Source location `bp:Pathway[@rdf:about="http://identifiers.org/smpdb/SMP0002038"]/bp:pathwayComponent; referenced reaction/transport sides and compound entityReference`
uridine + phosphate => alpha-D-ribose 1-phosphate + uracil `RHEA:24389`	provides_input_for Inferred chemical dependency within the complete source route; alternative uptake and metabolic fates remain possible.	alpha-D-ribose 1-phosphate => D-ribose 5-phosphate `RHEA:18794`	PathBank:SMP0002038 Source assertion: Curator inference: alpha-D-ribose1-phosphate product/substrate connect these native steps. BioPAX pathway membership is explicit; flux, exclusivity and obligatory use of NupG are not measured by the diagram. Source location `bp:Pathway[@rdf:about="http://identifiers.org/smpdb/SMP0002038"]/bp:pathwayComponent; referenced reaction/transport sides and compound entityReference`

References

PathBank:SMP0002038 PathBank Pyrimidine Ribonucleosides Degradation, native PW002024 BioPAX (source version: Primary BioPAX archive; exact PW002024.owl member retrieved 2026-10-10)
MetaCyc:CPDB-MONOMER MetaCyc CPDB-MONOMER (source version: 22.5; native mirror retrieved 2026-10-11)
MetaCyc:RXN-14091 MetaCyc RXN-14091 (source version: 22.5; native mirror retrieved 2026-10-11)
MetaCyc:RXN-14115 MetaCyc RXN-14115 (source version: 22.5; native mirror retrieved 2026-10-11)
MetaCyc:URPHOS-CPLX MetaCyc URPHOS-CPLX (source version: 22.5; native mirror retrieved 2026-10-11)
MetaCyc:URPHOS-MONOMER MetaCyc URPHOS-MONOMER (source version: 22.5; native mirror retrieved 2026-10-11)
MetaCyc:URPHOS-RXN MetaCyc URPHOS-RXN (source version: 22.5; native mirror retrieved 2026-10-11)
MetaCyc:CYTIDEAM2-RXN MetaCyc CYTIDEAM2-RXN (source version: 22.5; native mirror retrieved 2026-10-11)
MetaCyc:PPENTOMUT-MONOMER MetaCyc PPENTOMUT-MONOMER (source version: 22.5; native mirror retrieved 2026-10-11)
MetaCyc:NUPG-MONOMER MetaCyc NUPG-MONOMER (source version: 22.5; native mirror retrieved 2026-10-11)
MetaCyc:PWY0-1295 MetaCyc PWY0-1295 (source version: 22.5; native mirror retrieved 2026-10-11)
UniProtKB:P08331 Reviewed UniProtKB P08331 (source version: 2026_03; actual X-UniProt-Release header; retrieved 2026-10-11)
UniProtKB:P0ABF6 Reviewed UniProtKB P0ABF6 (source version: 2026_03; actual X-UniProt-Release header; retrieved 2026-10-11)
UniProtKB:P12758 Reviewed UniProtKB P12758 (source version: 2026_03; actual X-UniProt-Release header; retrieved 2026-10-11)
UniProtKB:P0A6K6 Reviewed UniProtKB P0A6K6 (source version: 2026_03; actual X-UniProt-Release header; retrieved 2026-10-11)
UniProtKB:P0AFF4 Reviewed UniProtKB P0AFF4 (source version: 2026_03; actual X-UniProt-Release header; retrieved 2026-10-11)
RHEA:27879 Rhea 27879 directional reaction (source version: 142 (2026-09-02))
RHEA:27891 Rhea 27891 directional reaction (source version: 142 (2026-09-02))
RHEA:16070 Rhea 16070 directional reaction (source version: 142 (2026-09-02))
RHEA:24389 Rhea 24389 directional reaction (source version: 142 (2026-09-02))
RHEA:18794 Rhea 18794 directional reaction (source version: 142 (2026-09-02))
RHEA:29953 Rhea 29953 directional reaction (source version: 142 (2026-09-02))
RHEA:29985 Rhea 29985 directional reaction (source version: 142 (2026-09-02))
GO:0042597 GO periplasmic space replacement authority (source version: Independent cached GO sqlite authority; inspected2026-10-11; SHA covers sqlite body)
PMID:6251162 Isolation of Escherichia coli mutants (cpdB) deficient in periplasmic cyclic phosphodiesterase. (source version: 1980 primary full paper; author-repository scan inspected pp31–34, Table2 visually checked; retrieved2026-10-11)
PMID:12499542 Structure of Escherichia coli uridine phosphorylase at2.0A. (source version: 2003 primary abstract only; Europe PMC core response retrieved2026-10-11)
PMID:27294396 Biochemical characterization of recombinant E. coli CpdB. (source version: Primary full text; retrieved2026-10-11)
PMID:33640454 Molecular basis for substrate recognition by bacterial NupG. (source version: Primary full text; retrieved2026-10-11)
PMID:1089430 Multiple forms of phosphodeoxyribomutase from Escherichia coli. Physical and chemical characterization. (source version: Primary abstract only; Europe PMC core response retrieved2026-10-11)
PMID:16751 Uridine phosphorylase from Escherichia coli. Physical and chemical characterization. (source version: Primary abstract only; Europe PMC core response retrieved2026-10-11)
PMID:15513740 Purification and properties of the Escherichia coli nucleoside transporter NupG, a paradigm for a major facilitator transporter sub-family. (source version: Primary abstract only; Europe PMC core response retrieved2026-10-11)
PMID:374403 Nucleoside transport in cells and membrane vesicles from Escherichia coli K12. (source version: Primary abstract only; Europe PMC core response retrieved2026-10-11)
PMID:4202859 The purification and properties of cytidine deaminase from Escherichia coli. (source version: 1973 primary full text, pp.797-803)

Curation history

2026-10-11T01:17:27Z Codex
- CREATE — Add the complete pyrimidine ribonucleoside degradation and uptake route.
  Curated exact PathBank:SMP0002038 with all five chemical reactions and two proton-coupled imports, separate periplasmic/cytosolic states, exact directed Rhea chemistry and current periplasm identity. Independent review found two NupG citations misplaced on CpdB edge029; removed those copies while preserving their transport-edge evidence. Source replay and the finding/fix are retained in research/pathway_additions/2026-10-10-next-cohort/pyrimidine-ribo-*. Root rebuilt independent identifier authorities while preserving the baseline; final corpus gates and independent scientific reviews are retained separately.
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