allantoin degradation to glyoxylate III

MetaCyc:PWY-5705

The Escherichia coli K-12 glyoxylate branch converts S-allantoin through allantoate and S-ureidoglycine to S-ureidoglycolate, then AllA releases urea and glyoxylate. AllC and AllE release ammonium in separate steps, distinguishing this four-step route from the yeast allantoicase route. Native PWY-5705 contains the complete PWY-5698 module and the terminal ureidoglycolate lyase reaction. K-12 ECL1 experiments support anaerobic allantoin nitrogen utilization, not growth on allantoin as sole carbon source; deleting allA did not abolish nitrogen-supported growth because the alternative oxamate branch remained available. Native assemblies are annotated for MG1655, while reviewed proteins and primary experiments support the broader K-12 scope. AllB is tetrameric and AllC dimeric; AllE monomer status is inferred and AllA homodimer status is structural annotation. Metal alternatives and source evidence tiers are retained. The urea-releasing AllA reaction corrects historical ammonia-releasing hydrolase assignments; glyoxylate hydration in solution does not establish a different net enzymatic mechanism. Downstream glycerate metabolism, transport, transcriptional regulation and the separate oxamate branch are outside this defined route.

Pathway type

allantoin degradation

Organism scope

Escherichia coli K-12 NCBITaxon:83333

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Pathway network

26 nodes · 41 asserted directed edges

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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
(S)-(+)-allantoin `CHEBI:15678`	small molecule
water `CHEBI:15377`	small molecule
allantoate `CHEBI:17536`	small molecule
hydron `CHEBI:15378`	small molecule
(S)-2-ureidoglycine zwitterion `CHEBI:59947`	small molecule
ammonium `CHEBI:28938`	small molecule
carbon dioxide `CHEBI:16526`	small molecule
(-)-ureidoglycolate `CHEBI:57296`	small molecule
urea `CHEBI:16199`	small molecule
glyoxylate `CHEBI:36655`	small molecule
zinc(2+) `CHEBI:29105`	cofactor
nickel(2+) `CHEBI:49786`	cofactor
cobalt(2+) `CHEBI:48828`	cofactor
manganese(2+) `CHEBI:29035`	cofactor
Allantoinase `UniProtKB:P77671`	protein
Allantoate amidohydrolase `UniProtKB:P77425`	protein
(S)-ureidoglycine aminohydrolase `UniProtKB:P75713`	protein
Ureidoglycolate lyase `UniProtKB:P77731`	protein
allantoinase `MetaCyc:CPLX-64`	complex
allantoate amidohydrolase `MetaCyc:CPLX-7524`	complex
cytoplasm `GO:0005737`	cellular component
(S)-allantoin + H2O => allantoate + H(+) `RHEA:17030`	molecular activity	left to right
allantoate + H2O + 2 H(+) => (S)-2-ureidoglycine + NH4(+) + CO2 `RHEA:27486`	molecular activity	left to right
(S)-2-ureidoglycine + H2O => (S)-ureidoglycolate + NH4(+) `RHEA:25242`	molecular activity	left to right
(S)-ureidoglycolate => urea + glyoxylate `RHEA:11305`	molecular activity	left to right

Mechanistic edges

Mechanistic edges and their cited evidence
Subject	Predicate and description	Object	Evidence
(S)-(+)-allantoin `CHEBI:15678`	consumes Coefficient 1 in the selected directed Rhea equation; source charge and stereochemistry are retained.	(S)-allantoin + H2O => allantoate + H(+) `RHEA:17030`	RHEA:17029 Source assertion: RHEA:17030 substrates contain CHEBI:15678 with coefficient 1. Source location `http://rdf.rhea-db.org/17030 rh:substrates; http://rdf.rhea-db.org/17029_L rh:contains1 http://rdf.rhea-db.org/Participant_17029_compound_2545; http://rdf.rhea-db.org/Participant_17029_compound_2545 rh:compound http://rdf.rhea-db.org/Compound_2545; http://rdf.rhea-db.org/Compound_2545 rh:accession`
water `CHEBI:15377`	consumes Coefficient 1 in the selected directed Rhea equation; source charge and stereochemistry are retained.	(S)-allantoin + H2O => allantoate + H(+) `RHEA:17030`	RHEA:17029 Source assertion: RHEA:17030 substrates contain CHEBI:15377 with coefficient 1. Source location `http://rdf.rhea-db.org/17030 rh:substrates; http://rdf.rhea-db.org/17029_L rh:contains1 http://rdf.rhea-db.org/Participant_17029_compound_1283; http://rdf.rhea-db.org/Participant_17029_compound_1283 rh:compound http://rdf.rhea-db.org/Compound_1283; http://rdf.rhea-db.org/Compound_1283 rh:accession`
(S)-allantoin + H2O => allantoate + H(+) `RHEA:17030`	produces Coefficient 1 in the selected directed Rhea equation; source charge and stereochemistry are retained.	allantoate `CHEBI:17536`	RHEA:17029 Source assertion: RHEA:17030 products contain CHEBI:17536 with coefficient 1. Source location `http://rdf.rhea-db.org/17030 rh:products; http://rdf.rhea-db.org/17029_R rh:contains1 http://rdf.rhea-db.org/Participant_17029_compound_4604; http://rdf.rhea-db.org/Participant_17029_compound_4604 rh:compound http://rdf.rhea-db.org/Compound_4604; http://rdf.rhea-db.org/Compound_4604 rh:accession`
(S)-allantoin + H2O => allantoate + H(+) `RHEA:17030`	produces Coefficient 1 in the selected directed Rhea equation; source charge and stereochemistry are retained.	hydron `CHEBI:15378`	RHEA:17029 Source assertion: RHEA:17030 products contain CHEBI:15378 with coefficient 1. Source location `http://rdf.rhea-db.org/17030 rh:products; http://rdf.rhea-db.org/17029_R rh:contains1 http://rdf.rhea-db.org/Participant_17029_compound_3249; http://rdf.rhea-db.org/Participant_17029_compound_3249 rh:compound http://rdf.rhea-db.org/Compound_3249; http://rdf.rhea-db.org/Compound_3249 rh:accession`
allantoate `CHEBI:17536`	consumes Coefficient 1 in the selected directed Rhea equation; source charge and stereochemistry are retained.	allantoate + H2O + 2 H(+) => (S)-2-ureidoglycine + NH4(+) + CO2 `RHEA:27486`	RHEA:27485 Source assertion: RHEA:27486 substrates contain CHEBI:17536 with coefficient 1. Source location `http://rdf.rhea-db.org/27486 rh:substrates; http://rdf.rhea-db.org/27485_L rh:contains1 http://rdf.rhea-db.org/Participant_27485_compound_4604; http://rdf.rhea-db.org/Participant_27485_compound_4604 rh:compound http://rdf.rhea-db.org/Compound_4604; http://rdf.rhea-db.org/Compound_4604 rh:accession`
water `CHEBI:15377`	consumes Coefficient 1 in the selected directed Rhea equation; source charge and stereochemistry are retained.	allantoate + H2O + 2 H(+) => (S)-2-ureidoglycine + NH4(+) + CO2 `RHEA:27486`	RHEA:27485 Source assertion: RHEA:27486 substrates contain CHEBI:15377 with coefficient 1. Source location `http://rdf.rhea-db.org/27486 rh:substrates; http://rdf.rhea-db.org/27485_L rh:contains1 http://rdf.rhea-db.org/Participant_27485_compound_1283; http://rdf.rhea-db.org/Participant_27485_compound_1283 rh:compound http://rdf.rhea-db.org/Compound_1283; http://rdf.rhea-db.org/Compound_1283 rh:accession`
hydron `CHEBI:15378`	consumes Coefficient 2 in the selected directed Rhea equation; source charge and stereochemistry are retained.	allantoate + H2O + 2 H(+) => (S)-2-ureidoglycine + NH4(+) + CO2 `RHEA:27486`	RHEA:27485 Source assertion: RHEA:27486 substrates contain CHEBI:15378 with coefficient 2. Source location `http://rdf.rhea-db.org/27486 rh:substrates; http://rdf.rhea-db.org/27485_L rh:contains2 http://rdf.rhea-db.org/Participant_27485_compound_3249; http://rdf.rhea-db.org/Participant_27485_compound_3249 rh:compound http://rdf.rhea-db.org/Compound_3249; http://rdf.rhea-db.org/Compound_3249 rh:accession`
allantoate + H2O + 2 H(+) => (S)-2-ureidoglycine + NH4(+) + CO2 `RHEA:27486`	produces Coefficient 1 in the selected directed Rhea equation; source charge and stereochemistry are retained.	(S)-2-ureidoglycine zwitterion `CHEBI:59947`	RHEA:27485 Source assertion: RHEA:27486 products contain CHEBI:59947 with coefficient 1. Source location `http://rdf.rhea-db.org/27486 rh:products; http://rdf.rhea-db.org/27485_R rh:contains1 http://rdf.rhea-db.org/Participant_27485_compound_6148; http://rdf.rhea-db.org/Participant_27485_compound_6148 rh:compound http://rdf.rhea-db.org/Compound_6148; http://rdf.rhea-db.org/Compound_6148 rh:accession`
allantoate + H2O + 2 H(+) => (S)-2-ureidoglycine + NH4(+) + CO2 `RHEA:27486`	produces Coefficient 1 in the selected directed Rhea equation; source charge and stereochemistry are retained.	ammonium `CHEBI:28938`	RHEA:27485 Source assertion: RHEA:27486 products contain CHEBI:28938 with coefficient 1. Source location `http://rdf.rhea-db.org/27486 rh:products; http://rdf.rhea-db.org/27485_R rh:contains1 http://rdf.rhea-db.org/Participant_27485_compound_1012; http://rdf.rhea-db.org/Participant_27485_compound_1012 rh:compound http://rdf.rhea-db.org/Compound_1012; http://rdf.rhea-db.org/Compound_1012 rh:accession`
allantoate + H2O + 2 H(+) => (S)-2-ureidoglycine + NH4(+) + CO2 `RHEA:27486`	produces Coefficient 1 in the selected directed Rhea equation; source charge and stereochemistry are retained.	carbon dioxide `CHEBI:16526`	RHEA:27485 Source assertion: RHEA:27486 products contain CHEBI:16526 with coefficient 1. Source location `http://rdf.rhea-db.org/27486 rh:products; http://rdf.rhea-db.org/27485_R rh:contains1 http://rdf.rhea-db.org/Participant_27485_compound_4391; http://rdf.rhea-db.org/Participant_27485_compound_4391 rh:compound http://rdf.rhea-db.org/Compound_4391; http://rdf.rhea-db.org/Compound_4391 rh:accession`
(S)-2-ureidoglycine zwitterion `CHEBI:59947`	consumes Coefficient 1 in the selected directed Rhea equation; source charge and stereochemistry are retained.	(S)-2-ureidoglycine + H2O => (S)-ureidoglycolate + NH4(+) `RHEA:25242`	RHEA:25241 Source assertion: RHEA:25242 substrates contain CHEBI:59947 with coefficient 1. Source location `http://rdf.rhea-db.org/25242 rh:substrates; http://rdf.rhea-db.org/25241_L rh:contains1 http://rdf.rhea-db.org/Participant_25241_compound_6148; http://rdf.rhea-db.org/Participant_25241_compound_6148 rh:compound http://rdf.rhea-db.org/Compound_6148; http://rdf.rhea-db.org/Compound_6148 rh:accession`
water `CHEBI:15377`	consumes Coefficient 1 in the selected directed Rhea equation; source charge and stereochemistry are retained.	(S)-2-ureidoglycine + H2O => (S)-ureidoglycolate + NH4(+) `RHEA:25242`	RHEA:25241 Source assertion: RHEA:25242 substrates contain CHEBI:15377 with coefficient 1. Source location `http://rdf.rhea-db.org/25242 rh:substrates; http://rdf.rhea-db.org/25241_L rh:contains1 http://rdf.rhea-db.org/Participant_25241_compound_1283; http://rdf.rhea-db.org/Participant_25241_compound_1283 rh:compound http://rdf.rhea-db.org/Compound_1283; http://rdf.rhea-db.org/Compound_1283 rh:accession`
(S)-2-ureidoglycine + H2O => (S)-ureidoglycolate + NH4(+) `RHEA:25242`	produces Coefficient 1 in the selected directed Rhea equation; source charge and stereochemistry are retained.	(-)-ureidoglycolate `CHEBI:57296`	RHEA:25241 Source assertion: RHEA:25242 products contain CHEBI:57296 with coefficient 1. Source location `http://rdf.rhea-db.org/25242 rh:products; http://rdf.rhea-db.org/25241_R rh:contains1 http://rdf.rhea-db.org/Participant_25241_compound_4140; http://rdf.rhea-db.org/Participant_25241_compound_4140 rh:compound http://rdf.rhea-db.org/Compound_4140; http://rdf.rhea-db.org/Compound_4140 rh:accession`
(S)-2-ureidoglycine + H2O => (S)-ureidoglycolate + NH4(+) `RHEA:25242`	produces Coefficient 1 in the selected directed Rhea equation; source charge and stereochemistry are retained.	ammonium `CHEBI:28938`	RHEA:25241 Source assertion: RHEA:25242 products contain CHEBI:28938 with coefficient 1. Source location `http://rdf.rhea-db.org/25242 rh:products; http://rdf.rhea-db.org/25241_R rh:contains1 http://rdf.rhea-db.org/Participant_25241_compound_1012; http://rdf.rhea-db.org/Participant_25241_compound_1012 rh:compound http://rdf.rhea-db.org/Compound_1012; http://rdf.rhea-db.org/Compound_1012 rh:accession`
(-)-ureidoglycolate `CHEBI:57296`	consumes Coefficient 1 in the selected directed Rhea equation; source charge and stereochemistry are retained. This is the urea-releasing lyase equation; the primary study notes glyoxylate hydration in solution and does not experimentally exclude water participation in the elementary mechanism.	(S)-ureidoglycolate => urea + glyoxylate `RHEA:11305`	RHEA:11304 Source assertion: RHEA:11305 substrates contain CHEBI:57296 with coefficient 1. Source location `http://rdf.rhea-db.org/11305 rh:substrates; http://rdf.rhea-db.org/11304_L rh:contains1 http://rdf.rhea-db.org/Participant_11304_compound_4140; http://rdf.rhea-db.org/Participant_11304_compound_4140 rh:compound http://rdf.rhea-db.org/Compound_4140; http://rdf.rhea-db.org/Compound_4140 rh:accession`
(S)-ureidoglycolate => urea + glyoxylate `RHEA:11305`	produces Coefficient 1 in the selected directed Rhea equation; source charge and stereochemistry are retained. This is the urea-releasing lyase equation; the primary study notes glyoxylate hydration in solution and does not experimentally exclude water participation in the elementary mechanism.	urea `CHEBI:16199`	RHEA:11304 Source assertion: RHEA:11305 products contain CHEBI:16199 with coefficient 1. Source location `http://rdf.rhea-db.org/11305 rh:products; http://rdf.rhea-db.org/11304_R rh:contains1 http://rdf.rhea-db.org/Participant_11304_compound_3216; http://rdf.rhea-db.org/Participant_11304_compound_3216 rh:compound http://rdf.rhea-db.org/Compound_3216; http://rdf.rhea-db.org/Compound_3216 rh:accession`
(S)-ureidoglycolate => urea + glyoxylate `RHEA:11305`	produces Coefficient 1 in the selected directed Rhea equation; source charge and stereochemistry are retained. This is the urea-releasing lyase equation; the primary study notes glyoxylate hydration in solution and does not experimentally exclude water participation in the elementary mechanism.	glyoxylate `CHEBI:36655`	RHEA:11304 Source assertion: RHEA:11305 products contain CHEBI:36655 with coefficient 1. Source location `http://rdf.rhea-db.org/11305 rh:products; http://rdf.rhea-db.org/11304_R rh:contains1 http://rdf.rhea-db.org/Participant_11304_compound_3124; http://rdf.rhea-db.org/Participant_11304_compound_3124 rh:compound http://rdf.rhea-db.org/Compound_3124; http://rdf.rhea-db.org/Compound_3124 rh:accession`
(S)-allantoin + H2O => allantoate + H(+) `RHEA:17030`	part_of Membership in the complete four-step native glyoxylate branch, with the exact selected Rhea direction.	`MetaCyc:PWY-5705`	MetaCyc:PWY-5705 Source assertion: PWY-5705 contains the PWY-5698 subpathway followed by UREIDOGLYCOLATE-LYASE-RXN, forming the native route to glyoxylate. Source location `Pathway/reaction-list; Pathway/sub-pathways; Pathway/reaction-layout` MetaCyc:PWY-5698 Source assertion: PWY-5698 explicitly contains ALLANTOINASE-RXN in its three-step reaction list. Source location `Pathway/reaction-list; Pathway/reaction-layout` MetaCyc:ALLANTOINASE-RXN Source assertion: The native reaction has Rhea cross-reference 17030. Source location `Reaction/dblink[dblink-db=RHEA]/dblink-oid` UniProtKB:P77671 Source assertion: The reviewed protein catalytic-activity entry identifies RHEA:17029; this grounds the current reaction-family choice. Source location `comments[1].reaction.reactionCrossReferences[database=Rhea]` RHEA:17029 Source assertion: RHEA:17029 rh:directionalReaction includes RHEA:17030, whose substrates and products define the selected left-to-right reaction. Source location `http://rdf.rhea-db.org/17029 rh:directionalReaction http://rdf.rhea-db.org/17030; http://rdf.rhea-db.org/17030 rh:substrates and rh:products`
allantoate + H2O + 2 H(+) => (S)-2-ureidoglycine + NH4(+) + CO2 `RHEA:27486`	part_of Membership in the complete four-step native glyoxylate branch, with the exact selected Rhea direction. The native 13594 cross-reference is stale; current AllC annotation and matched native chemistry ground the 27485 family without treating 13594 as a current exact match.	`MetaCyc:PWY-5705`	MetaCyc:PWY-5705 Source assertion: PWY-5705 contains the PWY-5698 subpathway followed by UREIDOGLYCOLATE-LYASE-RXN, forming the native route to glyoxylate. Source location `Pathway/reaction-list; Pathway/sub-pathways; Pathway/reaction-layout` MetaCyc:PWY-5698 Source assertion: PWY-5698 explicitly contains ALLANTOATE-DEIMINASE-RXN in its three-step reaction list. Source location `Pathway/reaction-list; Pathway/reaction-layout` MetaCyc:ALLANTOATE-DEIMINASE-RXN Source assertion: The native allantoate deiminase reaction forms ureidoglycine, ammonium and carbon dioxide; its legacy Rhea cross-reference is 13594. Source location `Reaction/left; Reaction/right; Reaction/dblink[dblink-db=RHEA]` UniProtKB:P77425 Source assertion: The reviewed protein catalytic-activity entry identifies RHEA:27485; this grounds the current reaction-family choice. Source location `comments[1].reaction.reactionCrossReferences[database=Rhea]` RHEA:27485 Source assertion: RHEA:27485 rh:directionalReaction includes RHEA:27486, whose substrates and products define the selected left-to-right reaction. Source location `http://rdf.rhea-db.org/27485 rh:directionalReaction http://rdf.rhea-db.org/27486; http://rdf.rhea-db.org/27486 rh:substrates and rh:products`
(S)-2-ureidoglycine + H2O => (S)-ureidoglycolate + NH4(+) `RHEA:25242`	part_of Membership in the complete four-step native glyoxylate branch, with the exact selected Rhea direction.	`MetaCyc:PWY-5705`	MetaCyc:PWY-5705 Source assertion: PWY-5705 contains the PWY-5698 subpathway followed by UREIDOGLYCOLATE-LYASE-RXN, forming the native route to glyoxylate. Source location `Pathway/reaction-list; Pathway/sub-pathways; Pathway/reaction-layout` MetaCyc:PWY-5698 Source assertion: PWY-5698 explicitly contains URUR-RXN in its three-step reaction list. Source location `Pathway/reaction-list; Pathway/reaction-layout` MetaCyc:URUR-RXN Source assertion: The native reaction has Rhea cross-reference 25242. Source location `Reaction/dblink[dblink-db=RHEA]/dblink-oid` UniProtKB:P75713 Source assertion: The reviewed protein catalytic-activity entry identifies RHEA:25241; this grounds the current reaction-family choice. Source location `comments[1].reaction.reactionCrossReferences[database=Rhea]` RHEA:25241 Source assertion: RHEA:25241 rh:directionalReaction includes RHEA:25242, whose substrates and products define the selected left-to-right reaction. Source location `http://rdf.rhea-db.org/25241 rh:directionalReaction http://rdf.rhea-db.org/25242; http://rdf.rhea-db.org/25242 rh:substrates and rh:products`
(S)-ureidoglycolate => urea + glyoxylate `RHEA:11305`	part_of Membership in the complete four-step native glyoxylate branch, with the exact selected Rhea direction.	`MetaCyc:PWY-5705`	MetaCyc:PWY-5705 Source assertion: PWY-5705 contains the PWY-5698 subpathway followed by UREIDOGLYCOLATE-LYASE-RXN, forming the native route to glyoxylate. Source location `Pathway/reaction-list; Pathway/sub-pathways; Pathway/reaction-layout` MetaCyc:UREIDOGLYCOLATE-LYASE-RXN Source assertion: The native reaction has Rhea cross-reference 11305. Source location `Reaction/dblink[dblink-db=RHEA]/dblink-oid` UniProtKB:P77731 Source assertion: The reviewed protein catalytic-activity entry identifies RHEA:11304; this grounds the current reaction-family choice. Source location `comments[1].reaction.reactionCrossReferences[database=Rhea]` RHEA:11304 Source assertion: RHEA:11304 rh:directionalReaction includes RHEA:11305, whose substrates and products define the selected left-to-right reaction. Source location `http://rdf.rhea-db.org/11304 rh:directionalReaction http://rdf.rhea-db.org/11305; http://rdf.rhea-db.org/11305 rh:substrates and rh:products`
Allantoinase `UniProtKB:P77671`	part_of The native assembly contains 4 copies of the P77671 subunit; no isolated-subunit catalysis is assigned.	allantoinase `MetaCyc:CPLX-64`	MetaCyc:CPLX-64 Source assertion: The native Protein/component contains 4 copies of G6281-MONOMER. Source location `Protein/component/Protein; Protein/component/coefficient` UniProtKB:P77671 Source assertion: The SUBUNIT annotation is homotetramer (ECO:0000269); the BioCyc cross-reference identifies the corresponding native monomer. Source location `comments[6] SUBUNIT; uniProtKBCrossReferences[database=BioCyc]` PMID:11092864 Source assertion: Purified AllB gel filtration and chemical cross-linking support a homotetramer. Source location `Results, molecular mass and cross-linking; Figure 4`
Allantoate amidohydrolase `UniProtKB:P77425`	part_of The native assembly contains 2 copies of the P77425 subunit; no isolated-subunit catalysis is assigned.	allantoate amidohydrolase `MetaCyc:CPLX-7524`	MetaCyc:CPLX-7524 Source assertion: The native Protein/component contains 2 copies of G6285-MONOMER. Source location `Protein/component/Protein; Protein/component/coefficient` UniProtKB:P77425 Source assertion: The SUBUNIT annotation is homodimer (ECO:0000269); the BioCyc cross-reference identifies the corresponding native monomer. Source location `comments[6] SUBUNIT; uniProtKBCrossReferences[database=BioCyc]` PMID:17362992 Source assertion: The AllC structural abstract describes a dimerization domain and the binuclear zinc active center. Source location `resultList.result[id=17362992].abstractText`
allantoinase `MetaCyc:CPLX-64`	catalyzes Purified E. coli AllB hydrolyzes S-allantoin. The native homotetramer is the catalyst; cobalt-substituted preparations also turn over R-allantoin more slowly, outside this S-specific route.	(S)-allantoin + H2O => allantoate + H(+) `RHEA:17030`	UniProtKB:P77671 Source assertion: Catalytic activity assigns RHEA:17029 with experimental evidence from PMID:11092864. Source location `comments[1].reaction; comments[1].reaction.evidences` MetaCyc:CPLX-64 Source assertion: The complex catalyzes ENZRXN0-268, whose reaction is ALLANTOINASE-RXN. Source location `Protein/catalyzes/Enzymatic-Reaction/reaction` PMID:11092864 Source assertion: The purified AllB protein has allantoinase activity and tetrameric molecular size. Source location `Results, purification and molecular mass determination; Figures 3B and 4` PMID:12486048 Source assertion: The zinc enzyme consumes S-allantoin; cobalt preparations prefer S but also turn over R at about one tenth the rate. Source location `Results, Enantioselectivity; Figure 6`
allantoate amidohydrolase `MetaCyc:CPLX-7524`	catalyzes AllC generates S-ureidoglycine; it does not replace the distinct AllE step. The earlier structural paper described a combined downstream product, corrected by the later product-identification study.	allantoate + H2O + 2 H(+) => (S)-2-ureidoglycine + NH4(+) + CO2 `RHEA:27486`	UniProtKB:P77425 Source assertion: AllC catalytic activity is RHEA:27485 with experimental evidence PMID:20038185. Source location `comments[1].reaction; comments[1].reaction.evidences` MetaCyc:CPLX-7524 Source assertion: The complex catalyzes ENZRXN-323, whose reaction is ALLANTOATE-DEIMINASE-RXN. Source location `Protein/catalyzes/Enzymatic-Reaction/reaction` PMID:20038185 Source assertion: NMR identifies S-ureidoglycine as the true AAH product; the bacterial AllE protein performs a separate manganese-dependent hydrolysis. Source location `resultList.result[id=20038185].abstractText`
(S)-ureidoglycine aminohydrolase `UniProtKB:P75713`	catalyzes AllE hydrolyzes S-ureidoglycine to S-ureidoglycolate and ammonium. Its monomer assignment is curator inference; it is not upgraded to an experimentally measured oligomeric state.	(S)-2-ureidoglycine + H2O => (S)-ureidoglycolate + NH4(+) `RHEA:25242`	UniProtKB:P75713 Source assertion: Catalytic activity assigns RHEA:25241 with experimental PMID:19935661 and curator-inference PMID:20038185 evidence; the monomer annotation is ECO:0000305. Source location `comments[1].reaction; comments[3] SUBUNIT` PMID:20038185 Source assertion: E. coli YlbA catalyzes manganese-dependent hydrolysis of S-ureidoglycine, yielding S-ureidoglycolate with configurational inversion. Source location `resultList.result[id=20038185].abstractText`
Ureidoglycolate lyase `UniProtKB:P77731`	enables AllA supplies the experimentally demonstrated urea-releasing activity. Current structural annotation describes a homodimer; this gene-product role does not assert that an isolated subunit suffices. Older ammonia-releasing hydrolase annotations are rejected.	(S)-ureidoglycolate => urea + glyoxylate `RHEA:11305`	UniProtKB:P77731 Source assertion: Catalytic activity assigns RHEA:11304 with experimental PMID:24107613 evidence. SUBUNIT is homodimer, supported by structural submission Ref.6 and HAMAP inference. Source location `comments[1].reaction; comments[4] SUBUNIT; references[citation.id=CI-4ICJD7CSP0B6L]` PMID:24107613 Source assertion: Recombinant E. coli AllA releases urea, detected as ammonia only after urease addition; the expressed clone is JW0493. Source location `Results and discussion, Nickel-dependent urea-release activity of AllA; Figure 2A-B; Methods, Biochemistry` PMID:10601204 Source assertion: allA disruption abolishes ureidoglycolate-cleaving activity but does not impair growth on xylose-allantoin medium. Source location `HTML section#sec13, allA disruption and JA174 growth paragraph`
allantoinase `MetaCyc:CPLX-64`	has_cofactor Alternative AllB metal preparation, not a simultaneous four-metal requirement. Zinc is favored as the physiological metal in the 2003 study; alternative activity and occupancy depend on preparation.	zinc(2+) `CHEBI:29105`	UniProtKB:P77671 Source assertion: AllB is annotated to use zinc and alternatively nickel, cobalt or manganese; this combines ECO:0000269 and ECO:0000305 evidence. Source location `comments[2] COFACTOR; cofactors; note` PMID:12486048 Source assertion: Metal-substituted preparations show different occupancy, activity and stereoselectivity; nickel and cobalt substitution does not establish their physiological necessity. Source location `Abstract; Results, metal content; Discussion`
allantoinase `MetaCyc:CPLX-64`	has_cofactor Alternative AllB metal preparation, not a simultaneous four-metal requirement. Zinc is favored as the physiological metal in the 2003 study; alternative activity and occupancy depend on preparation.	nickel(2+) `CHEBI:49786`	UniProtKB:P77671 Source assertion: AllB is annotated to use zinc and alternatively nickel, cobalt or manganese; this combines ECO:0000269 and ECO:0000305 evidence. Source location `comments[2] COFACTOR; cofactors; note` PMID:12486048 Source assertion: Metal-substituted preparations show different occupancy, activity and stereoselectivity; nickel and cobalt substitution does not establish their physiological necessity. Source location `Abstract; Results, metal content; Discussion`
allantoinase `MetaCyc:CPLX-64`	has_cofactor Alternative AllB metal preparation, not a simultaneous four-metal requirement. Zinc is favored as the physiological metal in the 2003 study; alternative activity and occupancy depend on preparation.	cobalt(2+) `CHEBI:48828`	UniProtKB:P77671 Source assertion: AllB is annotated to use zinc and alternatively nickel, cobalt or manganese; this combines ECO:0000269 and ECO:0000305 evidence. Source location `comments[2] COFACTOR; cofactors; note` PMID:12486048 Source assertion: Metal-substituted preparations show different occupancy, activity and stereoselectivity; nickel and cobalt substitution does not establish their physiological necessity. Source location `Abstract; Results, metal content; Discussion`
allantoinase `MetaCyc:CPLX-64`	has_cofactor Alternative AllB metal preparation, not a simultaneous four-metal requirement. Zinc is favored as the physiological metal in the 2003 study; alternative activity and occupancy depend on preparation.	manganese(2+) `CHEBI:29035`	UniProtKB:P77671 Source assertion: AllB is annotated to use zinc and alternatively nickel, cobalt or manganese; this combines ECO:0000269 and ECO:0000305 evidence. Source location `comments[2] COFACTOR; cofactors; note`
allantoate amidohydrolase `MetaCyc:CPLX-7524`	has_cofactor Two bound zinc ions per AllC subunit are reported in the earlier structure; this does not make zinc the unique physiological metal.	zinc(2+) `CHEBI:29105`	UniProtKB:P77425 Source assertion: AllC binds two Zn2+ ions per subunit, with experimental evidence PMID:17362992. Source location `comments[2] COFACTOR; note` PMID:17362992 Source assertion: The active center contains two co-catalytic zinc ions. Source location `resultList.result[id=17362992].abstractText`
allantoate amidohydrolase `MetaCyc:CPLX-7524`	has_cofactor AllC also binds manganese, and its functional manganese dependence is supported separately from the earlier zinc structure.	manganese(2+) `CHEBI:29035`	UniProtKB:P77425 Source assertion: AllC is also able to bind Mn2+, with experimental evidence PMID:25020232. Source location `comments[2].note` PMID:20038185 Source assertion: Allantoate amidohydrolase is described as a manganese-dependent enzyme found in plants and bacteria. Source location `resultList.result[id=20038185].abstractText`
(S)-ureidoglycine aminohydrolase `UniProtKB:P75713`	has_cofactor Manganese and cobalt support alternative AllE preparations; they are not simultaneous requirements.	manganese(2+) `CHEBI:29035`	UniProtKB:P75713 Source assertion: AllE uses Mn2+ and can also use Co2+, supported by ECO:0000269 from PMID:20038185. Source location `comments[2] COFACTOR; note`
(S)-ureidoglycine aminohydrolase `UniProtKB:P75713`	has_cofactor Manganese and cobalt support alternative AllE preparations; they are not simultaneous requirements.	cobalt(2+) `CHEBI:48828`	UniProtKB:P75713 Source assertion: AllE uses Mn2+ and can also use Co2+, supported by ECO:0000269 from PMID:20038185. Source location `comments[2] COFACTOR; note`
Ureidoglycolate lyase `UniProtKB:P77731`	has_cofactor AllA urea-release activity is nickel dependent in the purified-protein experiment. This protein-level relation does not resolve metal occupancy per protomer or imply isolated-subunit catalysis.	nickel(2+) `CHEBI:49786`	UniProtKB:P77731 Source assertion: Ni2+ is the annotated AllA cofactor, with experimental PMID:24107613 and HAMAP evidence. Source location `comments[2] COFACTOR` PMID:24107613 Source assertion: EDTA treatment abolishes AllA urea-release activity; only Ni2+ rescues it among the tested divalent ions. Source location `Results and discussion, Nickel-dependent urea-release activity of AllA; Figure 2C; Methods, Biochemistry`
Allantoate amidohydrolase `UniProtKB:P77425`	located_in Protein-level cytoplasmic localization at the source evidence tier; this is not propagated to the other pathway proteins.	cytoplasm `GO:0005737`	UniProtKB:P77425 Source assertion: The protein is annotated in the cytoplasm with ECO:0000305; GO cross-reference IEA:UniProtKB-SubCell. Source location `comments[7] SUBCELLULAR LOCATION; uniProtKBCrossReferences[database=GO,id=GO:0005737]`
(S)-ureidoglycine aminohydrolase `UniProtKB:P75713`	located_in Protein-level cytoplasmic localization at the source evidence tier; this is not propagated to the other pathway proteins.	cytoplasm `GO:0005737`	UniProtKB:P75713 Source assertion: The protein is annotated in the cytoplasm with ECO:0000269; GO cross-reference EXP:UniProtKB. Source location `comments[4] SUBCELLULAR LOCATION; uniProtKBCrossReferences[database=GO,id=GO:0005737]`
(S)-allantoin + H2O => allantoate + H(+) `RHEA:17030`	provides_input_for The product CHEBI:17536 is the shared intermediate in the native ordered sequence; this states metabolite handoff, not a physical channeling complex.	allantoate + H2O + 2 H(+) => (S)-2-ureidoglycine + NH4(+) + CO2 `RHEA:27486`	MetaCyc:PWY-5698 Source assertion: Native reaction-ordering places ALLANTOINASE-RXN before ALLANTOATE-DEIMINASE-RXN. Source location `Pathway/reaction-ordering; Pathway/reaction-layout` RHEA:17029 Source assertion: RHEA:17030 produces CHEBI:17536, the intermediate used by the next selected reaction. Source location `http://rdf.rhea-db.org/17030 rh:products http://rdf.rhea-db.org/17029_R; http://rdf.rhea-db.org/17029_R rh:contains1 http://rdf.rhea-db.org/Participant_17029_compound_4604; rh:compound http://rdf.rhea-db.org/Compound_4604; rh:accession` RHEA:27485 Source assertion: RHEA:27486 consumes CHEBI:17536, matching the preceding selected reaction product. Source location `http://rdf.rhea-db.org/27486 rh:substrates http://rdf.rhea-db.org/27485_L; http://rdf.rhea-db.org/27485_L rh:contains1 http://rdf.rhea-db.org/Participant_27485_compound_4604; rh:compound http://rdf.rhea-db.org/Compound_4604; rh:accession`
allantoate + H2O + 2 H(+) => (S)-2-ureidoglycine + NH4(+) + CO2 `RHEA:27486`	provides_input_for The product CHEBI:59947 is the shared intermediate in the native ordered sequence; this states metabolite handoff, not a physical channeling complex.	(S)-2-ureidoglycine + H2O => (S)-ureidoglycolate + NH4(+) `RHEA:25242`	MetaCyc:PWY-5698 Source assertion: Native reaction-ordering places ALLANTOATE-DEIMINASE-RXN before URUR-RXN. Source location `Pathway/reaction-ordering; Pathway/reaction-layout` RHEA:27485 Source assertion: RHEA:27486 produces CHEBI:59947, the intermediate used by the next selected reaction. Source location `http://rdf.rhea-db.org/27486 rh:products http://rdf.rhea-db.org/27485_R; http://rdf.rhea-db.org/27485_R rh:contains1 http://rdf.rhea-db.org/Participant_27485_compound_6148; rh:compound http://rdf.rhea-db.org/Compound_6148; rh:accession` RHEA:25241 Source assertion: RHEA:25242 consumes CHEBI:59947, matching the preceding selected reaction product. Source location `http://rdf.rhea-db.org/25242 rh:substrates http://rdf.rhea-db.org/25241_L; http://rdf.rhea-db.org/25241_L rh:contains1 http://rdf.rhea-db.org/Participant_25241_compound_6148; rh:compound http://rdf.rhea-db.org/Compound_6148; rh:accession`
(S)-2-ureidoglycine + H2O => (S)-ureidoglycolate + NH4(+) `RHEA:25242`	provides_input_for The product CHEBI:57296 is the shared intermediate in the native ordered sequence; this states metabolite handoff, not a physical channeling complex.	(S)-ureidoglycolate => urea + glyoxylate `RHEA:11305`	MetaCyc:PWY-5705 Source assertion: Native reaction-ordering places URUR-RXN before UREIDOGLYCOLATE-LYASE-RXN. Source location `Pathway/reaction-ordering; Pathway/reaction-layout` RHEA:25241 Source assertion: RHEA:25242 produces CHEBI:57296, the intermediate used by the next selected reaction. Source location `http://rdf.rhea-db.org/25242 rh:products http://rdf.rhea-db.org/25241_R; http://rdf.rhea-db.org/25241_R rh:contains1 http://rdf.rhea-db.org/Participant_25241_compound_4140; rh:compound http://rdf.rhea-db.org/Compound_4140; rh:accession` RHEA:11304 Source assertion: RHEA:11305 consumes CHEBI:57296, matching the preceding selected reaction product. Source location `http://rdf.rhea-db.org/11305 rh:substrates http://rdf.rhea-db.org/11304_L; http://rdf.rhea-db.org/11304_L rh:contains1 http://rdf.rhea-db.org/Participant_11304_compound_4140; rh:compound http://rdf.rhea-db.org/Compound_4140; rh:accession`

References

MetaCyc:PWY-5705 MetaCyc PWY-5705 (source version: 22.5; complete native XML; retrieved or digest-verified 2026-10-11 UTC)
MetaCyc:PWY-5698 MetaCyc PWY-5698 (source version: 22.5; complete native XML; retrieved or digest-verified 2026-10-11 UTC)
MetaCyc:CPLX-64 MetaCyc CPLX-64 (source version: 22.5; complete native XML; retrieved or digest-verified 2026-10-11 UTC)
MetaCyc:CPLX-7524 MetaCyc CPLX-7524 (source version: 22.5; complete native XML; retrieved or digest-verified 2026-10-11 UTC)
MetaCyc:ALLANTOINASE-RXN MetaCyc ALLANTOINASE-RXN (source version: 22.5; complete native XML; retrieved or digest-verified 2026-10-11 UTC)
MetaCyc:ALLANTOATE-DEIMINASE-RXN MetaCyc ALLANTOATE-DEIMINASE-RXN (source version: 22.5; complete native XML; retrieved or digest-verified 2026-10-11 UTC)
MetaCyc:URUR-RXN MetaCyc URUR-RXN (source version: 22.5; complete native XML; retrieved or digest-verified 2026-10-11 UTC)
MetaCyc:UREIDOGLYCOLATE-LYASE-RXN MetaCyc UREIDOGLYCOLATE-LYASE-RXN (source version: 22.5; complete native XML; retrieved or digest-verified 2026-10-11 UTC)
UniProtKB:P77671 Reviewed UniProtKB P77671 (source version: 2026_03 (2026-09-02); complete response retrieved 2026-10-11 UTC)
UniProtKB:P77425 Reviewed UniProtKB P77425 (source version: 2026_03 (2026-09-02); complete response retrieved 2026-10-11 UTC)
UniProtKB:P75713 Reviewed UniProtKB P75713 (source version: 2026_03 (2026-09-02); complete response retrieved 2026-10-11 UTC)
UniProtKB:P77731 Reviewed UniProtKB P77731 (source version: 2026_03 (2026-09-02); complete response retrieved 2026-10-11 UTC)
PMID:11092864 Functional expression and characterization of the two cyclic amidohydrolase enzymes, allantoinase and a novel phenylhydantoinase, from Escherichia coli. (source version: Full primary article HTML; preserved original response rehashed 2026-10-11 UTC)
PMID:12486048 Metal ion dependence of recombinant Escherichia coli allantoinase. (source version: Full primary article HTML; preserved original response rehashed 2026-10-11 UTC)
PMID:17362992 Structural analysis of a ternary complex of allantoate amidohydrolase from Escherichia coli reveals its mechanics. (source version: Indexed primary abstract only; complete retained multi-publication core JSON body digest; rehashed 2026-10-11 UTC)
PMID:20038185 Chemical basis of nitrogen recovery through the ureide pathway: formation and hydrolysis of S-ureidoglycine in plants and bacteria. (source version: Indexed primary abstract only; complete retained multi-publication core JSON body digest; rehashed 2026-10-11 UTC)
PMID:19935661 Ureide catabolism in Arabidopsis thaliana and Escherichia coli. (source version: Indexed primary abstract only; complete retained multi-publication core JSON body digest; rehashed 2026-10-11 UTC)
PMID:10601204 Genetic Analysis of a Chromosomal Region Containing Genes Required for Assimilation of Allantoin Nitrogen and Linked Glyoxylate Metabolism in Escherichia coli (source version: Full primary article HTML; retrieved 2026-10-11 UTC)
PMID:24107613 Ureidoglycolate hydrolase, amidohydrolase, lyase: how errors in biological databases are incorporated in scientific papers and vice versa (source version: Full primary article XML; retrieved 2026-10-11 UTC)
RHEA:17029 Rhea 17029 reaction family; selected 17030 (source version: 142 (2026-09-02); SHA256 covers complete compressed RDF gzip)
RHEA:27485 Rhea 27485 reaction family; selected 27486 (source version: 142 (2026-09-02); SHA256 covers complete compressed RDF gzip)
RHEA:25241 Rhea 25241 reaction family; selected 25242 (source version: 142 (2026-09-02); SHA256 covers complete compressed RDF gzip)
RHEA:11304 Rhea 11304 reaction family; selected 11305 (source version: 142 (2026-09-02); SHA256 covers complete compressed RDF gzip)

Curation history

2026-10-11T05:30:53Z codex
- CREATE — Add the complete four-reaction allantoin-to-glyoxylate III pathway
  MetaCyc:PWY-5705 contains the three-reaction PWY-5698 module followed by AllA ureidoglycolate cleavage: four reactions, 41 edges and 80 evidence items. This is mechanistically distinct from the maintained anaerobic oxamate route and the yeast allantoicase route. Verified native/primary evidence retains AllB/AllC assemblies, AllA homodimer limitations without inventing a complex identity, conditional metal/cofactor observations, reaction stereochemistry and directions, and E. coli K-12 scope. Duplicate searches include hidden/ignored content in both checkouts with explicit exclusions. Source provenance, chemical replay and coverage belong to research/pathway_additions/2026-10-11-next-192. Independent scientific review and full frozen-corpus gates remain pending at creation; final results are recorded separately in the cohort receipt.
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