L-arginine degradation IV (arginine decarboxylase/agmatine deiminase pathway)

MetaCyc:ARGDEG-III-PWY

L-arginine degradation through arginine decarboxylase and the agmatine deiminase pathway converts L-arginine to agmatine, N-carbamoylputrescine, putrescine, ammonium, and carbon dioxide.

Pathway type

amino acid degradation

Organism scope

Pseudomonas aeruginosa NCBITaxon:287

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Pathway network

18 nodes · 23 asserted directed edges

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Reaction / activity
Chemical / cofactor
Protein / complex
Other participant
Solid arrow: mechanistic relation
Dashed arrow: membership, location or cofactor relation

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Components and activities

Declared biological components and source reaction directions
Node	Kind or role	Source direction
Pseudomonas aeruginosa `NCBITaxon:287`	taxon
arginine decarboxylase `EC:4.1.1.19`	molecular activity
agmatine deiminase `EC:3.5.3.12`	molecular activity
N-carbamoylputrescine amidase `EC:3.5.1.53`	molecular activity
L-arginine `CHEBI:32682`	small molecule
H+ `CHEBI:15378`	small molecule
agmatine `CHEBI:58145`	small molecule
CO2 `CHEBI:16526`	small molecule
H2O `CHEBI:15377`	small molecule
N-carbamoylputrescine `CHEBI:58318`	small molecule
ammonium `CHEBI:28938`	small molecule
putrescine `CHEBI:326268`	small molecule
Biosynthetic arginine decarboxylase `UniProtKB:Q9HUX1`	protein
magnesium(2+) `CHEBI:18420`	cofactor
pyridoxal 5'-phosphate(2-) `CHEBI:597326`	cofactor
Agmatine deiminase `UniProtKB:Q9I6J9`	protein
L-arginine decarboxylase reaction `RHEA:17642`	reaction	left to right
agmatine deiminase reaction `RHEA:18038`	reaction	left to right
N-carbamoylputrescine amidohydrolase reaction `RHEA:22285`	reaction	left to right

Mechanistic edges

Mechanistic edges and their cited evidence
Subject	Predicate and description	Object	Evidence
H+ `CHEBI:15378`	consumes	L-arginine decarboxylase reaction `RHEA:17642`	RHEA:17642 Source assertion: Rhea lists CHEBI:15378 on the substrates side of RHEA:17642 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/17642']/rh:substrates; rh:contains/rh:compound/rh:accession`
L-arginine `CHEBI:32682`	consumes	L-arginine decarboxylase reaction `RHEA:17642`	RHEA:17642 Source assertion: Rhea lists CHEBI:32682 on the substrates side of RHEA:17642 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/17642']/rh:substrates; rh:contains/rh:compound/rh:accession`
L-arginine decarboxylase reaction `RHEA:17642`	produces	CO2 `CHEBI:16526`	RHEA:17642 Source assertion: Rhea lists CHEBI:16526 on the products side of RHEA:17642 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/17642']/rh:products; rh:contains/rh:compound/rh:accession`
L-arginine decarboxylase reaction `RHEA:17642`	produces	agmatine `CHEBI:58145`	RHEA:17642 Source assertion: Rhea lists CHEBI:58145 on the products side of RHEA:17642 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/17642']/rh:products; rh:contains/rh:compound/rh:accession`
H2O `CHEBI:15377`	consumes	agmatine deiminase reaction `RHEA:18038`	RHEA:18038 Source assertion: Rhea lists CHEBI:15377 on the substrates side of RHEA:18038 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/18038']/rh:substrates; rh:contains/rh:compound/rh:accession`
agmatine `CHEBI:58145`	consumes	agmatine deiminase reaction `RHEA:18038`	RHEA:18038 Source assertion: Rhea lists CHEBI:58145 on the substrates side of RHEA:18038 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/18038']/rh:substrates; rh:contains/rh:compound/rh:accession`
agmatine deiminase reaction `RHEA:18038`	produces	ammonium `CHEBI:28938`	RHEA:18038 Source assertion: Rhea lists CHEBI:28938 on the products side of RHEA:18038 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/18038']/rh:products; rh:contains/rh:compound/rh:accession`
agmatine deiminase reaction `RHEA:18038`	produces	N-carbamoylputrescine `CHEBI:58318`	RHEA:18038 Source assertion: Rhea lists CHEBI:58318 on the products side of RHEA:18038 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/18038']/rh:products; rh:contains/rh:compound/rh:accession`
H2O `CHEBI:15377`	consumes	N-carbamoylputrescine amidohydrolase reaction `RHEA:22285`	RHEA:22285 Source assertion: Rhea lists CHEBI:15377 on the substrates side of RHEA:22285 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/22285']/rh:substrates; rh:contains/rh:compound/rh:accession`
H+ `CHEBI:15378`	consumes	N-carbamoylputrescine amidohydrolase reaction `RHEA:22285`	RHEA:22285 Source assertion: Rhea lists CHEBI:15378 on the substrates side of RHEA:22285 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/22285']/rh:substrates; rh:contains/rh:compound/rh:accession`
N-carbamoylputrescine `CHEBI:58318`	consumes	N-carbamoylputrescine amidohydrolase reaction `RHEA:22285`	RHEA:22285 Source assertion: Rhea lists CHEBI:58318 on the substrates side of RHEA:22285 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/22285']/rh:substrates; rh:contains/rh:compound/rh:accession`
N-carbamoylputrescine amidohydrolase reaction `RHEA:22285`	produces	CO2 `CHEBI:16526`	RHEA:22285 Source assertion: Rhea lists CHEBI:16526 on the products side of RHEA:22285 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/22285']/rh:products; rh:contains/rh:compound/rh:accession`
N-carbamoylputrescine amidohydrolase reaction `RHEA:22285`	produces	ammonium `CHEBI:28938`	RHEA:22285 Source assertion: Rhea lists CHEBI:28938 on the products side of RHEA:22285 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/22285']/rh:products; rh:contains/rh:compound/rh:accession`
N-carbamoylputrescine amidohydrolase reaction `RHEA:22285`	produces	putrescine `CHEBI:326268`	RHEA:22285 Source assertion: Rhea lists CHEBI:326268 on the products side of RHEA:22285 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/22285']/rh:products; rh:contains/rh:compound/rh:accession`
arginine decarboxylase `EC:4.1.1.19`	catalyzes	L-arginine decarboxylase reaction `RHEA:17642`	RHEA:17641 Source assertion: Rhea associates EC:4.1.1.19 with the reaction family containing RHEA:17642. Source location `rh:ec`
agmatine deiminase `EC:3.5.3.12`	catalyzes	agmatine deiminase reaction `RHEA:18038`	RHEA:18037 Source assertion: Rhea associates EC:3.5.3.12 with the reaction family containing RHEA:18038. Source location `rh:ec` PMID:12634339 agmatine deiminase (the aguA product) and N-carbamoylputrescine amidohydrolase (the aguB product) Source location `PubMed Abstract`
N-carbamoylputrescine amidase `EC:3.5.1.53`	catalyzes	N-carbamoylputrescine amidohydrolase reaction `RHEA:22285`	RHEA:22284 Source assertion: Rhea associates EC:3.5.1.53 with the reaction family containing RHEA:22285. Source location `rh:ec` PMID:12634339 agmatine deiminase (the aguA product) and N-carbamoylputrescine amidohydrolase (the aguB product) Source location `PubMed Abstract`
L-arginine decarboxylase reaction `RHEA:17642`	precedes	agmatine deiminase reaction `RHEA:18038`	MetaCyc:ARGDEG-III-PWY Source assertion: MetaCyc pathway ordering places RHEA:17642 before RHEA:18038 in this pathway. Shared intermediate: CHEBI:58145. Source location `Pathway/reaction-ordering and reaction-layout; Rhea-to-MetaCyc cross-references`
agmatine deiminase reaction `RHEA:18038`	precedes	N-carbamoylputrescine amidohydrolase reaction `RHEA:22285`	MetaCyc:ARGDEG-III-PWY Source assertion: MetaCyc pathway ordering places RHEA:18038 before RHEA:22285 in this pathway. Shared intermediate: CHEBI:58318. Source location `Pathway/reaction-ordering and reaction-layout; Rhea-to-MetaCyc cross-references`
Biosynthetic arginine decarboxylase `UniProtKB:Q9HUX1`	enables	L-arginine decarboxylase reaction `RHEA:17642`	UniProtKB:Q9HUX1 Source assertion: UniProt annotates UniProtKB:Q9HUX1 with catalytic activity for the reaction family of RHEA:17642. Annotation evidence: ECO:0000255; organism taxon: NCBITaxon:208964. Source location `comments[commentType='CATALYTIC ACTIVITY'].reaction.reactionCrossReferences`
Biosynthetic arginine decarboxylase `UniProtKB:Q9HUX1`	has_cofactor	magnesium(2+) `CHEBI:18420`	UniProtKB:Q9HUX1 Source assertion: UniProt lists CHEBI:18420 as a cofactor of UniProtKB:Q9HUX1 (evidence: ECO:0000255). Source location `comments[commentType='COFACTOR'].cofactors and note`
Biosynthetic arginine decarboxylase `UniProtKB:Q9HUX1`	has_cofactor	pyridoxal 5'-phosphate(2-) `CHEBI:597326`	UniProtKB:Q9HUX1 Source assertion: UniProt lists CHEBI:597326 as a cofactor of UniProtKB:Q9HUX1 (evidence: ECO:0000255). Source location `comments[commentType='COFACTOR'].cofactors and note`
Agmatine deiminase `UniProtKB:Q9I6J9`	enables	agmatine deiminase reaction `RHEA:18038`	UniProtKB:Q9I6J9 Source assertion: UniProt annotates UniProtKB:Q9I6J9 with catalytic activity for the reaction family of RHEA:18038. Annotation evidence: ECO:0000269; organism taxon: NCBITaxon:208964. Source location `comments[commentType='CATALYTIC ACTIVITY'].reaction.reactionCrossReferences`

References

MetaCyc:ARGDEG-III-PWY MetaCyc L-arginine degradation IV pathway (source version: 22.5)
RHEA:17642 Rhea L-arginine decarboxylase direction (source version: 139)
RHEA:18038 Rhea agmatine deiminase direction (source version: 139)
RHEA:22285 Rhea N-carbamoylputrescine amidohydrolase direction (source version: 139)
PMID:12634339 Nakada and Itoh, Microbiology, 2003
RHEA:17641 RHEA:17641 authority record (source version: 139)
RHEA:18037 RHEA:18037 authority record (source version: 139)
RHEA:22284 RHEA:22284 authority record (source version: 139)
UniProtKB:Q9HUX1 UniProtKB:Q9HUX1 authority record (source version: 2026_03)
UniProtKB:Q9I6J9 UniProtKB:Q9I6J9 authority record (source version: 2026_03)

Curation history

2026-10-05T06:25:52Z codex
- EDIT — Review causal chemistry and add sourced molecular context
  Reviewed the entire record against MetaCyc 22.5 native pathway XML (including nested pathways), Rhea 139 explicit sides and directions, ENZYME 02-Sep-2026, PubMed records, and reviewed UniProt 2026_03 annotations within the record's taxon scope. Replaced generated structured-source quotations with source_assertion and source_locator. Typed molecular activities and participants. Reaction count 3 to 3; 0 directed-ID corrections; 2 protein annotations, 2 cofactor annotations and 0 sourced locations. All Rhea reaction substrate/product sets checked against independent Rhea authority; native pathway leaf coverage and source exceptions recorded in reports/causal_graph_review/metacyc-review.json. Full source URLs, versions and byte hashes are in metacyc-sources.json. All 50 MetaCyc records passed native schema validation; six targeted chemistry/evidence regression tests passed. Missing protein or cofactor annotations are not treated as biological absence; qualifications and exclusions are preserved in the ledger.
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