L-phenylalanine biosynthesis I

MetaCyc:PHESYN

L-phenylalanine biosynthesis I converts chorismate to prephenate, dehydrates and decarboxylates prephenate to 3-phenylpyruvate, and transaminates 3-phenylpyruvate with L-glutamate to form L-phenylalanine.

Pathway type

amino acid biosynthesis

Organism scope

Escherichia coli NCBITaxon:562

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Pathway network

18 nodes · 22 asserted directed edges

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Chemical / cofactor
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Cell / process context
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
Escherichia coli `NCBITaxon:562`	taxon
chorismate mutase `EC:5.4.99.5`	molecular activity
prephenate dehydratase `EC:4.2.1.51`	molecular activity
aromatic-amino-acid transaminase `EC:2.6.1.57`	molecular activity
chorismate `CHEBI:29748`	small molecule
prephenate `CHEBI:29934`	small molecule
H+ `CHEBI:15378`	small molecule
3-phenylpyruvate `CHEBI:18005`	small molecule
CO2 `CHEBI:16526`	small molecule
H2O `CHEBI:15377`	small molecule
L-glutamate `CHEBI:29985`	small molecule
L-phenylalanine `CHEBI:58095`	small molecule
2-oxoglutarate `CHEBI:16810`	small molecule
T-protein `UniProtKB:P07023`	protein
cytoplasm `GO:0005737`	cellular component
Bifunctional chorismate mutase/prephenate dehydratase `UniProtKB:P0A9J8`	protein
chorismate mutase reaction `RHEA:13898`	reaction	left to right
prephenate dehydratase reaction `RHEA:21649`	reaction	left to right
L-phenylalanine aminotransferase reaction `RHEA:25154`	reaction	right to left

Mechanistic edges

Mechanistic edges and their cited evidence
Subject	Predicate and description	Object	Evidence
chorismate `CHEBI:29748`	consumes	chorismate mutase reaction `RHEA:13898`	RHEA:13898 Source assertion: Rhea lists CHEBI:29748 on the substrates side of RHEA:13898 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/13898']/rh:substrates; rh:contains/rh:compound/rh:accession`
chorismate mutase reaction `RHEA:13898`	produces	prephenate `CHEBI:29934`	RHEA:13898 Source assertion: Rhea lists CHEBI:29934 on the products side of RHEA:13898 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/13898']/rh:products; rh:contains/rh:compound/rh:accession`
H+ `CHEBI:15378`	consumes	prephenate dehydratase reaction `RHEA:21649`	RHEA:21649 Source assertion: Rhea lists CHEBI:15378 on the substrates side of RHEA:21649 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/21649']/rh:substrates; rh:contains/rh:compound/rh:accession`
prephenate `CHEBI:29934`	consumes	prephenate dehydratase reaction `RHEA:21649`	RHEA:21649 Source assertion: Rhea lists CHEBI:29934 on the substrates side of RHEA:21649 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/21649']/rh:substrates; rh:contains/rh:compound/rh:accession`
prephenate dehydratase reaction `RHEA:21649`	produces	H2O `CHEBI:15377`	RHEA:21649 Source assertion: Rhea lists CHEBI:15377 on the products side of RHEA:21649 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/21649']/rh:products; rh:contains/rh:compound/rh:accession`
prephenate dehydratase reaction `RHEA:21649`	produces	CO2 `CHEBI:16526`	RHEA:21649 Source assertion: Rhea lists CHEBI:16526 on the products side of RHEA:21649 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/21649']/rh:products; rh:contains/rh:compound/rh:accession`
prephenate dehydratase reaction `RHEA:21649`	produces	3-phenylpyruvate `CHEBI:18005`	RHEA:21649 Source assertion: Rhea lists CHEBI:18005 on the products side of RHEA:21649 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/21649']/rh:products; rh:contains/rh:compound/rh:accession`
3-phenylpyruvate `CHEBI:18005`	consumes	L-phenylalanine aminotransferase reaction `RHEA:25154`	RHEA:25154 Source assertion: Rhea lists CHEBI:18005 on the substrates side of RHEA:25154 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/25154']/rh:substrates; rh:contains/rh:compound/rh:accession`
L-glutamate `CHEBI:29985`	consumes	L-phenylalanine aminotransferase reaction `RHEA:25154`	RHEA:25154 Source assertion: Rhea lists CHEBI:29985 on the substrates side of RHEA:25154 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/25154']/rh:substrates; rh:contains/rh:compound/rh:accession`
L-phenylalanine aminotransferase reaction `RHEA:25154`	produces	2-oxoglutarate `CHEBI:16810`	RHEA:25154 Source assertion: Rhea lists CHEBI:16810 on the products side of RHEA:25154 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/25154']/rh:products; rh:contains/rh:compound/rh:accession`
L-phenylalanine aminotransferase reaction `RHEA:25154`	produces	L-phenylalanine `CHEBI:58095`	RHEA:25154 Source assertion: Rhea lists CHEBI:58095 on the products side of RHEA:25154 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/25154']/rh:products; rh:contains/rh:compound/rh:accession`
chorismate mutase `EC:5.4.99.5`	catalyzes	chorismate mutase reaction `RHEA:13898`	RHEA:13897 Source assertion: Rhea associates EC:5.4.99.5 with the reaction family containing RHEA:13898. Source location `rh:ec` PMID:4261395 Chorismate mutase-prephenate dehydratase from Escherichia coli K-12. II. Kinetic properties. Source location `PubMed ArticleTitle`
prephenate dehydratase `EC:4.2.1.51`	catalyzes	prephenate dehydratase reaction `RHEA:21649`	RHEA:21648 Source assertion: Rhea associates EC:4.2.1.51 with the reaction family containing RHEA:21649. Source location `rh:ec` PMID:4261395 Chorismate mutase-prephenate dehydratase from Escherichia coli K-12. II. Kinetic properties. Source location `PubMed ArticleTitle`
aromatic-amino-acid transaminase `EC:2.6.1.57`	catalyzes	L-phenylalanine aminotransferase reaction `RHEA:25154`	RHEA:25152 Source assertion: Rhea associates EC:2.6.1.57 with the reaction family containing RHEA:25154. Source location `rh:ec` PMID:236311 Multispecific aspartate and aromatic amino acid aminotransferases in Escherichia coli. Source location `PubMed ArticleTitle`
chorismate mutase reaction `RHEA:13898`	precedes	prephenate dehydratase reaction `RHEA:21649`	MetaCyc:PHESYN Source assertion: MetaCyc pathway ordering places RHEA:13898 before RHEA:21649 in this pathway. Shared intermediate: CHEBI:29934. Source location `Pathway/reaction-ordering and reaction-layout; Rhea-to-MetaCyc cross-references`
prephenate dehydratase reaction `RHEA:21649`	precedes	L-phenylalanine aminotransferase reaction `RHEA:25154`	MetaCyc:PHESYN Source assertion: MetaCyc pathway ordering places RHEA:21649 before RHEA:25154 in this pathway. Shared intermediate: CHEBI:18005. Source location `Pathway/reaction-ordering and reaction-layout; Rhea-to-MetaCyc cross-references`
T-protein `UniProtKB:P07023`	enables	chorismate mutase reaction `RHEA:13898`	UniProtKB:P07023 Source assertion: UniProt annotates UniProtKB:P07023 with catalytic activity for the reaction family of RHEA:13898. Annotation evidence: curated source annotation; organism taxon: NCBITaxon:83333. Source location `comments[commentType='CATALYTIC ACTIVITY'].reaction.reactionCrossReferences`
T-protein `UniProtKB:P07023`	located_in	cytoplasm `GO:0005737`	UniProtKB:P07023 Source assertion: UniProt locates UniProtKB:P07023 in Cytoplasm (SL-0086, mapped by UniProt to GO:0005737). Annotation evidence: curated source annotation. Source location `comments[commentType='SUBCELLULAR LOCATION'].subcellularLocations; UniProt location vocabulary GO mapping`
Bifunctional chorismate mutase/prephenate dehydratase `UniProtKB:P0A9J8`	enables	chorismate mutase reaction `RHEA:13898`	UniProtKB:P0A9J8 Source assertion: UniProt annotates UniProtKB:P0A9J8 with catalytic activity for the reaction family of RHEA:13898. Annotation evidence: ECO:0000269; organism taxon: NCBITaxon:83333. Source location `comments[commentType='CATALYTIC ACTIVITY'].reaction.reactionCrossReferences`
Bifunctional chorismate mutase/prephenate dehydratase `UniProtKB:P0A9J8`	enables	prephenate dehydratase reaction `RHEA:21649`	UniProtKB:P0A9J8 Source assertion: UniProt annotates UniProtKB:P0A9J8 with catalytic activity for the reaction family of RHEA:21649. Annotation evidence: ECO:0000269; organism taxon: NCBITaxon:83333. Source location `comments[commentType='CATALYTIC ACTIVITY'].reaction.reactionCrossReferences`
L-phenylalanine `CHEBI:58095`	inhibits	Bifunctional chorismate mutase/prephenate dehydratase `UniProtKB:P0A9J8`	UniProtKB:P0A9J8 Source assertion: UniProt activity-regulation annotation: Both activities are inhibited by L-phenylalanine Source location `comments[commentType='ACTIVITY REGULATION'].texts`
Bifunctional chorismate mutase/prephenate dehydratase `UniProtKB:P0A9J8`	located_in	cytoplasm `GO:0005737`	UniProtKB:P0A9J8 Source assertion: UniProt locates UniProtKB:P0A9J8 in Cytoplasm (SL-0086, mapped by UniProt to GO:0005737). Annotation evidence: ECO:0000305. Source location `comments[commentType='SUBCELLULAR LOCATION'].subcellularLocations; UniProt location vocabulary GO mapping`

References

MetaCyc:PHESYN MetaCyc L-phenylalanine biosynthesis I pathway (source version: 22.5)
RHEA:13897 Rhea chorismate mutase reaction (source version: 139)
RHEA:13898 Rhea prephenate-forming chorismate mutase direction (source version: 139)
RHEA:21648 Rhea prephenate dehydratase reaction (source version: 139)
RHEA:21649 Rhea phenylpyruvate-forming prephenate dehydratase direction (source version: 139)
RHEA:25152 Rhea L-phenylalanine aminotransferase reaction (source version: 139)
RHEA:25154 Rhea L-phenylalanine-forming aminotransferase direction (source version: 139)
PMID:4261395 Dopheide et al., Journal of Biological Chemistry, 1972
PMID:236311 Mavrides and Orr, Journal of Biological Chemistry, 1975
UniProtKB:P07023 UniProtKB:P07023 authority record (source version: 2026_03)
UniProtKB:P0A9J8 UniProtKB:P0A9J8 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, 0 cofactor annotations and 2 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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