pheA

Gene Description

Bifunctional chorismate mutase/prephenate dehydratase (the bacterial P-protein). It catalyzes two consecutive steps that commit carbon from the shikimate pathway to L-phenylalanine biosynthesis. First, the chorismate mutase reaction (EC 5.4.99.5), a Claisen rearrangement converting chorismate to prephenate; second, the prephenate dehydratase reaction (EC 4.2.1.51), the decarboxylative dehydration of prephenate to phenylpyruvate, the keto-acid precursor of L-phenylalanine. The protein has a modular architecture comprising an N-terminal AroQ-type chorismate mutase domain, a central prephenate dehydratase domain, and a C-terminal ACT-like regulatory domain that mediates allosteric feedback inhibition by L-phenylalanine. In Pseudomonas putida KT2440 the enzyme is essential for endogenous phenylalanine synthesis; loss-of-function mutants are phenylalanine auxotrophs. The protein acts in the cytoplasm on intracellular chorismate and prephenate pools.

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0004106 chorismate mutase activity	IEA GO_REF:0000120	ACCEPT	Summary: Core molecular function. The N-terminal AroQ-type chorismate mutase domain catalyzes chorismate to prephenate (EC 5.4.99.5), supported by domain architecture, EC mapping, and the phenylalanine-auxotroph phenotype of KT2440 pheA mutants.
GO:0004664 prephenate dehydratase activity	IEA GO_REF:0000120	ACCEPT	Summary: Core molecular function. The prephenate dehydratase domain catalyzes prephenate to phenylpyruvate + CO2 + H2O (EC 4.2.1.51), the committed step toward L-phenylalanine. Well supported by domain architecture and EC mapping.
GO:0005737 cytoplasm	IEA GO_REF:0000120	ACCEPT	Summary: Cytoplasmic localization is consistent with this enzyme acting on intracellular chorismate/prephenate pools in core amino-acid metabolism. Distinct periplasmic AroQ chorismate mutases exist in pseudomonads but are a separate monofunctional class; this bifunctional P-protein is cytosolic.
GO:0008652 amino acid biosynthetic process	IEA GO_REF:0000104	KEEP AS NON CORE	Summary: Correct but a high-level parent of the specific process (L-phenylalanine biosynthesis). Retained as accurate but non-core given the more precise child terms are also annotated.
GO:0009073 aromatic amino acid biosynthetic process	IEA GO_REF:0000104	KEEP AS NON CORE	Summary: Correct grouping term; phenylalanine is an aromatic amino acid. Less specific than L-phenylalanine biosynthetic process. Retained as accurate but non-core.
GO:0009094 L-phenylalanine biosynthetic process	IEA GO_REF:0000120	ACCEPT	Summary: Core biological process. pheA catalyzes the committed steps of phenylalanine biosynthesis; KT2440 disruption mutants are phenylalanine auxotrophs rescued by phenylalanine but not tyrosine, directly supporting this term. Reason: Mini-Tn5 insertions in PP_1769 (pheA) produce phenylalanine auxotrophy in P. putida KT2440 (rescued by phenylalanine, not tyrosine), and the gene is operon-linked with serC and the tyrA-region genes, providing organism-specific experimental support beyond the IEA evidence (file:PSEPK/pheA/pheA-deep-research-falcon.md; PMID:21261884).
GO:0016829 lyase activity	IEA GO_REF:0000104	MARK AS OVER ANNOTATED	Summary: Uninformative grand-parent of prephenate dehydratase activity (a lyase). Over-annotation when the specific EC 4.2.1.51 activity is already captured.
GO:0016836 hydro-lyase activity	IEA GO_REF:0000117	MARK AS OVER ANNOTATED	Summary: Intermediate parent of prephenate dehydratase activity within the lyase branch. Less informative than the specific child term GO:0004664, which is annotated.
GO:0016853 isomerase activity	IEA GO_REF:0000104	MARK AS OVER ANNOTATED	Summary: Uninformative grand-parent of chorismate mutase activity (an intramolecular isomerase/transferase). Over-annotation when the specific EC 5.4.99.5 activity is already captured by GO:0004106.
GO:0046417 chorismate metabolic process	IEA GO_REF:0000002	KEEP AS NON CORE	Summary: Accurate; chorismate is the substrate of the chorismate mutase step. A broader metabolic grouping than L-phenylalanine biosynthesis. Retained as accurate but non-core.

Core Functions

Chorismate mutase activity converting chorismate to prephenate, the first committed step diverting shikimate-pathway flux toward phenylalanine/tyrosine.

Molecular Function:

chorismate mutase activity

Directly Involved In:

L-phenylalanine biosynthetic process

Supporting Evidence:

GO_REF:0000120
chorismate mutase activity (EC 5.4.99.5); RHEA:13897 chorismate = prephenate.

Prephenate dehydratase activity converting prephenate to phenylpyruvate, the committed step toward L-phenylalanine; allosterically feedback-inhibited by L-phenylalanine via the C-terminal ACT-like domain.

Molecular Function:

prephenate dehydratase activity

Directly Involved In:

L-phenylalanine biosynthetic process

Supporting Evidence:

GO_REF:0000120
prephenate dehydratase activity (EC 4.2.1.51); RHEA:21648 prephenate + H+ = 3-phenylpyruvate + CO2 + H2O.

Gene Description

Existing Annotations Review

Core Functions

Chorismate mutase activity converting chorismate to prephenate, the first committed step diverting shikimate-pathway flux toward phenylalanine/tyrosine.

Prephenate dehydratase activity converting prephenate to phenylpyruvate, the committed step toward L-phenylalanine; allosterically feedback-inhibited by L-phenylalanine via the C-terminal ACT-like domain.

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