paaF

UniProt ID: Q88HR9
Organism: Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)
Review Status: DRAFT
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Gene Description

PaaF is an enoyl-CoA hydratase-isomerase in the aerobic phenylacetate degradation pathway of Pseudomonas putida KT2440. It acts in the beta-oxidation-like lower segment of the pathway after aromatic-ring opening.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0003824 catalytic activity
IEA
GO_REF:0000002 		MARK AS OVER ANNOTATED
Summary: Correct in branch but less informative than the assigned activity.
Reason: UniProt assigns EC 4.2.1.17 and names PaaF an enoyl-CoA hydratase-isomerase.
Supporting Evidence:
file:PSEPK/paaF/paaF-uniprot.txt
SubName: Full=Enoyl-CoA hydratase-isomerase
GO:0004300 enoyl-CoA hydratase activity
IEA
GO_REF:0000003 		ACCEPT
Summary: Best available GO molecular-function term for the assigned enzyme.
Reason: The UniProt enzyme assignment is enoyl-CoA hydratase-isomerase, EC 4.2.1.17.
Supporting Evidence:
file:PSEPK/paaF/paaF-uniprot.txt
EC=4.2.1.17
file:PSEPK/paaF/paaF-deep-research-openscientist.md
encodes a **cytoplasmic enoyl-CoA hydratase** of the **crotonase superfamily** (EC 4.2.1.17)
GO:0006635 fatty acid beta-oxidation
IEA
GO_REF:0000118 		MARK AS OVER ANNOTATED
Summary: Likely family-level over-annotation rather than the physiological pathway.
Reason: PaaF is encoded in the phenylacetate catabolic locus and is assigned to the lower phenylacetate pathway. The fatty-acid process annotation was transferred from a broad enoyl-CoA hydratase family.
Supporting Evidence:
file:PSEPK/paaF/paaF-deep-research-openscientist.md
The physiological substrate is the CoA-thioester of a short **dicarboxylic** enoyl intermediate produced by ring opening of phenylacetyl-CoA — not generic long-chain fatty enoyl-CoAs.
GO:0016836 hydro-lyase activity
IEA
GO_REF:0000117 		MARK AS OVER ANNOTATED
Summary: Correct parent activity but redundant with the specific hydratase term.
Reason: Enoyl-CoA hydratase activity is the informative child term.
Supporting Evidence:
file:PSEPK/paaF/paaF-uniprot.txt
SubName: Full=Enoyl-CoA hydratase-isomerase
file:PSEPK/paaF/paaF-deep-research-openscientist.md
operates within the aerobic **phenylacetate (paa) catabolic pathway** of *Pseudomonas putida* KT2440
GO:0010124 phenylacetate catabolic process
IC
file:PSEPK/paaF/paaF-uniprot.txt 		NEW
Summary: Missing pathway annotation for the PaaF lower-pathway enzyme.
Reason: PaaF is the enoyl-CoA hydratase-isomerase encoded in the paa locus.
Supporting Evidence:
file:PSEPK/paaF/paaF-uniprot.txt
SubName: Full=Enoyl-CoA hydratase-isomerase

Core Functions

Catalyzes an enoyl-CoA hydration/isomerization step in the beta-oxidation-like lower segment of aerobic phenylacetate catabolism.

Molecular Function:
enoyl-CoA hydratase activity
Directly Involved In:
phenylacetate catabolic process
Supporting Evidence:
  • file:PSEPK/paaF/paaF-uniprot.txt
    SubName: Full=Enoyl-CoA hydratase-isomerase
  • file:PSEPK/paaF/paaF-deep-research-openscientist.md
    syn-hydration of the C2=C3 double bond of 2,3-dehydroadipyl-CoA to yield 3-hydroxyadipyl-CoA

References

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Suggested Questions for Experts

Q: Which open-chain phenylacetate intermediate is the preferred KT2440 PaaF substrate?

Q: Does KT2440 PaaF form the stable PaaFG complex observed for E. coli orthologs, and does complex formation affect pathway flux?

Suggested Experiments

Experiment: Measure PaaF kinetics with pathway-derived enoyl-CoA intermediates and representative fatty-acyl-CoAs to define physiological substrate preference.

Deep Research

OpenScientist

(paaF-deep-research-openscientist.md)

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📚 Additional Documentation

Notes

(paaF-notes.md)

paaF curation notes

  • UniProt accession Q88HR9 names PaaF Enoyl-CoA hydratase-isomerase and
    assigns EC 4.2.1.17
    [file:PSEPK/paaF/paaF-uniprot.txt,
    "SubName: Full=Enoyl-CoA hydratase-isomerase"].
  • The precise enoyl-CoA hydratase molecular-function annotation is accepted;
    its generic catalytic and hydro-lyase parents are replaced by that term.
  • fatty acid beta-oxidation is marked as over-annotated. It is a
    TreeGrafter family transfer, whereas this protein is the PaaF encoded in the
    phenylacetate catabolic locus and is modeled in the analogous lower
    phenylacetate pathway.

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