fadB

UniProt ID: Q88L02
Organism: Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)
Review Status: DRAFT
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Gene Description

fadB encodes the alpha subunit of the FadBA fatty acid beta-oxidation multienzyme complex. It provides hydroxyacyl-CoA dehydrogenase, enoyl-CoA hydratase, enoyl-CoA isomerase, and 3-hydroxybutyryl-CoA epimerase activities used in long-chain fatty acid beta-oxidation.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0003824 catalytic activity
IEA
GO_REF:0000002 		MARK AS OVER ANNOTATED
Summary: Generic catalytic activity is uninformative for a multi-activity beta-oxidation enzyme.
Reason: Retain the specific FadB enzymatic activities instead.
Supporting Evidence:
file:PSEPK/fadB/fadB-uniprot.txt
Catalyzes the formation of
GO:0003857 (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity
IEA
GO_REF:0000120 		ACCEPT
Summary: FadB has (3S)-3-hydroxyacyl-CoA dehydrogenase activity.
Reason: Retain as a core beta-oxidation enzymatic activity.
Supporting Evidence:
file:PSEPK/fadB/fadB-uniprot.txt
Reaction=a (3S)-3-hydroxyacyl-CoA + NAD(+) =
file:PSEPK/fadB/fadB-deep-research-falcon.md
Mechanistically, the review describes FadB catalyzing the hydration of **2‑trans‑enoyl‑CoA → (S)‑3‑hydroxyacyl‑CoA**, followed by oxidation of **(S)‑3‑hydroxyacyl‑CoA → 3‑ketoacyl‑CoA** with **NAD\+ reduction**, corresponding to two successive β‑oxidation steps.
GO:0004165 delta(3)-delta(2)-enoyl-CoA isomerase activity
IEA
GO_REF:0000120 		ACCEPT
Summary: FadB has delta(3)-delta(2)-enoyl-CoA isomerase activity.
Reason: Retain this beta-oxidation auxiliary activity.
Supporting Evidence:
file:PSEPK/fadB/fadB-uniprot.txt
Reaction=a (3Z)-enoyl-CoA = a 4-saturated (2E)-enoyl-CoA;
file:PSEPK/fadB/fadB-deep-research-falcon.md
also annotated with **cis-Δ3-trans-Δ2 enoyl-CoA isomerase** and **3-hydroxyacyl-CoA epimerase** activities
GO:0004300 enoyl-CoA hydratase activity
IEA
GO_REF:0000120 		ACCEPT
Summary: FadB has enoyl-CoA hydratase activity.
Reason: Retain this core beta-oxidation activity.
Supporting Evidence:
file:PSEPK/fadB/fadB-uniprot.txt
Reaction=a (3S)-3-hydroxyacyl-CoA = a (2E)-enoyl-CoA + H2O;
file:PSEPK/fadB/fadB-deep-research-falcon.md
A β‑oxidation/PHA study also annotates FadB as **enoyl‑CoA hydratase** and an **NAD\+‑dependent (S)‑3‑hydroxyacyl‑CoA dehydrogenase** (often denoted “FadB (NAD\+)”), consistent with the above reaction logic.
GO:0006631 fatty acid metabolic process
IEA
GO_REF:0000002 		MARK AS OVER ANNOTATED
Summary: Fatty acid metabolic process is true but broader than fatty acid beta-oxidation.
Reason: Retain GO:0006635 and GO:0009062 for the reviewed process context.
Supporting Evidence:
file:PSEPK/fadB/fadB-uniprot.txt
degradation of long-
GO:0006635 fatty acid beta-oxidation
IEA
GO_REF:0000120 		ACCEPT
Summary: FadB functions in fatty acid beta-oxidation.
Reason: Retain the core process annotation.
Supporting Evidence:
file:PSEPK/fadB/fadB-uniprot.txt
PATHWAY: Lipid metabolism; fatty acid beta-oxidation.
file:PSEPK/fadB/fadB-deep-research-falcon.md
FadB’s canonical role places it in the **β‑oxidation spiral** between acyl‑CoA dehydrogenation and thiolysis, producing 3‑ketoacyl‑CoA for **FadA thiolase** action.
GO:0008692 3-hydroxybutyryl-CoA epimerase activity
IEA
GO_REF:0000120 		KEEP AS NON CORE
Summary: FadB carries an annotated 3-hydroxybutyryl-CoA epimerase activity assigned by HAMAP/UniRule homology, but falcon deep research indicates this epimerase role may not be physiologically relevant in P. putida, so it is retained as non-core.
Reason: The epimerase reaction is supported by sequence-based annotation, but the KT2440-focused literature questions whether FadBA contributes a physiologically relevant epimerase route; downgraded from core to non-core auxiliary activity.
Supporting Evidence:
file:PSEPK/fadB/fadB-uniprot.txt
Reaction=(3S)-3-hydroxybutanoyl-CoA = (3R)-3-hydroxybutanoyl-CoA;
file:PSEPK/fadB/fadB-deep-research-falcon.md
although epimerase activity may be assigned to FadB by homology, this epimerase role **may not be physiologically relevant** in *Pseudomonas* under tested conditions
GO:0009062 fatty acid catabolic process
IEA
GO_REF:0000002 		ACCEPT
Summary: FadB participates in fatty acid catabolism via beta-oxidation.
Reason: Retain the catabolic process annotation.
Supporting Evidence:
file:PSEPK/fadB/fadB-uniprot.txt
degradation of long-
GO:0016042 lipid catabolic process
IEA
GO_REF:0000104 		MARK AS OVER ANNOTATED
Summary: Lipid catabolic process is a broad parent of the more specific fatty acid catabolic role.
Reason: Retain fatty acid catabolic process and beta-oxidation instead.
Supporting Evidence:
file:PSEPK/fadB/fadB-uniprot.txt
PATHWAY: Lipid metabolism; fatty acid beta-oxidation.
GO:0016491 oxidoreductase activity
IEA
GO_REF:0000002 		MARK AS OVER ANNOTATED
Summary: Generic oxidoreductase activity is less informative than the specific hydroxyacyl-CoA dehydrogenase terms.
Reason: Retain GO:0003857 and GO:0016509 instead.
Supporting Evidence:
file:PSEPK/fadB/fadB-uniprot.txt
Reaction=a (3S)-3-hydroxyacyl-CoA + NAD(+) =
GO:0016509 long-chain (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity
IEA
GO_REF:0000118 		ACCEPT
Summary: Long-chain (3S)-3-hydroxyacyl-CoA dehydrogenase activity is supported for FadB.
Reason: Retain as the most specific dehydrogenase annotation.
Supporting Evidence:
file:PSEPK/fadB/fadB-uniprot.txt
Involved in the aerobic and anaerobic degradation of long-
file:PSEPK/fadB/fadB-deep-research-falcon.md
Disruption of the **fadB homolog PP_2136** produces **severe fitness defects on fatty acids with chain length C6 and longer**, implicating PP_2136 as the **primary enoyl‑CoA hydratase/3‑hydroxyacyl‑CoA dehydrogenase** for **C6+** fatty-acid catabolism.
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
IEA
GO_REF:0000002 		MARK AS OVER ANNOTATED
Summary: This oxidoreductase parent is less specific than hydroxyacyl-CoA dehydrogenase activity.
Reason: Retain the specific dehydrogenase terms.
Supporting Evidence:
file:PSEPK/fadB/fadB-uniprot.txt
Reaction=a (3S)-3-hydroxyacyl-CoA + NAD(+) =
GO:0018812 3-hydroxyacyl-CoA dehydratase activity
IEA
GO_REF:0000116 		ACCEPT
Summary: FadB has 3-hydroxyacyl-CoA dehydratase/hydratase activity.
Reason: Retain as a specific beta-oxidation enzymatic activity.
Supporting Evidence:
file:PSEPK/fadB/fadB-uniprot.txt
Reaction=a (3S)-3-hydroxyacyl-CoA = a (2E)-enoyl-CoA + H2O;
GO:0036125 fatty acid beta-oxidation multienzyme complex
IEA
GO_REF:0000002 		ACCEPT
Summary: FadB is part of the fatty acid beta-oxidation multienzyme complex with FadA.
Reason: Retain the complex annotation.
Supporting Evidence:
file:PSEPK/fadB/fadB-uniprot.txt
Heterotetramer of two alpha chains (FadB) and two beta chains
file:PSEPK/fadB/fadB-deep-research-falcon.md
In *P. putida* KT2440, **FadB (PP_2136)** is described as a **multifunctional enzyme** within the **FadBA complex (PP_2136–PP_2137)**.
GO:0070403 NAD+ binding
IEA
GO_REF:0000002 		KEEP AS NON CORE
Summary: NAD+ binding is a supported cofactor feature of the dehydrogenase domain.
Reason: Retain as non-core cofactor binding.
Supporting Evidence:
file:PSEPK/fadB/fadB-uniprot.txt
Reaction=a (3S)-3-hydroxyacyl-CoA + NAD(+) =

Core Functions

FadB catalyzes long-chain 3-hydroxyacyl-CoA dehydrogenation in the FadBA beta-oxidation multienzyme complex.

Molecular Function:
long-chain (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity
Directly Involved In:
fatty acid beta-oxidation
In Complex:
fatty acid beta-oxidation multienzyme complex
Supporting Evidence:
  • file:PSEPK/fadB/fadB-uniprot.txt
    Involved in the aerobic and anaerobic degradation of long-
  • file:PSEPK/fadB/fadB-uniprot.txt
    Reaction=a (3S)-3-hydroxyacyl-CoA + NAD(+) =

FadB catalyzes enoyl-CoA hydration/dehydration steps in fatty acid beta-oxidation.

Molecular Function:
enoyl-CoA hydratase activity
Directly Involved In:
fatty acid beta-oxidation
In Complex:
fatty acid beta-oxidation multienzyme complex
Supporting Evidence:
  • file:PSEPK/fadB/fadB-uniprot.txt
    Reaction=a (3S)-3-hydroxyacyl-CoA = a (2E)-enoyl-CoA + H2O;

FadB provides auxiliary delta(3)-delta(2)-enoyl-CoA isomerase activity needed to reposition double bonds in unsaturated beta-oxidation intermediates.

Molecular Function:
delta(3)-delta(2)-enoyl-CoA isomerase activity
Directly Involved In:
fatty acid beta-oxidation
In Complex:
fatty acid beta-oxidation multienzyme complex
Supporting Evidence:
  • file:PSEPK/fadB/fadB-uniprot.txt
    Reaction=a (3Z)-enoyl-CoA = a 4-saturated (2E)-enoyl-CoA;

References

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Suggested Questions for Experts

Q: Which FadB activities are rate-limiting for KT2440 growth on long-chain versus unsaturated fatty acids?

Suggested experts: Pseudomonas lipid metabolism experts

Suggested Experiments

Experiment: Construct domain-specific FadB active-site mutants and compare fatty-acid growth profiles, acyl-CoA intermediate accumulation, and complementation of fadB deletion phenotypes.

Type: domain-specific mutagenesis with lipid metabolomics

Deep Research

Falcon

(fadB-deep-research-falcon.md)

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