GO_REF:0000002

Gene Ontology annotation through association of InterPro records with GO terms

GO_REF:0000120

Combined Automated Annotation using Multiple IEA Methods

PMID:12534463

Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440.

KT2440 is a metabolically versatile strain with broad encoded metabolic capacity

"Pseudomonas putida is a metabolically versatile saprophytic soil bacterium"

file:PSEPK/eda/eda-uniprot.txt

UniProt entry Q88P29

eda / PP_1024 encodes 2-dehydro-3-deoxy-phosphogluconate aldolase (EC 4.1.2.14)

"RecName: Full=2-dehydro-3-deoxy-phosphogluconate aldolase"
Eda cleaves KDPG to glyceraldehyde 3-phosphate and pyruvate

"Reaction=2-dehydro-3-deoxy-6-phospho-D-gluconate = D-glyceraldehyde 3-...phosphate + pyruvate"
Eda is placed in 2-dehydro-3-deoxy-D-gluconate degradation step 2/2

"PATHWAY: Carbohydrate acid metabolism; 2-dehydro-3-deoxy-D-gluconate...degradation; D-glyceraldehyde 3-phosphate and pyruvate from 2-dehydro-3-deoxy-D-gluconate: step 2/2."
Eda belongs to the KHG/KDPG aldolase family and is predicted to form a homotrimer

"SIMILARITY: Belongs to the KHG/KDPG aldolase family."

PMID:12393206

Analysis of the zwf-pgl-eda-operon in Pseudomonas putida strains H and KT2440.

In KT2440, eda is part of the zwf-pgl-eda operon, with the divergently transcribed regulator hexR nearby; the operon is induced by carbohydrates including glucose, gluconate, fructose, and glycerol.
Operon transcription in KT2440 was about 3-fold higher than in strain H, indicating strain-level differences in expression control.

PMID:23967821

Metabolic and regulatory rearrangements underlying glycerol metabolism in Pseudomonas putida KT2440.

An eda::mini-Tn5 mutant in KT2440 fails to grow on glucose but grows slowly on glycerol (mu=0.21+/-0.05 h^-1) and succinate (mu=0.34+/-0.02 h^-1).
Eda activity in extracts of glucose-grown KT2440 is 635+/-141 units, 2.2-fold higher than on glycerol; transcript expression hierarchy is glucose greater than glycerol greater than succinate.

PMID:26350459

Pseudomonas putida KT2440 strain metabolizes glucose through a cycle formed by enzymes of the Entner-Doudoroff, Embden-Meyerhof-Parnas, and pentose phosphate pathways.

In KT2440, more than 80 percent of glucose influx is routed through periplasmic oxidation and the Entner-Doudoroff pathway contributes about 50 percent of the flux to pyruvate, placing Eda at a high-flux node in central carbon metabolism.

PMID:16403639

Mechanism of the Class I KDPG aldolase.

Class I KDPG aldolases including the Pseudomonas putida enzyme operate via a Schiff-base (covalent imine) intermediate formed by a conserved active-site lysine, with a conserved glutamate as general acid/base; the fold is a TIM (alpha/beta) barrel forming a trimeric assembly.

PMID:39589324

GnuR Represses the Expression of Glucose and Gluconate Catabolism in Pseudomonas putida KT2440.

GnuR is a transcriptional repressor that directly represses glucose and gluconate catabolic genes including ED-pathway genes such as eda (ChIP-seq enrichment ~1.74 at the eda locus), participating in an incoherent feedforward loop with glucose/gluconate induction.
ΔgnuR shortens lag time on 22 mM glucose or 4 mM gluconate without changing exponential growth rate, indicating GnuR primarily tunes transition dynamics for catabolite switching.

file:PSEPK/eda/eda-deep-research-falcon.md

Falcon (Edison Scientific) deep research report: eda (PP_1024; UniProt Q88P29) in Pseudomonas putida KT2440

eda is PP_1024 and encodes KDPG aldolase (EC 4.1.2.14), matching UniProt Q88P29, disambiguating it from unrelated proteins sharing the eda symbol.

"In *Pseudomonas putida* KT2440, **eda is PP_1024** and encodes **2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase** (EC **4.1.2.14**), consistent with UniProt **Q88P29** and the KHG/KDPG aldolase family annotation."
Eda catalyzes the defining aldolase step of the Entner-Doudoroff pathway, cleaving KDPG to pyruvate and glyceraldehyde-3-phosphate.

"**Eda (KDPG aldolase)** catalyzes the defining aldolase step of the Entner–Doudoroff (ED) pathway: **cleavage of KDPG to pyruvate and glyceraldehyde-3-phosphate (GAP/G3P)**."
The ED route is a high-flux central node in KT2440 glucose catabolism, with most glucose influx via periplasmic oxidation and ~50% of pyruvate flux through the ED pathway.

"A ^13C-based flux analysis framework described that **>80% of glucose influx** is routed through periplasmic oxidation, and the ED pathway contributes **~50% of the flux to pyruvate formation** under the tested conditions."
Eda sits at a high-flux node in the characteristic glucose-utilization architecture of KT2440.

"Thus, Eda (PP_1024) sits at a high-flux node in KT2440’s characteristic glucose-utilization architecture."
A KT2440 eda mini-Tn5 mutant fails to grow on glucose, demonstrating that eda is required for hexose catabolism through the ED pathway.

"A KT2440 **eda::mini-Tn5** mutant **failed to grow on glucose**, consistent with ED pathway indispensability for glucose utilization in this organism."
Eda acts in the cytosol on the phosphorylated intermediate KDPG, downstream of periplasmic glucose oxidation.

"However, the functional placement of Eda in the ED pathway (acting on **KDPG**, a cytosolic phosphorylated intermediate formed from 6-phosphogluconate) and the separation of periplasmic oxidation from cytosolic catabolism in KT2440’s glucose architecture support that Eda operates in the **cytosol** rather than in the periplasm."
Eda belongs to the KDPG/KHG aldolase family; direct KT2440 biochemical specificity for KHG versus KDPG was not measured, so KHG activity remains an inference from family membership.

"The UniProt/domain context and one KT2440 paper’s annotation terminology reflect that Eda belongs to the **KDPG/KHG aldolase family** (sometimes annotated as ketodeoxyphosphogluconate/ketohydroxyglutarate aldolase)."
eda is part of the carbohydrate-induced zwf-pgl-eda operon adjacent to the divergent regulator hexR in KT2440.

"In KT2440, **eda is part of the zwf–pgl–eda operon**, and this operon was cloned together with part of the divergently transcribed regulator **hexR**. The operon is **induced by carbohydrates** including glucose, gluconate, fructose, and glycerol."