eda encodes the canonical 2-dehydro-3-deoxy-phosphogluconate (KDPG) aldolase of Pseudomonas putida KT2440. The 235 aa enzyme belongs to the KHG/KDPG aldolase family and catalyzes cleavage of KDPG to pyruvate and glyceraldehyde 3-phosphate, which is the carbon-splitting step of the Entner-Doudoroff route from 6-phosphogluconate. UniProt also places the protein in 2-dehydro-3-deoxy-D-gluconate degradation step 2/2 and predicts a homotrimeric enzyme.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0008675 2-dehydro-3-deoxy-phosphogluconate aldolase activity | IEA GO_REF:0000120 | ACCEPT | Summary: This annotation captures the specific catalytic activity named in UniProt and matches the recorded EC 4.1.2.14 reaction that cleaves KDPG into glyceraldehyde 3-phosphate and pyruvate. It is the core molecular function of Eda. Reason: The term exactly matches the enzyme name and reaction chemistry given in the UniProt record for Q88P29, so it should be retained as the primary functional annotation. Supporting Evidence: file:PSEPK/eda/eda-uniprot.txt RecName: Full=2-dehydro-3-deoxy-phosphogluconate aldolase file:PSEPK/eda/eda-uniprot.txt Reaction=2-dehydro-3-deoxy-6-phospho-D-gluconate = D-glyceraldehyde 3-...phosphate + pyruvate file:PSEPK/eda/eda-deep-research-falcon.md **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)**. file:PSEPK/eda/eda-deep-research-falcon.md 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. |
| GO:0016829 lyase activity | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: This broad parent term is technically correct because Eda is a lyase, but it adds little beyond the much more informative child term GO:0008675. It is a generic InterPro2GO (GO_REF:0000002) parent of the specific KDPG aldolase activity that is already annotated, so it represents an over-annotation rather than an informative independent function. The falcon deep research confirms the specific KDPG aldolase activity as the evolved function, leaving the generic lyase term redundant. Reason: The specific child term GO:0008675 already captures the evolved aldolase (lyase) activity, so the generic parent lyase term is a redundant high-level IEA over-annotation that should not be propagated as a distinct function. Supporting Evidence: file:PSEPK/eda/eda-uniprot.txt KW Lyase file:PSEPK/eda/eda-uniprot.txt SIMILARITY: Belongs to the KHG/KDPG aldolase family. file:PSEPK/eda/eda-deep-research-falcon.md **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)**. |
| GO:0061678 Entner-Doudoroff pathway | IEA file:PSEPK/eda/eda-uniprot.txt | NEW | Summary: The UniProt pathway statement places Eda in 2-dehydro-3-deoxy-D-gluconate degradation step 2/2, which is the terminal aldol-cleavage step of the Entner-Doudoroff pathway. This process-level annotation is missing from GOA and should be added. (Previously proposed as GO:0009255 Entner-Doudoroff pathway through 6-phosphogluconate, which GO obsoleted with replaced_by GO:0061678.) Reason: Eda performs the pathway-defining KDPG aldolase reaction that produces pyruvate and glyceraldehyde 3-phosphate from KDPG, so a process term for the Entner-Doudoroff route is warranted. Falcon deep research provides strong organism-specific support, including a KT2440 eda mutant that fails to grow on glucose and 13C flux data placing the ED route at a high-flux central node. Supporting Evidence: file:PSEPK/eda/eda-uniprot.txt 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. file:PSEPK/eda/eda-deep-research-falcon.md A KT2440 **eda::mini-Tn5** mutant **failed to grow on glucose**, consistent with ED pathway indispensability for glucose utilization in this organism. file:PSEPK/eda/eda-deep-research-falcon.md 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. |
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Download this section (compressed HTML)Q: Does PP_1024 act strictly on KDPG in vivo, or does it also process related 2-keto-3-deoxy sugar phosphates such as KHG?
Q: Under which carbon-source conditions does eda become rate-limiting for central carbon flux in KT2440?
Experiment: Construct an eda deletion and complemented strain, then compare growth and end-product formation on glucose, gluconate, and 2-ketogluconate.
Hypothesis: Eda is the primary KDPG aldolase required for Entner-Doudoroff flux from glucose oxidation products in KT2440.
Type: growth phenotype and complementation
Experiment: Purify recombinant Eda and measure steady-state kinetics with KDPG and structurally related substrates such as KHG.
Hypothesis: PP_1024 has strong substrate preference for KDPG over alternative 2-keto-3-deoxy sugar phosphates.
Type: enzymology
Experiment: Perform 13C-tracer metabolomics or flux analysis in wild-type and eda mutant strains during growth on gluconate or glucose.
Hypothesis: Loss of eda redirects carbon flux upstream of KDPG during oxidative glucose metabolism.
Type: metabolomics / flux analysis
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