| Claim/Aspect | Key finding | Quantitative data (if any) | Source (with year, DOI/URL) |
|---|---|---|---|
| Identity | The target gene in *Pseudomonas putida* KT2440 is **eda = PP_1024**, annotated as **2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase / 2-keto-3-deoxygluconate-6-P aldolase**, matching UniProt Q88P29. (pqac-00000000, pqac-00000003, pqac-00000005) | Locus: **PP_1024** | Nikel et al., 2014, *Environ. Microbiol.*, doi:10.1111/1462-2920.12224, https://doi.org/10.1111/1462-2920.12224; Petruschka et al., 2002, *FEMS Microbiol. Lett.*, doi:10.1016/S0378-1097(02)00923-0, https://doi.org/10.1016/S0378-1097(02)00923-0; Nikel et al., 2015, *J. Biol. Chem.*, doi:10.1074/jbc.M115.687749, https://doi.org/10.1074/jbc.M115.687749 |
| Reaction | Eda catalyzes cleavage of **KDPG** to **pyruvate + glyceraldehyde-3-phosphate (G3P/GAP)**, the defining aldolase step of the Entner–Doudoroff pathway. (pqac-00000003, pqac-00000015) | Products formed in equimolar terms from KDPG cleavage: pyruvate and GAP | Petruschka et al., 2002, *FEMS Microbiol. Lett.*, doi:10.1016/S0378-1097(02)00923-0, https://doi.org/10.1016/S0378-1097(02)00923-0; Fullerton et al., 2006, *Bioorg. Med. Chem.*, doi:10.1016/j.bmc.2005.12.022, https://doi.org/10.1016/j.bmc.2005.12.022 |
| Pathway role | In KT2440, Eda is a central **Entner–Doudoroff (ED) pathway** enzyme downstream of Edd; glucose catabolism relies strongly on peripheral oxidation to gluconate/2-ketogluconate feeding the ED route. (pqac-00000004, pqac-00000005) | **>80%** of glucose influx routed through periplasmic oxidation; ED pathway contributes **~50%** of flux to pyruvate formation. | Nikel et al., 2015, *J. Biol. Chem.*, doi:10.1074/jbc.M115.687749, https://doi.org/10.1074/jbc.M115.687749 |
| Operon/regulation | Early genetic analysis placed **eda** in the **zwf-pgl-eda operon**; the divergently transcribed regulator **hexR** lies nearby. The operon is induced by carbohydrates including glucose, gluconate, fructose, and glycerol. (pqac-00000003) | Operon transcription in KT2440 reported about **3-fold higher** than in strain H. | Petruschka et al., 2002, *FEMS Microbiol. Lett.*, doi:10.1016/S0378-1097(02)00923-0, https://doi.org/10.1016/S0378-1097(02)00923-0 |
| Localization | No direct localization experiment for Eda was captured in the gathered snippets, but the pathway context places Eda in the **cytoplasmic ED pathway** after transport/phosphorylation/periplasmic oxidation steps; no evidence supports periplasmic or extracellular localization in the cited snippets. (pqac-00000004, pqac-00000005) | Not directly quantified | Nikel et al., 2015, *J. Biol. Chem.*, doi:10.1074/jbc.M115.687749, https://doi.org/10.1074/jbc.M115.687749 |
| Mutant phenotype | An **eda::mini-Tn5** mutant in KT2440 **failed to grow on glucose**, but still showed slow growth on glycerol and succinate, supporting essentiality for hexose catabolism through ED. (pqac-00000009) | Growth rates of mutant: **0.21 ± 0.05 h⁻¹** on glycerol; **0.34 ± 0.02 h⁻¹** on succinate; no growth on glucose. | Nikel et al., 2014, *Environ. Microbiol.*, doi:10.1111/1462-2920.12224, https://doi.org/10.1111/1462-2920.12224 |
| Enzyme activity/expression | Eda activity is highest in glucose-grown cells and lower on glycerol/succinate, consistent with carbon-source-dependent ED pathway usage. Transcript data show **glucose > glycerol > succinate** expression hierarchy for ED genes including **eda**. (pqac-00000000, pqac-00000001, pqac-00000011) | Eda activity in glucose-grown cells: **635 ± 141 min⁻¹ mg protein⁻¹**; **2.2-fold** higher on glucose than glycerol. Transcript change for **eda**: log2(glycerol/succinate) **+2.481** (~**5.6-fold**), log2(glycerol/glucose) **−2.852** (glucose ~**7-fold** higher than glycerol). | Nikel et al., 2014, *Environ. Microbiol.*, doi:10.1111/1462-2920.12224, https://doi.org/10.1111/1462-2920.12224 |
| Recent 2024 regulation | A 2024 multi-omics study identified **GnuR** as a direct **repressor** of glucose/gluconate catabolic genes, including ED-pathway genes such as **eda**. ED genes were induced by both glucose and gluconate, and GnuR participates in an incoherent feedforward loop. (pqac-00000006, pqac-00000007, pqac-00000008, pqac-00000010) | **eda** was among GnuR-bound loci; ChIP-seq MACS2 fold enrichment for **eda = 1.74**. Physiologically, **ΔgnuR** shortened lag time on **22 mM glucose** or **4 mM gluconate**, with no significant change in exponential growth rate. Some glucose/gluconate catabolic genes increased **almost 100-fold** vs succinate. | Chen et al., 2024, *Microbial Biotechnology*, doi:10.1111/1751-7915.70059, https://doi.org/10.1111/1751-7915.70059 |
| Catalytic mechanism / family support | Broader structural work on class I KDPG aldolases supports annotation of Eda as a **Class I Schiff-base aldolase** with a conserved catalytic lysine/glutamate-centered mechanism; *P. putida* enzyme structure superimposes closely with homologs. (pqac-00000012, pqac-00000013, pqac-00000014, pqac-00000016) | *P. putida* enzyme superimposes with homologs at about **1.5 Å RMSD**; key residues discussed include Lys129/Lys133, Glu40/Glu45, Thr156, Ser179, and conserved waters. | Fullerton et al., 2006, *Bioorg. Med. Chem.*, doi:10.1016/j.bmc.2005.12.022, https://doi.org/10.1016/j.bmc.2005.12.022 |


*Table: This table compiles organism-specific and family-level evidence supporting the functional annotation of *Pseudomonas putida* KT2440 eda (PP_1024; UniProt Q88P29). It highlights identity, reaction, pathway placement, regulation, phenotype, and quantitative evidence most relevant for a research report.*