edd encodes the IlvD/Edd-family 6-phosphogluconate dehydratase that catalyzes dehydration of 6-phospho-D-gluconate to 2-keto-3-deoxy-6-phosphogluconate (KDPG; EC 4.2.1.12). In Pseudomonas putida KT2440 this reaction is the committed Entner-Doudoroff (ED) pathway step downstream of 6-phosphogluconate production from glucose, gluconate, or 2-ketogluconate. The protein is a predicted soluble cytosolic enzyme with an essential [4Fe-4S] cofactor and is part of the metabolic architecture that makes KT2440 rely strongly on ED catabolism during sugar utilization.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003824 catalytic activity | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: This parent term is technically correct for an enzyme, but it adds no useful specificity once the more precise phosphogluconate dehydratase activity annotation is present. Reason: GO:0003824 is fully subsumed by GO:0004456 for this gene product and is therefore not informative as a separate functional statement. |
| GO:0004456 phosphogluconate dehydratase activity | IEA GO_REF:0000120 | ACCEPT | Summary: This is the specific core molecular function of Edd. UniProt assigns the EC 4.2.1.12 activity and describes dehydration of 6-phospho-D-gluconate to 2-dehydro-3-deoxy-6-phospho-D-gluconate, and species-specific studies on KT2440 place PP_1010/Edd at this ED-pathway step. Reason: The term captures the exact catalytic activity of the protein and is the most informative GO molecular-function term in the current annotation set. Supporting Evidence: file:PSEPK/edd/edd-uniprot.txt Catalyzes the dehydration of 6-phospho-D-gluconate to 2-dehydro-3-deoxy-6-phospho-D-gluconate. |
| GO:0005829 cytosol | IEA GO_REF:0000118 | KEEP AS NON CORE | Summary: This localization is plausible for a soluble central-metabolism enzyme acting on cytosolic 6-phosphogluconate and KDPG. It is reasonable to keep, but it is less informative than the catalytic and pathway terms for defining the gene's core evolved role. Reason: Cytosolic localization is compatible with the known organization of sugar catabolism in KT2440, but the main biological value of this review is the enzyme activity and ED-pathway assignment. |
| GO:0009255 Entner-Doudoroff pathway through 6-phosphogluconate | IEA GO_REF:0000120 | MODIFY | Summary: This is the correct pathway-level annotation. In KT2440, 6-phosphogluconate enters the ED route by conversion to KDPG through Edd, and edd mutants are explicitly included in experimental analyses of glucose catabolism. Reason: The pathway assignment is correct, but GO:0009255 is obsolete in the GO release 2026-07-26 (replaced_by GO:0061678) and consolidated the Entner-Doudoroff sub-variants into the parent term. Edd performs the committed ED dehydration step, so the annotation should move to GO:0061678 Entner-Doudoroff pathway. Proposed replacements: Entner-Doudoroff pathway Supporting Evidence: file:PSEPK/edd/edd-deep-research-falcon.md The ED pathway is not a peripheral option; it is a major organizing principle of glucose catabolism...This supports the GO process term `Entner-Doudoroff pathway through 6-phosphogluconate` as the right pathway annotation. |
| GO:0016836 hydro-lyase activity | IEA GO_REF:0000120 | MARK AS OVER ANNOTATED | Summary: This mechanistic parent term is not wrong, but it is considerably less informative than the child term phosphogluconate dehydratase activity. Reason: The child term GO:0004456 already captures the relevant hydro-lyase chemistry for this protein with appropriate substrate specificity. |
| GO:0051539 4 iron, 4 sulfur cluster binding | IEA GO_REF:0000104 | KEEP AS NON CORE | Summary: Edd-family dehydratases typically require a [4Fe-4S] cluster, and the UniProt entry predicts the cofactor plus ligand residues for this protein. The annotation is therefore plausible, but it is best treated as a mechanistic supporting feature rather than the primary core function. Reason: Cofactor binding is important for catalysis, but the more central biological statement for this gene is its phosphogluconate dehydratase activity in the ED pathway. |
Loading supporting content…
Download this section (compressed HTML)Q: How strongly is Edd activity modulated at the protein or metabolite level during oxidative stress, beyond the pathway-level phenotypes already known for KT2440?
Suggested experts: Pablo I. Nikel, Victor de Lorenzo
Q: Does the predicted [4Fe-4S] cluster of PP_1010 show unusual stability or repair dynamics during oxidative stress compared with other IlvD-family dehydratases?
Suggested experts: Pablo I. Nikel
Experiment: Purify PP_1010 and measure conversion of 6-phosphogluconate to KDPG in vitro with and without Fe-S cluster reconstitution.
Hypothesis: PP_1010 is a bona fide [4Fe-4S]-dependent phosphogluconate dehydratase whose catalytic activity depends on intact Fe-S loading.
Experiment: Compare wild type, delta-edd, and complemented strains for growth, flux redistribution, and intracellular NADPH/NADP+ balance during glucose growth with and without oxidant challenge.
Hypothesis: Loss of edd will block normal ED flux and exacerbate the redox defects that accompany oxidative stress in KT2440.
Experiment: Quantify Edd protein abundance and enzyme activity after shifts from succinate to glucose, gluconate, or 2-ketogluconate.
Hypothesis: Edd activity will increase when KT2440 is routed into hexose catabolism even if transcriptional changes are modest.
Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)