AceK is a bifunctional isocitrate dehydrogenase kinase/phosphatase (IDHK/P) that both phosphorylates (inactivating) and dephosphorylates (reactivating) isocitrate dehydrogenase (IDH) on a specific serine residue. By switching IDH between its active and inactive states, AceK controls the partitioning of isocitrate between the tricarboxylic acid (TCA) cycle and the glyoxylate bypass in response to the carbon source. When cells grow on glucose, IDH is unphosphorylated and fully active and flux proceeds through the TCA cycle; when cells grow on acetate, ethanol, or fatty acids, AceK phosphorylates and inactivates IDH, causing isocitrate to accumulate and be diverted through isocitrate lyase and malate synthase (the glyoxylate shunt), enabling net carbon assimilation from C2 substrates. Both the kinase and the opposing phosphatase reactions are ATP-dependent and catalyzed by the same enzyme. AceK is a cytoplasmic protein with a conserved active site and ATP-binding region, and belongs to the AceK family.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004721 phosphoprotein phosphatase activity | IEA GO_REF:0000118 | ACCEPT | Summary: AceK dephosphorylates phosphoserine in isocitrate dehydrogenase. Reason: Both existing adjudications support phosphoprotein phosphatase activity in substance. A more specific substrate term is useful in the core summary, but its availability does not make the TreeGrafter parent assertion biologically incorrect. Supporting Evidence: file:PSEPK/aceK/aceK-uniprot.txt dephosphorylate isocitrate dehydrogenase (IDH) on a specific serine file:PSEPK/aceK/aceK-notes.md which is more precise than file:PSEPK/aceK/aceK-hypotheses/function-hypothesis-go-0004721/openscientist.md Verdict: Partially supported / too general - Failure mode #1 (granularity / family-vs-subfamily). file:PSEPK/aceK/aceK-hypotheses/function-hypothesis-go-0004721/openscientist.md AceK is a genuine bifunctional isocitrate dehydrogenase kinase/phosphatase whose phosphatase catalytic residues are fully conserved file:PSEPK/aceK/aceK-hypotheses/function-hypothesis-go-0004721/falcon.md AceK does remove phosphate from a phosphoprotein |
| GO:0005524 ATP binding | IEA GO_REF:0000120 | ACCEPT | Summary: ATP binding supports the conserved kinase/phosphatase mechanism of AceK. Reason: The UniProt record explicitly annotates ATP-binding residues, and the characterized AceK structure contains ATP. This functional ligand interaction is real and core; coexistence with kinase activity is not over-annotation. Supporting Evidence: file:PSEPK/aceK/aceK-uniprot.txt BINDING 318..324 file:PSEPK/aceK/aceK-notes.md broad relative to |
| GO:0005737 cytoplasm | IEA GO_REF:0000120 | ACCEPT | Summary: AceK is a cytoplasmic enzyme, consistent with the UniProt subcellular location and its role acting on soluble IDH in the cytoplasm. Reason: UniProt annotates the cytoplasmic location and this is consistent with the function of a soluble metabolic regulatory enzyme. Supporting Evidence: file:PSEPK/aceK/aceK-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm |
| GO:0006006 glucose metabolic process | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: AceK regulates the carbon-source-dependent IDH switch, but the glucose-specific process assignment is not established by that regulatory response alone. Reason: Glucose-versus-acetate growth changes the AceK/IDH regulatory state. That observation supports metabolic regulation but does not itself establish a glucose-specific metabolic pathway role, since TCA and glyoxylate partitioning also concerns other carbon sources. Retain the over-annotation judgment with this scope distinction, without claiming that AceK is inactive whenever cells grow on glucose. Supporting Evidence: file:PSEPK/aceK/aceK-uniprot.txt when grown on acetate or ethanol, the file:PSEPK/aceK/aceK-notes.md this term is misleading and over-broad |
| GO:0006097 glyoxylate cycle | IEA GO_REF:0000104 | ACCEPT | Summary: AceK is the regulatory switch that diverts isocitrate into the glyoxylate bypass by phosphorylating and inactivating IDH during growth on acetate/fatty acids; this is a core biological process for the enzyme. Reason: AceK enables flux through the glyoxylate shunt by inactivating IDH, partitioning isocitrate toward isocitrate lyase and malate synthase. This is a defining biological role of the enzyme. Supporting Evidence: file:PSEPK/aceK/aceK-uniprot.txt bypass the Krebs cycle via the glyoxylate shunt |
| GO:0006099 tricarboxylic acid cycle | IEA GO_REF:0000104 | ACCEPT | Summary: AceK regulates entry of isocitrate into the TCA cycle by controlling IDH activity; it does not itself catalyze a TCA-cycle reaction but governs flux through this pathway, so it is appropriately associated with the TCA cycle as a regulator. Reason: By reactivating IDH (dephosphorylation), AceK restores TCA-cycle flux; by inactivating IDH (phosphorylation) it diverts flux to the glyoxylate bypass. This regulatory role makes the TCA cycle association appropriate. Supporting Evidence: file:PSEPK/aceK/aceK-notes.md regulatory switch that partitions |
| GO:0008772 [isocitrate dehydrogenase (NADP+)] kinase activity | IEA GO_REF:0000120 | ACCEPT | Summary: This is the core molecular function of AceK, the ATP-dependent kinase that phosphorylates IDH on a specific serine (EC 2.7.11.5; Rhea RHEA:43540), inactivating it. Reason: Matches the UniProt-annotated catalytic activity (EC 2.7.11.5) and the kinase half of the bifunctional enzyme. This is a central, specific core function. Supporting Evidence: file:PSEPK/aceK/aceK-uniprot.txt phosphorylate or file:PSEPK/aceK/aceK-uniprot.txt EC=2.7.11.5 file:PSEPK/aceK/aceK-uniprot.txt PTHR39559:SF1; ISOCITRATE DEHYDROGENASE KINASE_PHOSPHATASE |
| GO:0016208 AMP binding | IEA GO_REF:0000118 | ACCEPT | Summary: AMP binding is a conserved allosteric mechanism of the AceK kinase/phosphatase switch. Reason: The E. coli AceK structure shows AMP at an interdomain allosteric site controlling the opposing catalytic activities. This provides positive family-level support for the TreeGrafter inference to the conserved P. putida AceK. An unmeasured target-specific binding constant is not sufficient reason to mark the inherited mechanism non-core. Supporting Evidence: file:PSEPK/aceK/aceK-notes.md a discrete "AMP binding" MF is weakly supported for the P. putida PMID:20505668 As an AceK phosphatase activator and kinase inhibitor, AMP is found to bind in an allosteric site between the two AceK domains. |
| GO:0016788 hydrolase activity, acting on ester bonds | IEA GO_REF:0000104 | ACCEPT | Summary: The AceK phosphatase reaction hydrolyzes a phosphoric ester bond. Reason: Hydrolase activity acting on ester bonds is a valid broad function of the enzyme. Redundancy with substrate-specific phosphatase activity is not a biological error. Supporting Evidence: file:PSEPK/aceK/aceK-notes.md broad parent of the phosphatase |
| GO:0016791 phosphatase activity | IEA GO_REF:0000002 | ACCEPT | Summary: AceK catalyzes phospho-IDH dephosphorylation. Reason: Phosphatase activity is entailed by the accepted specific phosphoprotein dephosphorylation reaction. Retain the correct InterPro parent term. Supporting Evidence: file:PSEPK/aceK/aceK-uniprot.txt dephosphorylate isocitrate dehydrogenase (IDH) on a specific serine |
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Download this section (compressed HTML)Q: Is the P. putida AceK phosphatase reaction ATP-dependent and carried out at the same active site as the kinase, as in the E. coli ortholog?
Suggested experts: Bacterial metabolism biochemists, Enzymologists
Q: Which metabolites (e.g. AMP, ADP, isocitrate, oxaloacetate, NADPH) allosterically bias AceK toward kinase versus phosphatase activity in P. putida?
Suggested experts: Metabolic regulation specialists, Structural enzymologists
Q: How is aceK expression and the glyoxylate-bypass switch regulated during growth of P. putida on fatty acids and other C2 substrates?
Suggested experts: Microbial physiologists, Systems biologists
Experiment: Reconstitute purified P. putida AceK with its cognate IDH and measure both ATP-dependent kinase and phosphatase activities, confirming bifunctionality and ATP dependence of dephosphorylation.
Type: Enzyme assay
Experiment: Construct an aceK (PP_4565) deletion mutant and assay growth on acetate, ethanol, and fatty acids versus glucose to confirm the glyoxylate-bypass switching role.
Type: Growth phenotyping
Experiment: Quantify IDH serine phosphorylation in P. putida across carbon sources (glucose vs acetate/fatty acids) to map AceK activity to in vivo IDH inactivation.
Type: Phosphoproteomics
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