Phosphoenolpyruvate carboxylase (PEPC/PEPCase; EC 4.1.1.31), a soluble cytosolic enzyme of the PEPCase type 1 family. It catalyzes the essentially irreversible, Mg2+-dependent carboxylation of phosphoenolpyruvate (PEP) using bicarbonate (hydrogencarbonate) to form oxaloacetate (OAA) and inorganic phosphate. In bacterial central carbon metabolism PEPC functions as an anaplerotic enzyme that replenishes oxaloacetate at the PEP-pyruvate-oxaloacetate node, supplying the tricarboxylic acid cycle and biosynthetic precursor pools (e.g., the aspartate family of amino acids) when TCA intermediates are withdrawn. Bacterial PEPCs are typically homotetramers subject to allosteric regulation, commonly activated by acetyl-CoA and fructose-1,6-bisphosphate and inhibited by aspartate and malate, allowing anaplerotic OAA formation to be tuned to glycolytic and biosynthetic demand.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000287 magnesium ion binding | IEA GO_REF:0000104 | KEEP AS NON CORE | Summary: PEPC requires Mg2+ as a catalytic cofactor, and the reviewed UniProt record assigns Mg2+ through HAMAP MF_00595. This is mechanistically valid but subordinate to phosphoenolpyruvate carboxylase activity. Reason: Retain the cofactor-binding annotation as supporting chemistry rather than treating generic magnesium binding as a core function. |
| GO:0005829 cytosol | IEA GO_REF:0000118 | ACCEPT | Summary: PEPC is a soluble enzyme of central carbon metabolism with no membrane or signal/transit-peptide features; cytosolic localization is the expected and consistent assignment. Reason: Consistent with the soluble enzyme class and TreeGrafter/PANTHER family inference; bacterial PEPC has no localization signals and acts in the cytoplasm. |
| GO:0006099 tricarboxylic acid cycle | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: PEPC is an anaplerotic enzyme that replenishes oxaloacetate feeding the TCA cycle, but it is not itself a reaction of the TCA cycle. The PEP->OAA carboxylation is an anaplerotic/CO2-fixation step at the PEP-pyruvate-OAA node, not a cyclic TCA reaction. This InterPro2GO inference over-states the role. Reason: PEPC supports TCA cycle function anaplerotically but does not participate in the cycle's reactions; the more precise process annotations (oxaloacetate metabolic process, carbon fixation) better capture the actual role. |
| GO:0006107 oxaloacetate metabolic process | IEA GO_REF:0000104 | ACCEPT | Summary: PEPC directly produces oxaloacetate from PEP, so participation in the oxaloacetate metabolic process is well supported and captures the core anaplerotic role. Reason: The catalytic product is oxaloacetate; this is a direct and accurate process annotation for an anaplerotic PEPC. |
| GO:0008964 phosphoenolpyruvate carboxylase activity | IEA GO_REF:0000120 | ACCEPT | Summary: This is the defining molecular function of the gene product (EC 4.1.1.31, RHEA:28370). Supported by the HAMAP rule, conserved active-site residues (His137, His542 region), and PEPCase type 1 family membership. Reason: Core catalytic activity of PEPC; carboxylation of PEP with bicarbonate to yield oxaloacetate and phosphate. Represents the primary function of the gene. Supporting Evidence: file:PSEPK/ppc/ppc-deep-research-falcon.md PEPC catalyzes PEP + HCO3- -> oxaloacetate + Pi, an essentially irreversible anaplerotic carboxylation at the PEP-pyruvate-oxaloacetate node (deep research; ppc-deep-research-falcon.md). |
| GO:0015977 carbon fixation | IEA GO_REF:0000120 | MODIFY | Summary: PEPC incorporates bicarbonate into oxaloacetate during heterotrophic anaplerosis, but GO:0015977 denotes carbon-fixation pathways rather than this individual replenishing reaction. Reason: Replace the autotrophic carbon-fixation process term with GO:0006107 oxaloacetate metabolic process. Ppc directly produces oxaloacetate for central metabolism, whereas its bicarbonate incorporation does not by itself establish a carbon-fixation pathway. Proposed replacements: oxaloacetate metabolic process Supporting Evidence: file:PSEPK/ppc/ppc-uniprot.txt Forms oxaloacetate, a four-carbon dicarboxylic acid source |
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Download this section (compressed HTML)Q: Has the allosteric regulation of P. putida KT2440 Ppc (e.g., activation by acetyl-CoA/fructose-1,6-bisphosphate, inhibition by aspartate/malate) been measured directly, or is it inferred from E. coli/C. glutamicum homologs?
Experiment: Determine kinetic parameters (Km for PEP and bicarbonate, kcat) and Mg2+ dependence of purified KT2440 Ppc, and test the effect of candidate effectors (acetyl-CoA, fructose-1,6-bisphosphate, aspartate, malate).
Experiment: Characterize a ppc deletion/overexpression strain for growth phenotypes and 13C-fluxomics of anaplerotic OAA supply on different carbon sources.
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