PycB (PP_5346) is the beta subunit of the two-subunit pyruvate carboxylase of Pseudomonas putida KT2440. It carries the pyruvate carboxyltransferase domain and a C-terminal biotin carboxyl carrier domain. After the PycA subunit carboxylates the biotin, PycB transfers the carboxyl group to pyruvate, forming oxaloacetate as an anaplerotic input to the TCA cycle. The same carboxyltransferase architecture occurs in the alpha subunit of sodium-pumping oxaloacetate decarboxylase (OadA, NCBIfam TIGR01108), and PycB has not been assayed directly; the assignment rests on its domain architecture and its operon partner PycA.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003824 catalytic activity | IEA GO_REF:0000002 | MODIFY | Summary: Catalytic activity is an uninformative parent of pyruvate carboxylase activity. Reason: Correct but general: GO:0004736, already on this gene, is the specific descendant supported by the PYR_CT domain behind this row. Proposed replacements: pyruvate carboxylase activity Supporting Evidence: file:PSEPK/pycB/pycB-uniprot.txt DR PROSITE; PS50991; PYR_CT; 1. |
| GO:0004736 pyruvate carboxylase activity | IEA GO_REF:0000120 | ACCEPT | Summary: PycB carries the pyruvate carboxyltransferase step of two-subunit PC. Reason: The carboxyltransferase domain (PYR_CT) plus biotin carrier domain, partnered with the adjacent biotin carboxylase PycA, constitute the beta subunit of a two-subunit pyruvate carboxylase; the carboxyl transfer to pyruvate occurs on PycB. Supporting Evidence: file:PSEPK/pycB/pycB-uniprot.txt DR PROSITE; PS50991; PYR_CT; 1. PMID:24157795 The carboxyltransferase (CT) domain of PC catalyzes the transfer of a carboxyl group from carboxybiotin to the accepting substrate, pyruvate. file:PSEPK/pycB/pycB-deep-research-openscientist.md encodes the Ξ² subunit of a two-subunit, biotin-dependent pyruvate carboxylase in *Pseudomonas putida* KT2440. |
| GO:0005737 cytoplasm | IEA GO_REF:0000118 | ACCEPT | Summary: Soluble cytoplasmic enzyme (TreeGrafter). Reason: Bacterial pyruvate carboxylases are soluble cytoplasmic enzymes; cytoplasm is as precise as the KT2440 evidence allows. Supporting Evidence: file:PSEPK/pycB/pycB-uniprot.txt DR PANTHER; PTHR43778; PYRUVATE CARBOXYLASE; 1. |
| GO:0006094 gluconeogenesis | IEA GO_REF:0000118 | KEEP AS NON CORE | Summary: Gluconeogenesis is a plausible but secondary role of bacterial pyruvate carboxylase. Reason: Pyruvate carboxylase supplies oxaloacetate that PEP carboxykinase can convert to PEP, so a gluconeogenic contribution from C3 substrates is plausible and is physiological for liver and yeast PCs. For KT2440 the demonstrated or expected primary role is anaplerotic oxaloacetate supply, and no gluconeogenic flux through this enzyme has been measured, so the row is kept as non-core. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: PANTHER:PTN001821756 SUPPORTS TRANSFER Seeded by liver and yeast pyruvate carboxylases; the process transfers to bacterial descendants as a secondary role. Supporting Evidence: file:PSEPK/pycB/pycB-uniprot.txt DR PANTHER; PTHR43778; PYRUVATE CARBOXYLASE; 1. |
| GO:0006814 sodium ion transport | IEA GO_REF:0000002 | REMOVE | Summary: Sodium ion transport is the OadA-complex process and does not apply to PycB. Reason: Na+ pumping is done by the membrane OadB subunit of oxaloacetate decarboxylase; the shared OadA carboxyltransferase signature does not make the soluble PC beta subunit a sodium transporter. The positive argument is that PycB is encoded next to PycA, an ATP-grasp biotin carboxylase; oxaloacetate decarboxylase has no biotin carboxylase subunit (it decarboxylates oxaloacetate to carboxylate its own biotin), so a BC partner is incompatible with the OadA reading. Supporting Evidence: file:PSEPK/pycB/pycB-uniprot.txt DR NCBIfam; TIGR01108; oadA; 1. |
| GO:0008948 oxaloacetate decarboxylase activity | IEA GO_REF:0000002 | REMOVE | Summary: Oxaloacetate decarboxylase is the OadA paralog function, not that of PycB. Reason: IPR005776 (OadA) is shared by the carboxyltransferase domains of PC and of the Na+-pumping oxaloacetate decarboxylase alpha subunit. PycB is paired with the biotin carboxylase PycA (the PC architecture), not with OadB/OadG membrane subunits, so the decarboxylase activity is a wrong family-signature mapping. The positive argument is that PycB is encoded next to PycA, an ATP-grasp biotin carboxylase; oxaloacetate decarboxylase has no biotin carboxylase subunit (it decarboxylates oxaloacetate to carboxylate its own biotin), so a BC partner is incompatible with the OadA reading. Supporting Evidence: file:PSEPK/pycB/pycB-uniprot.txt DR NCBIfam; TIGR01108; oadA; 1. PMID:27708276 the PC enzyme is encoded by two separate genes |
| GO:0006107 oxaloacetate metabolic process | IC PMID:24157795 Insights into the carboxyltransferase reaction of pyruvate c... | NEW | Summary: PycB forms oxaloacetate from pyruvate (anaplerosis). Reason: The carboxyltransferase reaction on PycB produces oxaloacetate, so PycB does the work of oxaloacetate formation; GO has no anaplerosis term, and this matches the process used for E. coli Ppc and B. subtilis PycA. Supporting Evidence: PMID:24157795 The carboxyltransferase (CT) domain of PC catalyzes the transfer of a carboxyl group from carboxybiotin to the accepting substrate, pyruvate. |
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Download this section (compressed HTML)Q: Under which carbon sources does KT2440 rely on PycAB rather than PEP carboxylase for anaplerosis?
Experiment: Compare growth of ΞpycB, Ξppc and double mutants of KT2440 on glucose, gluconate and pyruvate, with oxaloacetate-derived amino acid labelling.
Type: mutant growth and 13C labelling
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Download this section (compressed HTML)Curated by Claude (AI-assisted). Rows that quoted DR GO lines or ARBA-only text were
re-supported with family/domain classification (NCBIfam, PIRSF, HAMAP, PROSITE, InterPro) and,
where useful, orthologue literature. Correct-but-general parent terms are MODIFY to the specific
activity already on the gene. Verdicts were aligned with the experimentally anchored E. coli
(aceE, aceF, ppc, pykF, ppsA) and B. subtilis (pycA) reviews. The KT2440 PDH/OGDH E3 is LpdG
(PP_4187), not Lpd (PP_5366, LPD-3). No KT2440-specific enzymology was found for this gene.
- The OadA-derived oxaloacetate decarboxylase and sodium transport IEA rows were removed: shared
carboxyltransferase signature, but PycB partners with the biotin carboxylase PycA.
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