id: MODULE:bacterial_gallate_catabolism title: Bacterial gallate catabolism by the GalA-D-B-C route description: >- A reusable bacterial module for oxidative cleavage of gallate and conversion of the ring-opened product to pyruvate and oxaloacetate. An optional outer-membrane porin can facilitate substrate entry. GalA then cleaves the aromatic ring to the keto tautomer of 4-oxalomesaconate, GalD supplies the enol tautomer used by GalB, GalB hydrates that intermediate to 4-carboxy-4-hydroxy-2-oxoadipate, and GalC performs the terminal aldol cleavage. Regulation and downstream central metabolism are outside the module boundary. status: DRAFT scope: CONCRETE evidence: - source_id: PMID:16030014 title: Molecular characterization of the gallate dioxygenase from Pseudomonas putida KT2440. The prototype of a new subgroup of extradiol dioxygenases. statement: >- Biochemical characterization establishes the Fe(II)-dependent GalA gallate ring-cleavage reaction that initiates the pathway. - source_id: PMID:21219457 title: 'Unravelling the gallic acid degradation pathway in bacteria: the gal cluster from Pseudomonas putida' statement: >- Genetic and biochemical analysis establishes the GalA, GalD, GalB, and GalC sequence and connects the terminal products to central metabolism; homologous gal clusters outside Pseudomonas support a bacterial rather than KT2440-only scope. notes: >- GalP is optional because its porin activity and outer-membrane location are supported, but direct gallate specificity and pathway essentiality are not. The module begins chemically at extracellular or periplasm-accessible gallate and ends at pyruvate plus oxaloacetate. GalR regulation, the GalT inner-membrane transporter candidate, and metabolism of the terminal products are adjacent context rather than additional core reactions. Continuity of the GalA-D-B-C chain was manually verified against RHEA:28927, RHEA:28931, RHEA:17401, and RHEA:28935; the current derived chaining check is CoA-specific and does not evaluate these non-CoA intermediates. module: id: bacterial_gallate_catabolism label: Bacterial gallate catabolism by the GalA-D-B-C route module_type: METABOLIC_PATHWAY concepts: - preferred_term: gallate catabolic process term: id: GO:0019396 label: gallate catabolic process description: Oxidative ring cleavage and conversion of gallate to central-metabolic products. context: taxa: - preferred_term: bacteria term: id: NCBITaxon:2 label: Bacteria parts: - order: 1 role: optional outer-membrane substrate entry optional: true node: id: gallate_outer_membrane_entry label: GalP-associated outer-membrane entry module_type: TRANSPORT_STEP annotons: - id: galp_outer_membrane_porin label: Gallate-cluster outer-membrane porin participant: selector_type: FAMILY required_function: preferred_term: porin activity term: id: GO:0015288 label: porin activity family: preferred_term: experimentally supported gallate-cluster GalP ortholog family description: >- Porin activity alone is not family-specific; the verified Q88JX6 exemplar anchors this selector to the gallate-cluster GalP lineage. representative_members: - preferred_term: PSEPK GalP term: id: UniProtKB:Q88JX6 label: Porin-like protein GalP function: preferred_term: porin activity term: id: GO:0015288 label: porin activity processes: - preferred_term: transmembrane transport term: id: GO:0055085 label: transmembrane transport locations: - preferred_term: cell outer membrane term: id: GO:0009279 label: cell outer membrane role_description: >- Provides a porin route associated with gallate utilization. The transported substrate is deliberately not asserted as gallate. - order: 2 role: gallate ring cleavage node: id: gallate_dioxygenation label: GalA gallate ring cleavage module_type: REACTION annotons: - id: gala_gallate_dioxygenase label: Gallate dioxygenase participant: selector_type: FAMILY required_function: preferred_term: gallate dioxygenase activity term: id: GO:0036238 label: gallate dioxygenase activity family: preferred_term: experimentally supported GalA gallate dioxygenase family representative_members: - preferred_term: PSEPK GalA term: id: UniProtKB:Q88JX5 label: Gallate dioxygenase function: preferred_term: gallate dioxygenase activity term: id: GO:0036238 label: gallate dioxygenase activity substrates: - preferred_term: gallate - preferred_term: molecular oxygen products: - preferred_term: 4-oxalomesaconate keto tautomer evidence: - source_id: RHEA:28927 statement: >- Gallate and molecular oxygen are converted to the keto tautomer of 4-oxalomesaconate and protons. processes: - preferred_term: gallate catabolic process term: id: GO:0019396 label: gallate catabolic process role_description: Fe(II)-dependent extradiol cleavage opens the gallate ring. - order: 3 role: ring-cleavage product tautomerization node: id: oxalomesaconate_tautomerization label: GalD oxalomesaconate tautomerization module_type: REACTION annotons: - id: gald_oxalomesaconate_tautomerase label: 4-oxalomesaconate tautomerase participant: selector_type: FAMILY required_function: preferred_term: intramolecular oxidoreductase activity, transposing C=C bonds term: id: GO:0016863 label: intramolecular oxidoreductase activity, transposing C=C bonds family: preferred_term: experimentally supported GalD 4-oxalomesaconate tautomerase family description: >- GO:0016863 is broad; the verified Q88JY0 exemplar anchors this selector to the GalD 4-oxalomesaconate-tautomerase lineage. representative_members: - preferred_term: PSEPK GalD term: id: UniProtKB:Q88JY0 label: 4-oxalomesaconate tautomerase function: preferred_term: 4-oxalomesaconate tautomerization term: id: GO:0016863 label: intramolecular oxidoreductase activity, transposing C=C bonds substrates: - preferred_term: 4-oxalomesaconate keto tautomer products: - preferred_term: 4-oxalomesaconate enol tautomer evidence: - source_id: RHEA:28931 statement: >- Reversible tautomerization between keto and enol forms of 4-oxalomesaconate. processes: - preferred_term: gallate catabolic process term: id: GO:0019396 label: gallate catabolic process role_description: Supplies the enol tautomer accepted by GalB. - order: 4 role: oxalomesaconate hydration node: id: oxalomesaconate_hydration label: GalB oxalomesaconate hydration module_type: REACTION annotons: - id: galb_oxalomesaconate_hydratase label: 4-oxalomesaconate hydratase participant: selector_type: FAMILY required_function: preferred_term: 4-oxalmesaconate hydratase activity term: id: GO:0047584 label: 4-oxalmesaconate hydratase activity family: preferred_term: experimentally supported GalB 4-oxalomesaconate hydratase family representative_members: - preferred_term: PSEPK GalB term: id: UniProtKB:Q88JX8 label: 4-oxalmesaconate hydratase function: preferred_term: 4-oxalmesaconate hydratase activity term: id: GO:0047584 label: 4-oxalmesaconate hydratase activity substrates: - preferred_term: 4-oxalomesaconate enol tautomer - preferred_term: water products: - preferred_term: 4-carboxy-4-hydroxy-2-oxoadipate evidence: - source_id: RHEA:17401 statement: >- Reversible hydration of the enol form of 4-oxalomesaconate to CHA. processes: - preferred_term: gallate catabolic process term: id: GO:0019396 label: gallate catabolic process role_description: Hydrates the GalD-generated enol intermediate to CHA. - order: 5 role: terminal carbon-carbon cleavage node: id: cha_aldol_cleavage label: GalC terminal aldol cleavage module_type: REACTION annotons: - id: galc_cha_aldolase label: 4-carboxy-4-hydroxy-2-oxoadipate aldolase participant: selector_type: FAMILY required_function: preferred_term: 4-hydroxy-4-methyl-2-oxoglutarate aldolase activity term: id: GO:0047443 label: 4-hydroxy-4-methyl-2-oxoglutarate aldolase activity family: preferred_term: experimentally supported GalC CHA aldolase family representative_members: - preferred_term: PSEPK GalC term: id: UniProtKB:Q88JX9 label: 4-carboxy-4-hydroxy-2-oxoadipic acid aldolase function: preferred_term: 4-carboxy-4-hydroxy-2-oxoadipate aldol cleavage term: id: GO:0047443 label: 4-hydroxy-4-methyl-2-oxoglutarate aldolase activity substrates: - preferred_term: 4-carboxy-4-hydroxy-2-oxoadipate products: - preferred_term: pyruvate - preferred_term: oxaloacetate evidence: - source_id: RHEA:28935 statement: >- Reversible cleavage of CHA to pyruvate and oxaloacetate. processes: - preferred_term: gallate catabolic process term: id: GO:0019396 label: gallate catabolic process role_description: >- Cleaves CHA into pyruvate and oxaloacetate. GO:0047443 is the current EC-mapped term but does not name the physiological CHA substrate explicitly. connections: - source: gallate_outer_membrane_entry target: gallate_dioxygenation connection_type: PROVIDES_INPUT_FOR description: GalP-associated uptake can improve access of gallate-pathway substrate to the catalytic route. - source: gallate_dioxygenation target: oxalomesaconate_tautomerization connection_type: PROVIDES_INPUT_FOR description: GalA produces the keto tautomer processed by GalD. - source: oxalomesaconate_tautomerization target: oxalomesaconate_hydration connection_type: PROVIDES_INPUT_FOR description: GalD produces the enol tautomer used by GalB. - source: oxalomesaconate_hydration target: cha_aldol_cleavage connection_type: PROVIDES_INPUT_FOR description: GalB produces CHA for terminal GalC cleavage. knowledge_gaps: - gap_statement: >- The substrate specificity and pathway requirement of the GalP-associated outer-membrane porin are not established directly. boundary: >- GalP is retained only as an optional entry step; gallate-specific transport and the required inner-membrane uptake step are not asserted. gap_kind: - BIOLOGY - CURATION status: OPEN resolution: >- Direct GalP uptake/selectivity assays plus identification and testing of the inner-membrane gallate transporter would resolve the transport boundary. provenance: - reference_id: file:PSEPK/galP/galP-uniprot.txt supporting_text: Probable transporter, possibly involved in the gallate reference_section_type: RESULTS - gap_statement: >- GO:0047443 already maps to RHEA:28935 for CHA cleavage, but its label names only 4-hydroxy-4-methyl-2-oxoglutarate rather than the characterized physiological CHA substrate. boundary: >- The reaction is represented through RHEA:28935; the remaining gap is whether GO should add a CHA synonym or a narrower CHA-specific term. gap_kind: - ONTOLOGY status: OPEN resolution: >- GO molecular-function editors should determine whether GO:0047443 needs a CHA synonym or whether the physiological reaction warrants a narrower CHA-specific child term. provenance: - reference_id: file:PSEPK/galC/galC-ai-review.yaml supporting_text: >- Should GO represent GalC with a CHA-specific aldolase molecular-function term distinct from the current EC-name term? reference_section_type: RESULTS proposed_terms: - proposed_name: 4-carboxy-4-hydroxy-2-oxoadipate aldolase activity proposed_definition: >- Catalysis of the cleavage of 4-carboxy-4-hydroxy-2-oxoadipate to pyruvate and oxaloacetate. justification: >- GalC has a characterized physiological CHA cleavage reaction, while the current EC-mapped GO term label names only the HMG substrate. proposed_parent: id: GO:0016833 label: oxo-acid-lyase activity supported_by: - reference_id: PMID:21219457 supporting_text: >- galC encodes the aldolase catalysing CHA cleavage to pyruvic and oxaloacetic acids