Bacterial gallate catabolism via 4-oxalomesaconate

A bacterial aromatic-acid catabolic module that opens the gallate ring by extradiol dioxygenation and converts the ring-cleavage product to pyruvate and oxaloacetate. A two-domain type II extradiol gallate dioxygenase cleaves gallate to the keto tautomer of 4-oxalomesaconate (OMA). OMA is then converted to 4-carboxy-4-hydroxy-2-oxoadipate (CHA) by one of two enzyme pairs that are not homologous at the hydration step: a keto-enol tautomerase plus an OMA-enol hydratase of the PIG-L/MshB zinc-hydratase fold, or a 1,3-allylic isomerase that forms (3Z)-2-keto-4-carboxy-3-hexenedioate (KCH) plus a KCH hydratase of the amidohydrolase fold. A metal-dependent class II CHA aldolase of the RraA-like fold finally cleaves CHA to pyruvate and oxaloacetate. An outer-membrane porin encoded with the pathway genes can optionally support substrate entry. Upstream reactions that generate gallate (for example demethylation of syringate-derived 3-O-methylgallate), regulation, and the metabolism of the end products are outside the module boundary.

Taxonomic scope. The ring-cleavage, CHA-forming, and CHA-cleavage chemistry is characterized in two distantly related proteobacterial lineages: the Gammaproteobacterium Pseudomonas putida KT2440 (gal cluster: GalA, GalD, GalB, GalC, optional GalP porin) and the sphingomonads Sphingobium (Sphingomonas paucimobilis) SYK-6 and Novosphingobium KA1 (DesB, LigU, LigJ, LigK). In SYK-6 these enzymes serve gallate formed from syringate as well as the protocatechuate 4,5-cleavage pathway, which joins this module at 4-oxalomesaconate. The dioxygenase (NCBIfam NF009904) and CHA aldolase (PTHR33254:SF16) steps are homologous between lineages; the keto-enol tautomerase (GO:0016862, EC 5.3.2.8) and the C=C-transposing allylic isomerase (GO:0016863, EC 5.3.3.-) are paralogous members of PTHR43709:SF3 with different reaction classes; and the two hydratases belong to unrelated folds (PTHR12993 and PTHR21240), which is why the OMA-to-CHA segment is a variant set. The context taxon is Bacteria because homologs occur beyond Proteobacteria (the Arthrobacter keyseri CHA aldolase PcmE is cited by the LigK study), but every exemplar here is proteobacterial; no non-proteobacterial gallate catabolism of this type is grounded. Escherichia coli K-12, Bacillus subtilis, and eukaryotes are not added: no gallate dioxygenase of this type is characterized in them, and the E. coli YbhH paralog (PTHR43709:SF3) and RraA (PTHR33254:SF29) have no demonstrated role in gallate catabolism. Boundary. 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 gallate and ends at pyruvate plus oxaloacetate. GalR regulation, the GalT inner-membrane transporter candidate, the sphingomonad 3-O-methylgallate routes (DesZ, LigAB, LigM O-demethylation), and metabolism of the terminal products are adjacent context rather than additional core reactions. Grounding. Family terms adopt the PANTHER/NCBIfam groundings proposed for this module in the maintainer grounding batch (PTHR34596, NCBIfam NF009904, PTHR43709, PTHR12993, PTHR33254), each checked against panther.obo, the PANTHER member index, and InterPro (NF009904 matches both GalA Q88JX5 and DesB Q5NTE5). For the isomerase, hydratase and aldolase steps the grounding is narrowed to the subfamily that holds the exemplars (PTHR43709:SF3, PTHR12993:SF29, PTHR33254:SF16), because the family reviews restrict those activities to those subfamilies. That batch also listed the nicotinate-cluster porin NicP (Q88FY7) as a GalP-step representative; it is not adopted because NicP has no role in gallate catabolism. PTHR21240:SF28 for LigJ was added from the LigJ UniProt cross-reference and member index. PANTHER families are broad (chitoporins, PrpF-like isomerases, PIG-L deacetylases, RraA-like aldolases, ACMSD-like amidohydrolases); the module role is carried by the named subfamily members, as recorded in the family reviews. Chaining. Continuity of each route was manually verified against Rhea: RHEA:28927 (gallate to (1E)-4-oxobut-1-ene-1,2,4-tricarboxylate, the OMA keto form), RHEA:28931 (OMA to its enol, 4-carboxy-2-hydroxy-cis,cis-muconate), RHEA:17401 (enol plus water to CHA), RHEA:58504 (OMA to KCH), RHEA:58508 (KCH plus water to (2S)-CHA), and RHEA:28935 (CHA to pyruvate and oxaloacetate). The derived chaining check is CoA-specific and does not evaluate these intermediates. Ontology. GO:0047443 maps to RHEA:28935 for CHA cleavage but its label names only 4-hydroxy-4-methyl-2-oxoglutarate; a CHA synonym or a CHA-specific child term (proposed in the GalC review) would describe the physiological reaction better.