Catechol ortho-cleavage branch of the beta-ketoadipate pathway

A reusable bacterial aromatic-catabolism module for the catechol ortho-cleavage branch of the beta-ketoadipate pathway, which converts catechol to beta-ketoadipate enol-lactone in three cytoplasmic steps. A CatA-type Fe(III) intradiol catechol 1,2-dioxygenase first cleaves catechol between its hydroxylated carbons to cis,cis-muconate; a CatB-type muconate cycloisomerase of the enolase superfamily then forms (4S)-muconolactone; and a CatC-type muconolactone Delta-isomerase produces the enol-lactone. The same three-enzyme chain is found in Proteobacteria, as in Pseudomonas putida KT2440 (which carries two CatA paralogs) and Acinetobacter baylyi ADP1, and in Actinobacteria, as in Rhodococcus opacus 1CP, whose CatA and CatB come from lineages distinct from the proteobacterial enzymes. The module starts at catechol, the product of upper pathways such as benzoate dioxygenation, and stops before the enol-lactone hydrolase, CoA-transferase and thiolase steps that the catechol branch shares with the protocatechuate branch.

Scope: generalised from a first-pass P. putida KT2440 (PSEPK) instance to a Bacteria-wide module, because the same CatA -> CatB -> CatC chain is experimentally established in gammaproteobacteria (KT2440, A. baylyi ADP1) and in the actinobacterium R. opacus 1CP. KT2440 remains one exemplar; ADP1 and 1CP were added because each has direct structural, biochemical or genetic evidence for all three steps. Scope stays CONCRETE since every step is grounded to reviewed proteins. Fungal catechol branches are not modelled: some fungal intradiol dioxygenases fall in PANTHER PTHR33711, but the fungal cycloisomerase and isomerase steps were not reviewed. Family grounding uses NCBIfam models rather than PANTHER: CatA is split into proteobacterial (TIGR02439) and actinobacterial (TIGR02438) families, both inside the broader PANTHER PTHR33711:SF7; TIGR02534 covers muconate cycloisomerases that PANTHER divides between PTHR48073 (Proteobacteria) and PTHR48080 (Actinobacteria), each a heterogeneous enolase-superfamily family; TIGR03221 covers CatC, which has no PANTHER family. The KEGG ppu00361 bucket that seeded the PSEPK instance lacks CatC (a map-partitioning artefact) and over-broadly frames the branch as chlorinated-aromatic degradation; chlorocatechol modified ortho-cleavage is a separate neighbouring module. Downstream enol-lactone hydrolase, CoA-transferase and thiolase steps are shared lower beta-ketoadipate chemistry, modelled separately.