Aerobic phenylacetate catabolism

Representative members are given for two experimentally anchored bacterial lineages: Escherichia coli K-12, whose paa enzymes were purified and assayed (the PaaABCE oxygenase, PaaZ, PaaH and the PaaFG complex were characterized directly in E. coli, while the reconstitution study also used Pseudomonas sp. strain Y2 PaaABCE, PaaG, PaaJ and PaaF), and Pseudomonas putida KT2440, whose contiguous paa locus encodes orthologs of every step. Neither list is a species restriction. The route is bacterial (about 16% of sequenced bacteria, plus some Halobacteria by horizontal transfer) and has no eukaryotic counterpart, so no yeast or human members are given; the crotonase, 3-hydroxyacyl-CoA dehydrogenase and thiolase families that supply PaaF, PaaG, PaaH and PaaJ also contain eukaryotic fatty-acid beta-oxidation enzymes, but those homologs do not perform these steps. Family selectors use the most Paa-specific classification available. PANTHER 19.0 subfamilies named for the Paa protein itself are used for PaaK (PTHR43439:SF1), PaaA (PTHR30458:SF2), PaaC (PTHR30458:SF0) and PaaE (PTHR47354:SF8), and PTHR43111:SF1 for PaaZ, whose family review scopes both PaaZ activities to it. Where the PANTHER subfamily is broader than the role, the paa-specific NCBIfam model is used instead: PaaB has no PANTHER family (TIGR02157); PaaG's PTHR43459:SF1 also holds uncharacterized hydratase-like proteins (TIGR02280); PaaH's PTHR48075:SF5 is substrate-mixed and named for 3-hydroxybutyryl-CoA dehydrogenase, an activity the PaaH reviews reject (TIGR02279); and PaaF's PTHR11941:SF54 also holds mitochondrial ECHS1 and E. coli CaiD and ScpB (NF007239). The four NCBIfam labels are the entry names returned by the InterPro API (https://www.ebi.ac.uk/interpro/api/entry/ncbifam/<accession>), checked on 2026-11-02. Two exemplar placements disagree between PANTHER's 19.0 classification files and UniProt/InterPro: E. coli PaaG (PTHR11941:SF133 versus PTHR43459:SF1) and E. coli PaaJ (PTHR43853:SF2 versus PTHR18919:SF12). The tie-break rule is to keep the subfamily that holds both exemplars, so P. putida and E. coli PaaG are recorded in PTHR43459:SF1 and both PaaJ proteins in PTHR43853:SF2; both decisions are rows in interpro/panther/panther-members-overrides.tsv, and the conflicts are recorded in the family reviews. GO has no substrate-specific activity terms for the PaaG epoxide-oxepin isomerase (EC 5.3.3.18), the PaaZ oxepin-CoA hydrolase (EC 3.3.2.12) or the PaaZ semialdehyde dehydrogenase (EC 1.2.1.91), so those leaves use the closest EC-class parents (GO:0016863, GO:0016803 and GO:0033721). PaaD is a pathway-associated accessory protein but is not required by the minimal PaaABCE catalytic assembly in vitro; its proposed metallocenter maturation or assembly role remains unresolved and is not counted for module satisfiability. A stable PaaFG complex is known from E. coli, but obligate complex formation is not established across taxa, so PaaF and PaaG remain separate reaction annotons rather than a required complex selector. PaaI and PaaY thioesterases are pathway-associated proofreading or detoxification proteins, and PaaX is a regulator; none is a required reaction in this core linear module. Broad organism-level pathway maps are useful for candidate discovery, but the module boundary is the paa-specific phenylacetyl-CoA route.

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