pcaG notes

2026-03-20

Identity check: UniProt Q88E13 is pcaG / PP_4655 in Pseudomonas putida KT2440 and is annotated as the protocatechuate 3,4-dioxygenase alpha chain. The classical Pseudomonas putida cloning paper states that the cloned fragment contained pcaH and pcaG, "corresponding to the beta and alpha subunits, respectively, of 3,4-PCD" PMID:8407791.
Complex architecture: P. putida protocatechuate 3,4-dioxygenase is an alpha4beta4 enzyme with one ferric iron per alpha beta catalytic unit PMID:6273403.
KT2440-specific evidence: the 2018 KT2440 biosensor paper explicitly deleted pcaH/pcaG and describes them as the two-subunit protocatechuate 3,4-dioxygenase PMID:29765865. In that study, WT KT2440 metabolized PCA further through the beta-ketoadipate pathway whereas the pcaHG deletion strain accumulated PCA [PMID:29765865 "native (in which PCA is metabolized via the β-ketoadipate pathway)" ].
Key curation point: the seeded GOA iron-binding terms appear wrong for pcaG specifically. Structural work places the Fe3+ ligands on beta-subunit residues: "Tyr447 (147beta) and His462 (162beta), and equatorial ligands, Tyr408 (108beta), His460 (160beta)" PMID:9485360. A separate structure paper shows the alpha subunit contributes Tyr16 to the active-site environment after substrate binding: "Tyr447 is stabilized by hydrogen bonding to Tyr16 (16alpha) and Asp413 (113beta)" PMID:9254600.
Interpretation: keep the specific dioxygenase activity term for pcaG, but treat it as a complex-mediated activity of the alpha chain rather than evidence that the alpha monomer independently binds ferric iron.
Pathway context: pca genes are part of the central aromatic-catabolic branch. The Crc/BenR paper describes "the cat and pca genes of the central catechol and beta-ketoadipate pathways" PMID:18156252.
Conserved ortho-cleavage chemistry is also supported by a homologous Pseudomonas system: in strain HR199, pcaG/pcaH encode protocatechuate 3,4-dioxygenase homologs and "vanillin is degraded through the ortho-cleavage pathway" PMID:10049847 PMID:10049847.
Deep research was generated locally as genes/PSEPK/pcaG/pcaG-deep-research-openai.md; useful for orientation, but the YAML should rely mainly on the primary papers above.