pchB (Q51507, PA4230) notes

Review session 2026-10-28 (PseudoCAP IBA-seed protocol, worklist rank 66)

No deep-research provider was available; these notes are my own reading of the Swiss-Prot record and the
cached papers. Only PMID:21751784 has full text in the cache; PMID:7500944, 11937513, 16248620 and
19432488 are abstract-only.

Identity

P. aeruginosa PAO1 PA4230, Swiss-Prot Q51507, 101 aa, AroQ-class chorismate-mutase fold
(Pfam PF01817 CM_2; InterPro IPR008241 Isochorismate_pyruvate-lyase; PIRSF029775; PANTHER PTHR38041:SF1).
Intertwined three-helix homodimer; structures 2H9C/2H9D/3HGW/3HGX/3REM/3RET.
First gene of the iron-repressed pchBA operon (salicylate), upstream of the pyochelin NRPS genes.

Literature

Genetics: pchBA are necessary for salicylate formation PMID:7500944. pchB alone converts isochorismate to
salicylate in an E. coli entB background PMID:7500944. Crude-extract reconstitution PMID:7500944. Pathway conclusion PMID:7500944. Salicylate is a pyochelin
precursor PMID:7500944.
Purified enzyme: IPL, no cofactors PMID:11937513; "second enzyme of pyochelin
biosynthesis" PMID:11937513.
Secondary CM activity PMID:11937513 and complementation of an E. coli CM-deficient mutant PMID:11937513.
Mechanism: pericyclic hydrogen transfer PMID:16248620; the two activities are not covariant PMID:19432488.
The CM activity is non-physiological PMID:21751784; the physiological role
is salicylate for pyochelin PMID:21751784.

Annotation decisions

GO:0043904 isochorismate pyruvate lyase activity (EXP x4, IEA): ACCEPT, core MF.
GO:0016835 carbon-oxygen lyase activity (IDA x2, IEA): MODIFY to GO:0043904 (its is_a descendant,
already carried).
GO:0004106 chorismate mutase activity (EXP, IDA x2, IBA, IEA): KEEP_AS_NON_CORE; real in vitro and in
heterologous complementation, but adventitious (kcat/Km much lower than for IPL).
GO:0046417 chorismate metabolic process (IBA, IEA): KEEP_AS_NON_CORE; follows from the adventitious CM
activity; the physiological substrate is isochorismate.
GO:0009697 salicylic acid biosynthetic process (IDA PseudoCAP, IBA, IEA): ACCEPT, core BP. PchB catalyses
the final step (isochorismate -> salicylate + pyruvate).
GO:0042864 pyochelin biosynthetic process (IDA, UniProt): ACCEPT; salicylate is incorporated into
pyochelin and PchB is the second enzyme of the pathway. In GO the two process terms are not linked
(GO:0009697 is not part_of GO:0042864), so both are kept.

The node PTN002211012

QuickGO (2026-10-28) lists 17 leaves with the GO:0009697 IBA from PTN002211012, and the same 17 with the
GO:0004106 chorismate mutase IBA from the same node. They are the AroQ-class chorismate-mutase family as a
whole: Methanocaldococcus jannaschii AroQ (Q57696, the classic MjCM), Halobacterium VNG_1244C (Q9HQB1),
Methanosarcina MA_1377 (Q8TR07), M. tuberculosis Rv1885c (P9WIB9, secreted CM) and Rv0948c (P9WIC1,
intracellular CM), P. aeruginosa AroQ (Q9HU05), Yersinia PheA2 (Q7CHH5), Xanthomonas PheA (Q8PCZ3),
Salmonella STM1269, Coxiella, Geobacter, Streptococcus pneumoniae, Streptomyces SCO2019, and the
secreted CM effectors of the fungi Sclerotinia sclerotiorum (A7F9N9) and Puccinia graminis (E3LB91).
PchB is the only member with IPL activity. The chorismate mutase IBD at this node is well seeded (Mtb,
MjCM, PA AroQ, Yersinia); the salicylate IBD rests on PchB alone and transfers a pathway that the
comparators do not perform (mycobacteria and Yersinia make salicylate with a salicylate synthase,
MbtI/Irp9, not via CM-fold proteins). The node term is right for PchB and wrong for the clade.

PseudoCAP IBA-seed assessment

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale
PTN002211012	GO:0009697 salicylic acid biosynthetic process	1 (sole)	17 (15 taxa)	GO:0009697, IDA, PMID:7500944 (PseudoCAP)	OVER-SPECIFIC	The seed is sound for PchB: pchB alone converts isochorismate to salicylate in an E. coli entB strain, and the purified enzyme is an IPL (PMID:11937513). But the IBD sits at the root of the AroQ chorismate-mutase family, whose other 16 leaves (archaeal, mycobacterial, enterobacterial, fungal CMs) are chorismate mutases with no IPL activity. Withdraw the IBD or move it to a node confined to PchB-type IPLs.