pchB encodes isochorismate pyruvate lyase (IPL), a small (101 aa) cytoplasmic enzyme with the AroQ-class chorismate-mutase fold that forms an intertwined homodimer with two active sites. It catalyses the cofactor-independent elimination of pyruvate from isochorismate to give salicylate, by a pericyclic mechanism with hydrogen transfer from C2 to C9. Acting after the isochorismate synthase PchA, encoded by the downstream gene of the iron-repressed pchBA operon, PchB supplies the salicylate that the pyochelin synthetases incorporate into the siderophore pyochelin. Owing to its fold the enzyme also converts chorismate to prephenate in vitro, a non-physiological side activity with much lower catalytic efficiency.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004106 chorismate mutase activity | EXP PMID:21751784 pH Dependence of catalysis by Pseudomonas aeruginosa isochor... | KEEP AS NON CORE | Summary: UniProt experimental annotation from the pH-dependence study, which measures both lyase and mutase kinetics of PchB and its Lys42 mutants. Reason: The chorismate mutase activity is real and measured, but the paper itself calls it non-physiological and much less efficient than the lyase reaction. It is a side activity inherited from the fold, not the gene's function. Supporting Evidence: PMID:21751784 has non-physiological chorismate mutase activity, albeit with considerably lower catalytic efficiency than for the lyase activity |
| GO:0004106 chorismate mutase activity | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: PAINT IBA from PTN002211012, the AroQ chorismate-mutase family node, seeded by several characterised chorismate mutases and by PchB itself. Reason: The family-level IBD is well founded and PchB does have measurable CM activity, so the row is correct; for PchB the activity is adventitious and not the physiological function. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: PANTHER:PTN002211012 · PTN002211012 SUPPORTS TRANSFER Seeded by M. tuberculosis Rv1885c and Rv0948c, M. jannaschii AroQ, Yersinia PheA2 and P. aeruginosa AroQ, all chorismate mutases. UniProtKB:Q51507 · pchB SUPPORTS TRANSFER The target's own experimental annotation is among the seeds; expected, not circular. Supporting Evidence: PMID:11937513 Chorismate was shown to be converted to prephenate by purified PchB in vitro |
| GO:0004106 chorismate mutase activity | IDA PMID:11937513 Salicylate biosynthesis in Pseudomonas aeruginosa. Purificat... | KEEP AS NON CORE | Summary: PseudoCAP IDA; the purified enzyme converts chorismate to prephenate and complements an E. coli CM mutant. Reason: Directly shown, but a secondary activity with a kcat about 14-fold lower than for the lyase and a much higher Km; the physiological role is IPL. Supporting Evidence: PMID:11937513 Chorismate was shown to be converted to prephenate by purified PchB in vitro, with an apparent K(m) of 150 microm and a kcat of 7.8 min(-1). PMID:11937513 a CM-deficient Escherichia coli mutant, which is auxotrophic for phenylalanine and tyrosine, was functionally complemented by the cloned P. aeruginosa pchB gene |
| GO:0004106 chorismate mutase activity | IDA PMID:19432488 Structure-function analyses of isochorismate-pyruvate lyase ... | KEEP AS NON CORE | Summary: PseudoCAP IDA from the structure-function mutagenesis study, which measures kcat for both reactions. Reason: Directly measured; adventitious relative to the physiological IPL reaction. Supporting Evidence: PMID:19432488 PchB also produces prephenate from chorismate, most likely due to structural homology to the Escherchia coli chorismate mutase. |
| GO:0004106 chorismate mutase activity | IEA GO_REF:0000120 | KEEP AS NON CORE | Summary: Combined IEA from the Rhea/EC chorismate mutase reaction and InterPro family signatures. Reason: Consistent with the experimental rows; real but a non-physiological side activity. Supporting Evidence: PMID:21751784 has non-physiological chorismate mutase activity, albeit with considerably lower catalytic efficiency than for the lyase activity |
| GO:0009697 salicylic acid biosynthetic process | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA from PTN002211012 whose sole seed is this gene's PseudoCAP IDA (PMID:7500944). Correct for PchB; the node placement is too broad for the clade. Reason: For PchB itself the term is right and core (PchB catalyses the last step of salicylate formation). The IBD, however, sits at the AroQ chorismate-mutase family node and propagates salicylate biosynthesis to 16 chorismate mutases (archaeal, mycobacterial, enterobacterial and fungal) that have no isochorismate pyruvate lyase activity. Recorded as a GO_CENTRAL defect. Propagation Review Root cause: PROPAGATION BAD Failure modes: FUNCTIONAL DIVERGENCE Sources checked: PANTHER:PTN002211012 · PTN002211012 SUPPORTS SOURCE BUT NOT TARGET QuickGO (2026-10-28) lists 17 GO:0009697 IBA leaves, the same set that receives the chorismate mutase IBA, including M. jannaschii AroQ (Q57696), M. tuberculosis Rv1885c (P9WIB9) and Rv0948c (P9WIC1), P. aeruginosa AroQ (Q9HU05), Yersinia PheA2 (Q7CHH5), Xanthomonas PheA (Q8PCZ3), and secreted CMs of Sclerotinia (A7F9N9) and Puccinia (E3LB91). Correct for PchB, wrong for the other leaves. UniProtKB:Q51507 · pchB SUPPORTS TRANSFER The target's own experimental annotation is the IBD seed; expected, not circular. Supporting Evidence: PMID:7500944 an entB mutant of E. coli blocked in the conversion of isochorismate to 2,3-dihydro-2,3-dihydroxybenzoate formed salicylate when transformed with a pchB expression construct |
| GO:0009697 salicylic acid biosynthetic process | IDA PMID:7500944 Structural genes for salicylate biosynthesis from chorismate... | ACCEPT | Summary: PseudoCAP IDA; sole seed of the GO:0009697 IBD at PTN002211012. The paper shows pchB is required for, and alone sufficient to convert isochorismate into, salicylate. Reason: Expression of pchB alone in an E. coli entB strain (which accumulates isochorismate) yields salicylate, and extracts containing PchA and PchB convert chorismate to equimolar salicylate and pyruvate. This is direct evidence that PchB performs a step of salicylate biosynthesis, later confirmed with the purified enzyme (PMID:11937513). Supporting Evidence: PMID:7500944 an entB mutant of E. coli blocked in the conversion of isochorismate to 2,3-dihydro-2,3-dihydroxybenzoate formed salicylate when transformed with a pchB expression construct PMID:7500944 Our results are consistent with a pathway leading from chorismate to isochorismate and then to salicylate plus pyruvate, catalyzed consecutively by the iron-repressible PchA and PchB proteins in P. aeruginosa. |
| GO:0009697 salicylic acid biosynthetic process | IEA GO_REF:0000120 | ACCEPT | Summary: IEA from the IPL InterPro family and the UniPathway salicylate pathway. Reason: Consistent with the experimental evidence; IPR008241 is specific to isochorismate pyruvate lyases. Supporting Evidence: PMID:11937513 In the reaction catalyzed by this enzyme, isochorismate --> salicylate + pyruvate, no cofactors appear to be required. |
| GO:0016835 carbon-oxygen lyase activity | IDA PMID:11937513 Salicylate biosynthesis in Pseudomonas aeruginosa. Purificat... | MODIFY | Summary: PseudoCAP IDA to the generic C-O lyase parent of the measured IPL activity. Reason: Correct but less specific than the evidence; the paper measures isochorismate pyruvate lyase activity (GO:0043904, an is_a descendant that the gene already carries). Proposed replacements: isochorismate pyruvate lyase activity Supporting Evidence: PMID:11937513 At the pH optimum (pH 6.8), the enzyme displayed Michaelis-Menten kinetics, with an apparent K(m) of 12.5 microm for isochorismate and a kcat of 106 min(-1), calculated per monomer. |
| GO:0016835 carbon-oxygen lyase activity | IDA PMID:19432488 Structure-function analyses of isochorismate-pyruvate lyase ... | MODIFY | Summary: PseudoCAP IDA to the generic C-O lyase parent. Reason: Correct but general; the specific activity measured is GO:0043904 isochorismate pyruvate lyase activity. Proposed replacements: isochorismate pyruvate lyase activity Supporting Evidence: PMID:19432488 PchB physiologically produces salicylate and pyruvate from isochorismate for ultimate incorporation of the salicylate into the siderophore pyochelin. |
| GO:0016835 carbon-oxygen lyase activity | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO from IPR008241 Isochorismate_pyruvate-lyase. Reason: Correct but general; the family and the experiments support GO:0043904. Proposed replacements: isochorismate pyruvate lyase activity Supporting Evidence: PMID:11937513 In the reaction catalyzed by this enzyme, isochorismate --> salicylate + pyruvate, no cofactors appear to be required. |
| GO:0042864 pyochelin biosynthetic process | IDA PMID:7500944 Structural genes for salicylate biosynthesis from chorismate... | ACCEPT | Summary: UniProt IDA; PchB makes salicylate, the precursor incorporated into pyochelin. Reason: PchB catalyses the second enzymatic step of the pyochelin pathway (after PchA), producing the salicylate moiety that the pyochelin synthetases activate and incorporate. It does part of the work of the pathway, so this is participation, not mere necessity. GO:0009697 is not part_of GO:0042864, so both process terms are needed. Supporting Evidence: PMID:7500944 Salicylate is a precursor of pyochelin in Pseudomonas aeruginosa PMID:11937513 Isochorismate pyruvate-lyase (IPL), the second enzyme of pyochelin biosynthesis and the product of the pchB gene, was purified to homogeneity from Pseudomonas aeruginosa. |
| GO:0043904 isochorismate pyruvate lyase activity | EXP PMID:11937513 Salicylate biosynthesis in Pseudomonas aeruginosa. Purificat... | ACCEPT | Summary: Purified PchB converts isochorismate to salicylate and pyruvate with Michaelis-Menten kinetics. Reason: Direct enzymology on the purified protein; the core activity. Supporting Evidence: PMID:11937513 In the reaction catalyzed by this enzyme, isochorismate --> salicylate + pyruvate, no cofactors appear to be required. |
| GO:0043904 isochorismate pyruvate lyase activity | EXP PMID:16248620 Isochorismate pyruvate lyase: a pericyclic reaction mechanis... | ACCEPT | Summary: Mechanistic study with C2-deuterated isochorismate. Reason: Direct assay of the IPL reaction (product analysis by NMR and kinetic isotope effect). Supporting Evidence: PMID:16248620 Isochorismate pyruvate lyase (IPL) catalyzes the cleavage of isochorismate to give salicylate and pyruvate, a key step in bacterial siderophore biosynthesis. |
| GO:0043904 isochorismate pyruvate lyase activity | EXP PMID:19432488 Structure-function analyses of isochorismate-pyruvate lyase ... | ACCEPT | Summary: Structure-function mutagenesis with kinetics for wild type and Lys42/Ala43/Ile87 mutants. Reason: Direct kinetic measurements of the IPL reaction. Supporting Evidence: PMID:19432488 The isochorismate-pyruvate lyase from Pseudomonas aeruginosa (PchB) catalyzes two pericyclic reactions in a single active site. |
| GO:0043904 isochorismate pyruvate lyase activity | EXP PMID:21751784 pH Dependence of catalysis by Pseudomonas aeruginosa isochor... | ACCEPT | Summary: pH-dependence of IPL catalysis by wild type and K42H. Reason: Direct kinetic assays; full text cached. Supporting Evidence: PMID:21751784 The physiological function of the isochorismate-pyruvate lyase (PchB) from Pseudomonas aeruginosa is to convert isochorismate to salicylate and pyruvate |
| GO:0043904 isochorismate pyruvate lyase activity | IEA GO_REF:0000120 | ACCEPT | Summary: IEA from the curated Rhea reaction and EC 4.2.99.21. Reason: Consistent with the experimental evidence. Supporting Evidence: PMID:11937513 In the reaction catalyzed by this enzyme, isochorismate --> salicylate + pyruvate, no cofactors appear to be required. |
| GO:0046417 chorismate metabolic process | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: PAINT IBA from the chorismate-mutase family node, seeded by chorismate mutases. Reason: Sound for the family; for PchB the physiological substrate is isochorismate, and chorismate is turned over only by the adventitious mutase activity (which does complement an E. coli CM mutant), so the term is true but peripheral. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: PANTHER:PTN002211012 · PTN002211012 SUPPORTS TRANSFER Seeded by characterised chorismate mutases; PchB is not among the seeds for this term. Supporting Evidence: PMID:11937513 a CM-deficient Escherichia coli mutant, which is auxotrophic for phenylalanine and tyrosine, was functionally complemented by the cloned P. aeruginosa pchB gene |
| GO:0046417 chorismate metabolic process | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro2GO from chorismate-mutase fold signatures. Reason: As for the IBA; true via the side activity, not the physiological role. Supporting Evidence: PMID:21751784 has non-physiological chorismate mutase activity, albeit with considerably lower catalytic efficiency than for the lyase activity |
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Download this section (compressed HTML)Q: Which node in the PANTHER PTHR38041 tree, if any, groups the PchB-type isochorismate pyruvate lyases (P. aeruginosa PchB and its orthologs in other pyochelin or yersiniabactin-independent salicylate producers) apart from the AroQ chorismate mutases, so that the salicylate IBD can be placed there?
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