Shikimate pathway to chorismate

Seven-step shikimate pathway that converts phosphoenolpyruvate and D-erythrose 4-phosphate to chorismate in bacteria, fungi, plants and apicomplexan protists. DAHP synthase condenses the two central-carbon precursors and is the main point of feedback control; 3-dehydroquinate synthase, 3-dehydroquinate dehydratase, shikimate dehydrogenase, shikimate kinase and EPSP synthase then build 5-enolpyruvylshikimate 3-phosphate, and chorismate synthase performs a reduced-flavin-dependent elimination to give chorismate. The reaction chain is invariant, but its enzyme architecture differs by lineage: bacteria use separate enzymes (with either type I or type II dehydroquinases), plants fuse dehydroquinase and shikimate dehydrogenase in one polypeptide, and fungi and apicomplexa carry the five central activities on a single pentafunctional AROM polypeptide. In plants the pathway is plastidic; in fungi it is cytosolic. Chorismate is the branch point for phenylalanine, tyrosine, tryptophan, folate, ubiquinone and other aromatic compounds, which are outside this module.

GENERALIZE from YeastPathways ARO-PWY-1 (2026-10). The slug is kept for link stability even though the module is no longer bacterial-only; title, label and taxon context now cover bacteria, fungi, plants and apicomplexa. The former four-part bacterial structure was reorganised into three parts: DAHP synthase (enzyme-family variant set), the five central reactions (an architecture variant set: separate enzymes versus the pentafunctional AROM), and chorismate synthase. Steps are linked with PRECEDES. The separate-enzyme variant now has a type I versus type II dehydroquinase variant set; the plant bifunctional DHQ-SDH (Q9SQT8) is listed under both the type I dehydroquinase and shikimate dehydrogenase annotons. YeastCyc check: the seven reactions and the ARO3/ARO4, ARO1 and ARO2 assignments are all correct; no enzymes are missing. Compartment: every activity is cytosolic in both yeast GO-CAMs; in plants the pathway is plastidic, so the module asserts no compartment. GO-CAM disagreements: the PomBase model types aro7 chorismate mutase as part_of GO:0009423 (chorismate biosynthesis); chorismate mutase consumes chorismate and is modelled in phenylalanine_tyrosine_biosynthesis. PomBase names SPAP8A3.07c aro3 and SPAC24H6.10c aro4, whereas UniProt gives the gene name aro4 to SPAP8A3.07c; this module follows PomBase. The YeastPathways model has no causal or input/output links between activities. Pseudomonas putida KT2440 exemplars are kept from the earlier bacterial version. KT2440 has three DAHP synthases in two unrelated families, three type II dehydroquinases, and five PTHR21089 proteins. PP_2608/Q88JP1 (RifI2) is deliberately excluded from the shikimate dehydrogenase annoton (PMID:23142411), although the PTHR21089 family selector does not enforce that exclusion. The PP_2406/PP_2407 and PP_3002/PP_3003 SDH/dehydroquinase pairs have the gene arrangement typical of quinate/shikimate catabolism and are candidate rather than established biosynthetic implementations. AroA/PP_1770 is a fusion; only its EPSP synthase activity belongs here. COMPLETION (2026-11). Scope is CONCRETE: the reaction chain is universal, and every leaf is grounded to reviewed proteins. E. coli K-12 (aroB, aroD, aroE, aroK, aroA) and M. tuberculosis H37Rv (aroG type II DAHP synthase, aroQ type II dehydroquinase) were added beside KT2440 and the yeasts. They are the family-review reference proteins and carry experimental evidence. E. coli AroF/AroG/AroH (PTHR21225) were not added because the yeast ARO3/ARO4 members already ground that family experimentally. All 30 grounded accessions have COMPLETE gene reviews. Family groundings are PTHR21225 and PTHR21337 (DAHP synthase), PTHR43622:SF7 (dehydroquinate synthase), PTHR21272 (type II dehydroquinase), PTHR21089 (shikimate dehydrogenase), the PTHR21087 shikimate kinase subfamilies, PTHR21085 (chorismate synthase) and PTHR21090:SF5 (AROM). The type I dehydroquinase annoton uses family_terms PTHR43699 (standalone AroD; new family review) plus PTHR21089, as in PR #5076. The second covers the plant DHQ-SDH, which PANTHER places only in PTHR21089:SF1. Both representative members also match NCBIfam TIGR01093 (aroD). The discrete EPSP synthase annoton is grounded to NCBIfam TIGR01356 because PTHR21090:SF5 mixes monofunctional AroA with the fungal AROM polypeptides. PTHR21090 itself is reviewed, and its review scopes GO:0003866 to SF5, so the two groundings agree. The five FAMILY_FUNCTION_UNREVIEWED warnings are truthful UNRESOLVED family adjudications (four AROM domain activities on PTHR21090:SF5, and GO:0003855 on PTHR21089). These are domain-architecture properties of individual members (AROM, plant DHQ-SDH) that no PANTHER subfamily separates. The verified PANTHER ids are kept. The PTHR43699 review records a PAINT problem: its root IBD for 3,4-dihydroxybenzoate biosynthesis (GO:0046279) is on the wrong node, and the root carries no chorismate biosynthesis IBD.