trpF encodes N-(5'-phosphoribosyl)anthranilate isomerase (PRAI, EC 5.3.1.24), a cytoplasmic monomeric TIM-barrel ((beta/alpha)8) enzyme that catalyzes the third step of L-tryptophan biosynthesis from chorismate. It converts N-(5-phospho-beta-D-ribosyl)anthranilate (PRA) into 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate (CdRP) via an Amadori rearrangement that opens the ribose ring. This intermediate is subsequently used by TrpC (indole-3-glycerol-phosphate synthase) and tryptophan synthase (TrpAB) to complete tryptophan biosynthesis. In Pseudomonas putida KT2440 the gene (locus PP_1995) is unlinked to the other trp clusters and is most likely monocistronic; a targeted chromosomal knockout produces a tryptophan auxotroph that is rescued by tryptophan or indole but not by anthranilate, placing the enzyme downstream of anthranilate and upstream of indole as expected for PRAI.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000162 L-tryptophan biosynthetic process | IEA GO_REF:0000120 | ACCEPT | Summary: Correct and core. PRAI catalyzes step 3 of 5 in tryptophan biosynthesis from chorismate, and the KT2440 trpF knockout is a tryptophan auxotroph, directly confirming a required role in this process. Reason: The biological process is supported both by family/pathway assignment (UniPathway UPA00035) and by experimental auxotrophy/complementation evidence in KT2440 (PMID:21261884). |
| GO:0004640 phosphoribosylanthranilate isomerase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Correct core molecular function. This is the precise EC 5.3.1.24 activity (RHEA:21540) defining the TrpF family, consistent with the HAMAP rule, InterPro TrpF family (IPR044643) and PRAI domain (IPR001240), and the conserved TIM-barrel active site. Reason: Directly matches the curated catalytic activity in UniProt and the protein's family/domain assignment; this is the defining function of the gene product. |
| GO:0046394 carboxylic acid biosynthetic process | IEA GO_REF:0000117 | MARK AS OVER ANNOTATED | Summary: Not wrong but uninformative and over-general. Tryptophan is a carboxylic acid, so this high-level ARBA-derived term is technically true but adds nothing beyond the more specific GO:0000162 (L-tryptophan biosynthetic process), which is already annotated. Reason: Generic parent term auto-generated from sequence features; the specific L-tryptophan biosynthetic process annotation already captures the biology precisely. |
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