aroB (PP_5078) encodes 3-dehydroquinate synthase (DHQS; EC 4.2.3.4), a cytoplasmic enzyme that catalyzes the second step of the shikimate pathway. It converts 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) into 3-dehydroquinate (DHQ), the first carbocyclic intermediate of the pathway, with release of inorganic phosphate. Catalysis requires a tightly bound NAD(+) used catalytically (transiently reduced and reoxidized) and a divalent metal cation (Co2+ or Zn2+) per subunit, driving a multi-step cascade of alcohol oxidation, phosphate elimination, carbonyl reduction, ring opening, and intramolecular aldol cyclization within a single active site. The shikimate pathway proceeds through chorismate, the branch-point precursor for the aromatic amino acids (phenylalanine, tyrosine, tryptophan) and other aromatic metabolites such as folate and ubiquinone. The pathway is present in bacteria, fungi, algae, and plants but absent in animals. The protein belongs to the sugar phosphate cyclases superfamily, dehydroquinate synthase family.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003856 3-dehydroquinate synthase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Core molecular function. aroB/PP_5078 is the 3-dehydroquinate synthase of P. putida KT2440 (EC 4.2.3.4, RHEA:21968), supported by UniProt/HAMAP rule MF_00110, conserved domain architecture (TIGR01357 aroB, Pfam PF01761), and KT2440 literature mapping the locus to this activity. |
| GO:0005737 cytoplasm | IEA GO_REF:0000120 | ACCEPT | Summary: DHQS acts on soluble cytosolic metabolites (DAHP, NAD+, divalent cation) and is a soluble intracellular enzyme of central metabolism. Consistent with UniProt subcellular location (cytoplasm) and the general architecture of the bacterial shikimate pathway. No experimental KT2440 localization assay exists, but the inference is well supported. |
| GO:0009073 aromatic amino acid biosynthetic process | IEA GO_REF:0000120 | ACCEPT | Summary: DHQS provides the second step of the shikimate pathway that supplies chorismate, the precursor of phenylalanine, tyrosine, and tryptophan. This biological process annotation is correct and represents a core role of the gene. |
| GO:0009423 chorismate biosynthetic process | IEA GO_REF:0000120 | ACCEPT | Summary: DHQS catalyzes step 2 of 7 in chorismate biosynthesis from D-erythrose 4-phosphate and phosphoenolpyruvate (UniPathway UPA00053). This is the most precise biological-process term for the gene and is well supported. |
| GO:0016838 carbon-oxygen lyase activity, acting on phosphates | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: InterPro2GO-derived MF term that is a more general parent of the specific 3-dehydroquinate synthase activity (GO:0003856) already annotated. DHQS is classified under EC 4.2.3.- (carbon-oxygen lyases acting on phosphates), so the term is not wrong, but it is redundant with and less informative than the specific child term. Reason: The precise activity is already captured by GO:0003856. This broad lyase grouping term adds no information beyond the specific annotation and is a less informative restatement of the same molecular function. |
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