De novo riboflavin biosynthesis and bacterial flavin cofactor activation

Species-neutral bacterial pathway for making the riboflavin ring de novo from GTP and ribulose 5-phosphate and then converting riboflavin to the active flavin cofactors FMN and FAD. The ring pathway has two converging branches: a GTP-derived pyrimidine branch made by GTP cyclohydrolase II, the RibD deaminase/reductase activities, and pyrimidine-intermediate dephosphorylation, and a ribulose-5-phosphate branch made by 3,4-dihydroxy-2-butanone 4-phosphate synthase. These branches converge at lumazine synthase, followed by riboflavin synthase. In bacteria, riboflavin kinase and FMN adenylyltransferase are frequently combined in a bifunctional RibF/RibC-family enzyme, connecting vitamin B2 synthesis to FMN and FAD supply.

The module deliberately separates riboflavin-ring synthesis from general flavoprotein use, FMN-dependent reductases, prenylated-FMN cofactor formation, and cobalamin lower-ligand biosynthesis. Those processes consume or transform flavins but are not required steps in de novo riboflavin formation. The downstream FMN/FAD activation step is included because bacterial RibF-family enzymes often connect riboflavin synthesis directly to active flavin-cofactor supply; animal-only uptake of dietary riboflavin is covered separately by modules/flavin_cofactor_biosynthesis.yaml. Human RFK and FLAD1 are included below only as cross-organism representatives of the shared activation activities, not as members of the bacterial de novo route. In the Pseudomonas putida KT2440 instantiation, OpenScientist flagged ribAB-I and ribAB-II as RibBX-like DHBP synthase candidates with apparently degenerate C-terminal GTP-CHII-fold domains, so this module does not use them as GTP cyclohydrolase II exemplars.