Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5’-Phosphate Production in E. coli
Fig 2
Proposed novel pathway for promiscuous production of pyridoxal 5’-phosphate.
GEM-PROPER was used to predict the indirect target-replacer pair, ∆pdxB/thiG, which we then confirmed with experiments. The predicted secondary function of thiG is pyridoxal 5’-phosphate synthase (P5PS), which would bypass the known 6-enzymatic-step pathway for production of p5p in E. coli. (a) The two alternative pathways, along with known promiscuous pathways in E. coli for producing p5p after pdxB knockout (as reported in Kim: [8]). Abbreviations are: ru5p-D = D-Ribulose 5-phosphate; gln-L = L-glutamine; g3p = Glyceraldehyde 3-phosphate; glu-L = L-glutamate; Pi = Phosphate. (b) Structural alignment of a homology model of thiG (for E. coli, based on crystal structure of thiG from B. subtilis) with a crystal structure of B. subtilis pdxS, the gene that (in complex with another gene, pdxT) performs the P5PS function in B. subtilis. The proteins share the TIM barrel fold. (c) Close-up of the structural alignment in (b), focused on the active site of pdxS and the residues of thiG that we propose perform the pdxS function. The location of the close-up is shown with a box in (b).