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Fructose‐1‐phosphate (F1P) is the preferred effector of the catabolite repressor/activator (Cra) protein of the soil bacterium  Pseudomonas putida  but its ability to bind other metabolic intermediates  in vivo  is unclear. The Cra protein of this microorganism (Cra PP ) was submitted to mobility shift assays with target DNA sequences (the  P fruB   promoter) and candidate effectors fructose‐1,6‐bisphosphate (FBP), glucose 6‐phosphate (G6P), and fructose‐6‐phosphate (F6P). 1 mM F1P was sufficient to release most of the Cra protein from its operators but more than 10 mM of FBP or G6P was required to free the same complex. However, isothermal titration microcalorimetry failed to expose any specific interaction between Cra PP  and FBP or G6P. To solve this paradox, transcriptional activity of a  P fruB ‐lacZ  fusion was measured in wild‐type and Δ fruB  cells growing on substrates that change the intracellular concentrations of F1P and FBP. The data indicated that  P fruB   activity was stimulated by fructose but not by glucose or succinate. This suggested that Cra PP  represses expression  in vivo  of the cognate  fruBKA  operon in a fashion dependent just on F1P, ruling out any other physiological effector. Molecular docking and dynamic simulations of the Cra‐agonist interaction indicated that both metabolites can bind the repressor, but the breach in the relative affinity of Cra PP  for F1P  vs  FBP is three orders of magnitude larger than the equivalent distance in the  Escherichia coli  protein. This assigns the Cra protein of  P. putida  the sole role of transducing the presence of fructose in the medium into a variety of direct and indirect physiological responses.

Fructose 1‐phosphate is the one and only physiological effector of the Cra (FruR) regulator of Pseudomonas putida