Fructose-1,6-bisphosphatase (FBPase) operates at a control point in mammalian gluconeogenesis, being inhibited synergistically by fructose 2,6-bisphosphate (Fru-2,6-P 2 ) and AMP. AMP and Fru-2,6-P 2 bind to allosteric and active sites, respectively, but the mechanism responsible for AMP/Fru-2,6-P 2 synergy is unclear. Demonstrated here for the first time is a global conformational change in porcine FBPase induced by Fru-2,6-P 2 in the absence of AMP. The Fru-2,6-P 2 complex exhibits a subunit pair rotation of 13°from the R-state (compared with the 15°rotation of the T-state AMP complex) with active site loops in the disengaged conformation. A three-state thermodynamic model in which Fru-2,6-P 2 drives a conformational change to a T-like intermediate state can account for AMP/Fru-2,6-P 2 synergism in mammalian FBPases. AMP and Fru-2,6-P 2 are not synergistic inhibitors of the Type I FBPase from Escherichia coli, and consistent with that model, the complex of E. coli FBPase with Fru-2,6-P 2 remains in the R-state with dynamic loops in the engaged conformation. Evidently in porcine FBPase, the actions of AMP at the allosteric site and Fru-2,6-P 2 at the active site displace engaged dynamic loops by distinct mechanisms, resulting in similar quaternary end-states. Conceivably, Type I FBPases from all eukaryotes may undergo similar global conformational changes in response to Fru-2,6-P 2 ligation.