Mechanism of Coordinated Gating and Signal Transduction in Purine Biosynthetic Enzyme Formylglycinamidine Synthetase

Enzymes that harbor transient tunnels have a complex interplay of allostery that links their assembly/disassembly with the catalytic cycle. Here, by employing PurL, a purine biosynthetic enzyme, as a model system, we decipher the mechanism of catalytic coupling, precise orchestration of signal transduction, associated conformational changes, and their link with formation of the transient ammonia tunnel. We show that ammonia passage in PurL is controlled by two gates "mouth-gate" and "end-gate", with the seed of the allosteric cycle residing at the "end-gate". It was established that substrate entry at the formylglycinamidine ribonucleotide (FGAM) synthetase domain both initiates end-gate opening and triggers conformational changes in the catalytic loop, which then passes the signal to the glutaminase domain. Molecular dynamics simulations indicate that during the catalytic cycle, the transient tunnel vacillates between open and partially closed states, which gives rise to a breathing ammonia channel that likely acts as a selectivity filter, which occludes solvent and provides directionality for ammonia passage. The mouth-gate network observed here was found to be a conserved feature in class 1 amidotransferases, hinting that a common mode of ammonia control exists across these enzymes.