Pentameric ligand-gated ion channels (pLGICs) mediate chemical signaling through a succession of allosteric transitions that are yet not completely understood as intermediate states remain poorly characterized by structural approaches. In a previous study on the prototypic bacterial proton-gated channel GLIC, we generated several fluorescent sensors of the protein conformation that report a fast transition to a pre-active state, which precedes the slower process of activation with pore opening. Here, we explored the phenotype of a series of allosteric mutations, using paralleled steady-state fluorescence and electrophysiological measurements over a broad pH range. Our data, fitted to a 3-states Monod-Wyman-Changeux (MWC) model, show that mutations at the subunit interface in the extracellular domain (ECD) principally alter pre-activation, while mutations in the lower ECD and in the transmembrane domain principally alter activation. We also show that propofol alters both transitions. Data are discussed in the framework of transition pathways generated by normal mode analysis (iModFit) that suggest collective protein motions concerted with pore opening. It further supports that pre-activation involves major quaternary compaction of the ECD, and suggests that activation involves principally a re-organization of a 'central gating region' involving a contraction of the ECD β-sandwich and the tilt of the channel lining M2 helix.