Structural and Functional Insights into Alkaline-pH Sensing by the Alka Channel

The ability to detect environmental pH is essential for survival. In Drosophila melanogaster , the taste receptor Alka mediates alkaline food sensing, but the structural and functional mechanisms of Alka-mediated high-pH sensation have remained unclear. Here, we report the cryo-electron microscopy structure of Alka at near-atomic resolution. Alka assembles into a homopentamer and undergoes conformational changes between neutral and alkaline pH conditions. At nearly neutral conditions, a lysine residue (K229) in the channel activation domain forms a stabilizing salt bridge, maintaining the channel in a closed state. Under alkaline conditions, deprotonation of the K229 side chain disrupts this interaction, resulting in channel opening. Functional studies in heterologous cells and intact flies show that mutation of K229 significantly impairs alkaline pH-dependent Alka activation, demonstrating its essential role in pH sensing. Our findings uncover a previously unrecognized structural mechanism underlying alkaline pH detection and identify a lysine residue as a molecular switch for alkaline pH-mediated channel gating. Moreover, our work establishes hydroxide ions as a distinct class of ion channel ligands and reveals a molecular innovation of chemosensory receptors by which animals broaden their range of chemical senses to detect and avoid strongly alkaline environments.