The membrane protein Photosystem II subunit S (PsbS) is a pH sensor that plays an essential role in signaling light stress in plants to prevent photo oxidation and generation of detrimental reactive species. PsbS detects thylakoid lumen acidification in excess light conditions via two glutamates facing the lumen, however, its molecular mechanism for activation is elusive. We performed a spectroscopic analysis of wild type Physcomitrella patens PsbS and of mutants in which the active glutamates have been replaced (E69Q, E174Q and E69Q / E174Q). We discovered that E69 exerts allosteric control of PsbS dimerization, while E174 is essential for the secondary structural response to low pH. Based on our results, we propose a molecular pH response mechanism that involves a change in the amphiphatic short helix containing E174 facing the lumen, moving from the aqeuous phase into the hydrophobic membrane phase. This structural mechanism may be a shared motif of protein molecular switches of the light-harvesting family and its elucidation could open new routes for crops engineering to improve photosynthetic production of biomass.