<p>Bacterial carboxyl-terminal processing proteases (CTPs) are essential for protein quality control, signal transduction, and cell adaptation. Typically, activation of CTPs involves substrate binding to the PDZ domain or an adaptor protein. Recent studies of CTPs from various bacterial species have indicated structural diversity in CTP oligomerisation. However, the activation mechanisms and rationale for these different oligomeric forms are not well characterised or understood. Here, we present biophysical analyses of CtpA from <i>Helicobacter pylori</i>, which assembles into a trimer-of-dimer (hexameric) configuration. Hydrogen–deuterium exchange mass spectrometry shows that CtpA transitions between resting and active states independently of substrate binding. Cryo-electron microscopy and crystal structural analysis of CtpA further reveal that only one subunit per dimer is active at a time, driven by asymmetric conformational changes. This asymmetric activation supports a cooperative mechanism in which hexameric subunits synchronise to regulate proteolytic activity. Coordinated inter-subunit interactions and concerted movements of the PDZ domain and motile loop generate three self-compartmentalised catalytic units that enable processive substrate degradation. We also identify intra- and intermolecular interactions that stabilise functional states, allowing adaptor-independent activation. These findings open a new avenue towards understanding the key elements of oligomeric assembly in protease activation.</p>