HipA is a bacterial serine/threonine protein kinase that phosphorylates targets, bringing about persistence and multidrug tolerance. Autophosphorylation of residue Ser150 is a critical regulatory mechanism of HipA function. Intriguingly, Ser150 is not located on the activation loop, as are other kinases; instead, it is in the protein core, where it forms part of the ATP-binding " P loop motif." How this buried residue is phosphorylated and regulates kinase activity is unclear. Here, we report multiple structures that reveal the P loop motif's exhibition of a remarkable " in-out" conformational equilibrium, which allows access to Ser150 and its intermolecular autophosphorylation. Phosphorylated Ser150 stabilizes the " out state," which inactivates the kinase by disrupting the ATP-binding pocket. Thus, our data reveal a mechanism of protein kinase regulation that is vital for multidrug tolerance and persistence, as kinase inactivation provides the critical first step in allowing dormant cells to revert to the growth phenotype and to reinfect the host. Bacterial multidrug tolerance (MDT) or persistence is largely responsible for the inability of antibiotics to eradicate infections and is caused by a small subpopulation of dormant cells called persisters. How reversion to a growth phenotype occurs is unknown. Schumacher and colleagues show that the key Escherichia coli persistence factor HipA, a protein kinase, undergoes a dramatic ejection of its catalytic P loop, thereby allowing its trans-autophosphorylation, which deactivates HipA. Such inactivation is a crucial early step in phenotypic reversion and MDT.