The loop domains of the E. coli β sliding clamp are required for Hda-dependent inactivation of DnaA

Failure to negatively regulate the activity of the bacterial DnaA initiator protein leads to overinitiation. The resultant elevated number of closely spaced replication forks increases the likelihood of lethal double strand DNA breaks when these forks encounter single stranded DNA gaps formed as an intermediate during excision repair. The principal mechanism underlying the regulation of DnaA relies on the ability of the Hda-β sliding clamp complex to stimulate DnaA’s intrinsic ATPase activity to convert active DnaA-ATP into less active DnaA-ADP. Although an x-ray crystal structure of the Hda-β clamp complex was described (PDB: 5X06), it represents an inactive conformation. Using genetic and biochemical approaches, we identified two loop domains of the β clamp required for Hda function, but the enigma is that these loops do not interact with Hda in the crystal structure. Their possible roles in supporting Hda function are discussed.