The DnaA protein binds to a region of the chromosome known as the origin of replication (oriC). In Escherichia coli, oriC contains several nonamer DnaA binding sites (DnaA boxes), some of which bind DnaA strongly and are occupied throughout the cell cycle. DnaA is conserved in bacteria, in agreement with the importance of its function. Based on its modular organization, the DnaA protein can be divided into four domains: the N-terminal domain, a linker of an unknown function, the central highly conserved AAA+-motif-containing ATPase domain and the C-terminal DnaA-box DNA binding domain (DBD).

This entry represents the DNA binding domain (DBD) which is entirely alpha-helical and binds its cognate DNA through sequence-specific interactions with bases spanning 9 bp and through non-specific interactions with the phosphodiester backbone. The DnaA DBD resembles several transcription factors in its protein fold and interaction with DNA, for example, the Trp repressor TrpR.

PMID:21620858