Figure 7.

Structural model for DnaB helicase in complex with DnaA domains I–II. A, ribbon model of a DnaB hexamer structure (PDB code 6QEL) and the positions of Leu¹⁶⁰ residues exposed on the surface are shown. DnaB regions are colored as shown in Fig. 1. B, docking model of DnaB and DnaA domain I is shown using a ribbon model. The overall structure with only one DnaA domain I molecule was calculated using the Rosetta server and optimized. DnaA is shown in light blue. DnaB is shown in gray, except for the DnaA-bound protomer, which is shown in brown. C, close-up view of the interface between DnaB and DnaA domains I and II. A part of the docking model (A) is enlarged. DnaB Leu¹⁶⁰ and DnaA Phe⁴⁶ (yellow), DnaA Asp¹⁵, Glu¹⁶, and Glu²¹ (red), and DnaB Arg⁶³, Arg⁶⁶, His⁶⁷, Arg¹⁶⁴, and Lys¹⁶⁷ (blue) are shown as stick models. D and E, a possible structure of the DnaA–DnaB–DnaC complex is shown using a space-filling mode. Based on the above and the DnaB–DnaC complex structure (PDB code 6QEM), overall structure of the DnaB–DnaC complex bound to three molecules of DnaA domains I and II (orange) is shown. The DnaB hexamer, which is colored as shown in A, binds six molecules of DnaC (yellow) and three molecules of DnaA domains I and II (orange). An essential DnaG binding site in DnaB, Tyr¹⁰⁵, is also shown.