BioMed Research International / 2014 / Article / Fig 11

Research Article

C-Terminal Domain Swapping of SSB Changes the Size of the ssDNA Binding Site

Figure 11

Possible models for explaining why SSBs are with different binding site sizes. Two modeled structures of KpSSB1–142 (blue), StSSB1–142 (pink), and PaSSB1–160 (green) complexed with ssDNA (gold) are shown. For clarity, only one C-terminal domain was shown for each SSB tetramer. By using the electrophoretic mobility shift assay and the protein chimeragenesis, we characterized that the binding site sizes of KpSSB, StSSB, PaSSB, KpSSBnStSSBc, and KpSSBnPaSSBc were 26, 21, 29, 21, and 29 nt per tetramer, respectively. KpSSB, StSSB, and PaSSB are similar proteins whose N-terminal ssDNA-binding domains are almost identical. Thus, the C-terminal domain of SSB may indirectly contribute to ssDNA binding and wrapping and affects the binding site size by the steric hindrance.