Fig. 4: Role of the Catcher Loop in DNA strand separation.
From: Structural basis for intrinsic strand displacement activity of mitochondrial DNA polymerase
A Interactions of the Catcher loop with downstream DNA and flap subdomain in Structure III. The structure of Mip1 (res 1-998, surface representation) is shown along with a loop connecting a flap (grey) to the C-terminal Domain (invisible in the Cryo-EM density). B A close-up view of Catcher loop interactions with downstream DNA and the flap subdomain in Structure IV (grey). C Conservation of the Catcher loop in yeast species. Conserved residues are highlighted in yellow, while positively charged residues are highlighted in red. Residues targeted in Mip1 mutagenesis are indicated by grey arrows. D Primer extension assay performed using the Catcher loop mutant (Tetra) and a primer-template construct with single or double-stranded downstream DNA, performed at 30 oC (left panel) and room temperature (right panel). E Electrophoretic Mobility Shift Assay (EMSA) using WT Mip1 (top panel) and TETRA Mip1 mutant (bottom panel). F. Relative affinity of WT and Tetra Mip1 mutant for DNA, as observed in (E).
