Fig. 3

Entry path of the primer strand into the PHP-exonuclease. a 2D cryo-EM class of the Mtb DnaE1–clamp-DNA complex. b Fitting of the crystal structures of DnaE1 and β-clamp, and modeling of DNA into the 2D cryo-EM class. c Hydrogen–deuterium exchange experiments map the areas of the polymerase that are most affected by DNA binding, including the long loop in the PHP domain in contact with the modeled DNA. d Close up of the entry path and active site, with mutated residues indicated in sticks. The path of the modeled DNA is indicated by the blue line. e Primer extension rates of different DnaE1 mutants on a matched and mismatched DNA substrate calculated from three–five independent experiments. Error bars indicate standard deviation (Supplementary Fig. 5). f Differential scanning fluorimetry analysis of WT and mutant DnaE1