Fig. 5

The PHP-exonuclease active site is analogous to endonuclease IV. a Overlay of the catalytic residues of DnaE1 (in gray) and E. coli Endo IV (in green). Note the mirrored position of Endo IV H109 and DnaE1 H107. b Schematic view of the positions of the residues that coordinate the zinc ions in Endo IV (left) and DnaE1 (right). The zinc-coordinating residues originate from entirely different locations, indicating the two enzymes do not have a common evolutionary origin. c Histidine 109 that ligands Zn₁ in Endo IV is positioned to the ‘right’ of the active site and pulls Zn₁ away from the center line. d In DnaE1, the analogous histidine (His 107) has moved to the other side of the active site, moving Zn₁ with it. e In DnaE1, glutamate 73 (E73) ligands both Zn₁ and Zn₂, whereas aspartate 226 (D226) only ligands Zn₂ and makes a hydrogen bond with a water molecule. Electron density show at 2.3σ in yellow mesh