Figure 6. Substrate recognition features of GEN1.
(A) Superposition of the protein part of the FEN1-DNA complex (PDB 3q8k, protein in gray, DNA in black) onto the GEN1-HJ complex (protein in green and the DNA strands in different colors). The FEN1-DNA aligns with the same register as the GEN1-DNA at the upstream interface. (B) Model for the recognition of a 5’ flap substrate by GEN1. The DNA was extended using the superimposition from A. Homology modeling suggests an additional helix α4 (disordered residues 79–92) forming an arch with helix α6. The protein is shown in a simplified surface representation with the same colors as in Figure 1 and structural elements are highlighted. The insert shows a zoomed in view of the hydrophobic wedge with the modeled FEN1-DNA in gray. (C) Model for the dimerization of GEN1 upon binding to a HJ substrate based on the 5’ flap model in B. The monomers interlock via both arches (α4-α6) and the hydrophobic wedges (α2-α3) contact each other. (D) Structure of the Thermus thermophilus RuvC-HJ complex (PDB 4ld0). (E) Structure of the T4 endonuclease VII-HJ complex (PDB 2qnc). (F) Structure of the T7 endonuclease I-HJ complex (PDB 2pfj). Individual monomers are in surface representation, colored in light blue and beige, respectively. DNA strands are shown as ladders in different colors.