Crystal structure of the ds-HP92/DbpA complex in the closed state. (A) Interaction of the substrate duplex including a 3 nt 5′ overhang with the active site of the helicase core. For clarity, only the substrate duplex (chain D) and one DbpA molecule (chain B) are shown (top). Schematic diagram of the 2:2 complex observed in the crystal (bottom). (B) SEC chromatograms of free ds-HP92 (black), the ds-HP92/DbpA complex (orange), and the ds-HP92/DbpA/ADP/BeF3 (blue) complex. (C) Close-up of the interaction between the substrate duplex (chain D, orange) and the active site of the helicase core (chain B, RecA_N blue, RecA_C cyan). The nucleotides that interact with the active site are numbered 1–6. The substrate duplex is shown in the upper-right, with identical numbering. (D) Close-up of the active site in the vicinity of α-helix α7 (left). Extension of the duplex by the addition of 2 nt at the 3′ end (green) leads to severe clashes with α-helix α7 of the RecA_N domain (right). Residues that show van der Waals clashes >1 Å with the RNA are shown in pink.
