Crystal structure of the hp-HP92/DbpA complex in the closed state. (A) Overall structure (top) and schematic diagram (bottom) of the complex between two DbpA molecules (chains A/B) and two hp-HP92 RNAs (chains F/G), as observed in the crystal. HP92 (red), the substrate hairpin (orange), and the 3 nt linker that base pairs with the 3′ overhang of HP92 (green) are shown in ribbon representation. The RecA_N (blue), RecA_C (cyan), and RRM (gray) domains of DbpA are shown in sphere representation. (B) Model of the 1:1 complex obtained by connecting HP92 and the substrate hairpin bound to one DbpA molecule by a flexible 3 nt linker (green). (C) SEC chromatograms of free hp-HP92 (black), the hp-HP92/DbpA complex (orange), and the hp-HP92/DbpA/ADP/BeF3 (blue) complex. (D) Close-up of the interaction between substrate hairpin (chain F, 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 hairpin is shown in the upper-right, with identical numbering. The distorted base pair between the adenosine in position 4 and the opposite uridine is indicated by a dashed line. (E) Comparison between the substrate hairpin bound to DbpA (only nt 1–7 are shown for clarity) and the complex between a 6 nt ssRNA (pink) and the DEAD-box helicase VASA (gray; PDB ID 2db3).
