Model of the unwinding mechanism for duplexes with 5′ ssRNA overhangs. HP92 and ATP are omitted for clarity. The nucleotides that interact with the active site of DbpA are colored orange. DbpA transiently adopts the closed conformation in the absence of substrate RNA (upper left). (1) The closed conformation binds to the ss/dsRNA junction, whereby nt 1–3 are single-stranded and nt 4–6 are still part of the duplex (as depicted in the structure of the DbpA/ds-HP92 complex). (2) Duplex breathing leads to a ssRNA-bound state with continuous base stacking (DbpA/ss-HP92 complex in conformation 2). (3) The nucleotides in positions 5/6 rearrange to a conformation that is incompatible with duplex formation (DbpA/ss-HP92 complex in conformation 1). (4) The loss of these three base pairs leads to the dissociation of the upper RNA strand.
