A translocation model for DEAH/RHA ATPases. (A) Two alternative translocation models, differing in the coupling of the ATPase cycle to RecA domain movement and in the number of stacked bases after Pi release. (B) All current structures of DExH box ATPases bound to RNA—Prp43 (this work), MLE (PDB 5AOR), NS3 bound and not bound to nucleotide (PDB 3O8R and 3O8C), HEL308 (PDB 2P6R), and MTR4 (PDB 2XGJ)—show that closed, ATP-bound states bookend 4-nt RNA stacks (top), whereas open, apo states bookend 5-nt stacks (bottom). Stacked nucleotides are red; nonstacked residues are gray; blue indicates residues of a complementary strand that has been partially unwound in Hel308. Motif Ib is in green and corresponds to the 3′ bookend in Prp43 and MLE; the 3′ bookend in NS3, Hel308, and Mtr4, which derives from an auxiliary domain, is cyan, and the proline similarly positioned in Prp43 and MLE is also cyan; the 5′ bookends are yellow. (C) Schematic representation of the chimeric structure of DEAH/RHA ATPases, which include elements structurally paralogous to NS3/NPHII or Ski2-like ATPases. The 3′- and 5′-bookends are represented as 3′ and 5′, respectively.
