ATP utilization by DExD/H‐box RNA helicases – molecular motor proteins that couple ATPase activity with RNA rearrangement.

Abstract

DExD/H‐box proteins (DBPs) utilize the free energy associated with ATPase cycling to perform work on RNA substrates. DBPs are found across all phyla, from RNA viruses to humans, and have evolved biological roles throughout RNA metabolism involving RNA unwinding, rearrangement of (mis)folded RNAs, and/or disruption of RNA‐protein complexes. DBPs share several highly conserved structural motifs that couple ATPase and RNA rearrangement activities. However, enzymatic adaptations alter the rate and equilibrium constants of the ATPase cycle, which affect both the efficiency and processivity of these enzymes. We have investigated the ATP utilization mechanisms of DBPs involved in bacterial rRNA folding, eukaryotic mRNA splicing, and RNA virus replication. The partially rate‐limiting formation of the DBP‐ADP‐ Pi intermediate on RNA is a likely candidate for the dominant force‐producing transition of the RNA‐activated DBP ATPase cycle. This step precedes ATP‐dependent duplex RNA strand dissociation during non‐processive unwinding. Evaluation of ATP utilization during processive RNA translocation requires parsing of initiation, stepping and dissociation. These studies reveal enzymatic features associated with ATPase coupling to RNA rearrangement and processive translocation by different DBP classes. An NSF CAREER Award (MCB‐0546353) supported this research.