Crystal structure of the ATPase domain of translation initiation factor 4A from Saccharomyces cerevisiae – the prototype of the DEAD box protein family

AbstractBackground: Translation initiation factor 4A (eIF4A) is the prototype of the DEAD-box family of proteins. DEAD-box proteins are involved in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. Energy from ATP hydrolysis is used to perform RNA unwinding during initiation of mRNA translation. The presence of eIF4A is required for the 43S preinitiation complex to bind to and scan the mRNA.Results: We present here the crystal structure of the nucleotide-binding domain of eIF4A at 2.0 Å and the structures with bound adenosinediphosphate and adenosinetriphosphate at 2.2 Å and 2.4 Å resolution, respectively. The structure of the apo form of the enzyme has been determined by multiple isomorphous replacement. The ATPase domain contains a central seven-stranded β sheet flanked by nine α helices. Despite low sequence homology to the NTPase domains of RNA and DNA helicases, the three-dimensional fold of eIF4A is nearly identical to the DNA helicase PcrA of Bacillus stearothermophilus and to the RNA helicase NS3 of hepatitis C virus.Conclusions: We have determined the crystal structure of the N-terminal domain of the eIF4A from yeast as the first structure of a member of the DEAD-box protein family. The complex of the protein with bound ADP and ATP offers insight into the mechanism of ATP hydrolysis and the transfer of energy to unwind RNA. The identical fold of the ATPase domain of the DNA helicase PcrA of B. stearothermophilus and the RNA helicase of hepatitis C virus suggests a common fold for all ATPase domains of DExx- and DEAD-box proteins