Crystal Structure of the Superfamily 1 Helicase from Tomato Mosaic Virus

The genomes of the Tomato mosaic virus and many other plant and animal positive-strand RNA viruses of agronomic and medi-cal importance encode superfamily 1 helicases. Although helicases play important roles in viral replication, the crystal structures of viral superfamily 1 helicases have not been determined. Here, we report the crystal structure of a fragment (S666 to Q1116) of the replication protein from Tomato mosaic virus. The structure reveals a novel N-terminal domain tightly associated with a helicase core. The helicase core contains two RecA-like / domains without any of the accessory domain insertions that are found in other superfamily 1 helicases. The N-terminal domain contains a flexible loop, a long -helix, and an antiparallel six-stranded-sheet. On the basis of the structure, we constructed deletion mutants of the S666-to-Q1116 fragment and performed split-ubiquitin-based interaction assays in Saccharomyces cerevisiaewith TOM1 and ARL8, host proteins that are essential for tomato mosaic virus RNA replication. The results suggested that both TOM1 and ARL8 interact with the long -helix in the N-terminal domain and that TOM1 also interacts with the helicase core. Prediction of secondary structures in other viral super-family 1 helicases and comparison of those structures with the S666-to-Q1116 structure suggested that these helicases have a similar fold. Our results provide a structural basis of viral superfamily 1 helicases. Helicases are motor proteins that use the free energy of nucle-oside triphosphate (NTP) hydrolysis to unwind nucleic acid duplexes during gene replication, transcription, translation, re-combination, and repair (1). Helicases are encoded in the ge