W0019

Crystal Structure of RNA Helicase from Genotype 1B Hepatitis C Virus: a Feasible Mechanism of Unwinding Duplex RNA. Hyun-Soo Cho, Nam-Chul Ha, Lin-Woo Kang, Kyung Min Chung, Sung Hoon Back, Sung Key Jang, Byung-Ha Oh, Dept. of Life Sciences, Pohang Science & Technology University, Hyojadong Pohang 790-784 South Korea

Crystal structure of RNA helicase domain from genotype 1b Hepatitis C Virus (HCV) has been determined at 2.1 Å resolution by the multiple isomorphous replacement method. The structure consists of three domains that form a Y-shaped molecule. One of them can be readily identified as a NTPase domain owing to the presence of two highly conserved NTP binding motifs. Another one is an RNA binding domain containing a conserved RNA binding motif. The third one is a helical domain that contains no [beta]-strand. The RNA binding domain of the molecule is distinctively separated from the other two domains forming an interdomain cleft into which single stranded RNA (ssRNA) can be modeled in the 3' to 5' direction. A channel is found between a pair of symmetry-related molecules which exhibit the most extensive crystal packing interactions. The channel is helical in shape and adequate to accommodate ssRNA along with the interdomain cleft. A stretch of ssRNA can be modeled with electrostatic complementarity into the interdomain cleft, and continuously through the channel. These observations suggest that some form of this dimer is likely to be the functional form that unwinds double stranded RNA processively by passing one strand of RNA through the channel and passing the other strand outside of the dimer. A `descending molecular see-saw' model is proposed which is analogous in concept to the functional model of F1-ATPase. In this model, the putative functional dimer entraps ssRNA containing the 3' overhang and moves along the same strand in the 5' direction coupled with NTP hydrolysis. Energy released by the NTP hydrolysis is used to detach ssRNA from the interdomain cleft, and energy released from favorable interactions between the interdomain cleft and ssRNA is used to disrupt base pairings of duplex RNA. This model is consistent with directionality of unwinding and other physicochemical properties of RNA helicases.