Biochemistry (Moscow)

, Volume 74, Issue 10, pp 1132–1141

Structure-function analysis of mutant RNA-dependent RNA polymerase complexes with VPg


DOI: 10.1134/S0006297909100095

Cite this article as:
Gu, C., Zeng, T., Li, Y. et al. Biochemistry Moscow (2009) 74: 1132. doi:10.1134/S0006297909100095


The replication of the foot-and-mouth disease virus (FMDV) genome is critically dependent upon the activity of a virally encoded RNA-dependent RNA polymerase (RdRp). In this study, four mutant RdRps of FMDV were isolated from viral quasi-species treated with ribavirin, of which two were single mutants (L123F and T381A) and two were double mutants (T291I/T381I and L123F/F244L). The mutant proteins were expressed in Escherichia coli and purified by His-bind resin chromatography. In combination with real-time RT-PCR, an in vitro RNA replication system that uses genome RNA/VPg as template-primers was used to determine polymerase activity. Mutant L123F exhibited a 0.6-fold decrease (p < 0.001) in polymerase activity relative to wild-type RdRp, whereas the activity of L123F/F244L and T381A was undetectable. Surprisingly, the activity of T291I/T381I yielded a 0.7-fold increase (p < 0.001) as compared to wild-type. In order to study the structure-function relationship of RdRp, all structures of the RdRp-RNA template-primer complex were obtained through homology modeling and molecular docking. The VPg1 orientation in the RdRp-VPg1 complexes was determined and analyzed with mathematical methods. Our results reveal that the orientation of VPg after binding to the polymerase determines the FMDV RdRp catalytic activity, which provides a basis for the rational design of novel antiviral agents.

Key words

foot-and-mouth disease virusRNA-dependent RNA polymerase activityhomogenous modelingmolecular dockingVPg orientation



foot-and-mouth disease (virus)


RNA-dependent RNA polymerase


root mean square deviation



Supplementary material

10541_2009_Article_9097_MOESM1_ESM.pdf (166 kb)
Appendix (PDF 166 KB)

Copyright information

© Pleiades Publishing, Ltd. 2009

Authors and Affiliations

  1. 1.State Key Laboratory of Virology, College of Life SciencesWuhan UniversityWuhanChina
  2. 2.Division of Molecular Virology, St. Luke’s-Roosevelt Hospital CenterColumbia UniversityNew YorkUSA
  3. 3.School of Mathematics and StatisticsWuhan UniversityWuhanChina
  4. 4.School of Computer ScienceWuhan UniversityWuhanChina