Biochemistry (Moscow)

, Volume 74, Issue 10, pp 1132–1141 | Cite as

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

  • Chaojiang Gu
  • Tao Zeng
  • Yong Li
  • Zhenghui Xu
  • Zhongxi MoEmail author
  • Congyi ZhengEmail author


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 virus RNA-dependent RNA polymerase activity homogenous modeling molecular docking VPg orientation 



foot-and-mouth disease (virus)


RNA-dependent RNA polymerase


root mean square deviation




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Supplementary material

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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

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