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Int. J. Mol. Sci. 2015, 16(6), 12943-12957; doi:10.3390/ijms160612943

A Structural Overview of RNA-Dependent RNA Polymerases from the Flaviviridae Family

1,2,3
,
1,2,3
and
1,2,*
1
Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, No. 44 Xiao Hong Shan, Wuchang District, Wuhan 430071, China
2
State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
3
University of Chinese Academy of Sciences, Beijing 100049, China
*
Author to whom correspondence should be addressed.
Academic Editor: Charles A. Collyer
Received: 1 April 2015 / Revised: 27 May 2015 / Accepted: 28 May 2015 / Published: 8 June 2015
(This article belongs to the Special Issue Protein Crystallography in Molecular Biology 2015)
View Full-Text   |   Download PDF [3057 KB, uploaded 24 June 2015]   |  

Abstract

RNA-dependent RNA polymerases (RdRPs) from the Flaviviridae family are representatives of viral polymerases that carry out RNA synthesis through a de novo initiation mechanism. They share a ≈ 600-residue polymerase core that displays a canonical viral RdRP architecture resembling an encircled right hand with palm, fingers, and thumb domains surrounding the active site. Polymerase catalytic motifs A–E in the palm and motifs F/G in the fingers are shared by all viral RdRPs with sequence and/or structural conservations regardless of the mechanism of initiation. Different from RdRPs carrying out primer-dependent initiation, Flaviviridae and other de novo RdRPs utilize a priming element often integrated in the thumb domain to facilitate primer-independent initiation. Upon the transition to the elongation phase, this priming element needs to undergo currently unresolved conformational rearrangements to accommodate the growth of the template-product RNA duplex. In the genera of Flavivirus and Pestivirus, the polymerase module in the C-terminal part of the RdRP protein may be regulated in cis by the N-terminal region of the same polypeptide. Either being a methyltransferase in Flavivirus or a functionally unclarified module in Pestivirus, this region could play auxiliary roles for the canonical folding and/or the catalysis of the polymerase, through defined intra-molecular interactions. View Full-Text
Keywords: Flaviviridae; RNA-dependent RNA polymerase; catalytic motif; de novo initiation; elongation; in cis regulation Flaviviridae; RNA-dependent RNA polymerase; catalytic motif; de novo initiation; elongation; in cis regulation
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Wu, J.; Liu, W.; Gong, P. A Structural Overview of RNA-Dependent RNA Polymerases from the Flaviviridae Family. Int. J. Mol. Sci. 2015, 16, 12943-12957.

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