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Viruses 2018, 10(1), 24; https://doi.org/10.3390/v10010024

Visualizing the Nucleotide Addition Cycle of Viral RNA-Dependent RNA Polymerase

1,2
and
1,*
1
Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
2
University of Chinese Academy of Sciences, Beijing 100049, China
*
Author to whom correspondence should be addressed.
Received: 21 October 2017 / Revised: 2 January 2018 / Accepted: 3 January 2018 / Published: 4 January 2018
(This article belongs to the Special Issue Structure-Function Relationships in Viral Polymerases)
View Full-Text   |   Download PDF [1090 KB, uploaded 4 January 2018]   |  

Abstract

Viral RNA-dependent RNA polymerases (RdRPs) are a class of nucleic acid polymerases bearing unique features from global architecture to catalytic mechanisms. In recent years, numerous viral RdRP crystal structures have improved the understanding of these molecular machines, in particular, for how they carry out each nucleotide addition cycle (NAC) as directed by the RNA template. This review focuses on a visual introduction of viral RdRP NAC mechanisms through a combination of static pictures of structural models, a user-friendly software-based assembly of the structural models, and two videos illustrating key conformational changes in the NAC. View Full-Text
Keywords: RNA viruses; RNA-dependent RNA polymerase; nucleotide addition cycle; active site closure; translocation RNA viruses; RNA-dependent RNA polymerase; nucleotide addition cycle; active site closure; translocation
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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).

Supplementary materials

  • Supplementary File 1:

    NAC (ZIP, 8991 KB)

    This is a PyMOL session file that shows seven viral RdRP NAC reference states (S1, S2, S2-3, S3, S4, S5, S6), five states derived from the reference state by removing the magnesium ions and pyrophosphate (S2m, S2-3m, S3m, S4m, S6m), one norovirus RdRP reference state (nvS3), three movies that connects S2m and S2-3m (closure1), S2-3m and S3m (closure2), S4m and S6m (translocation), and key distance changes during the active site closure (dist01-dist05 for closure1 ; dist06-dist10 for closure2).

  • Supplementary File 2:

    PSE-Document (PSE, 1919 KB)

    This is a simplified version of NAC.pse with only the seven reference states included and all hidden atoms deleted from the models, to help reduce the file size for web based PyMOL visualization.

  • Supplementary File 3:

    Active site closure (MPG, 1320 KB)

  • Supplementary File 4:

    Translocation (MPG, 1776 KB)

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Wu, J.; Gong, P. Visualizing the Nucleotide Addition Cycle of Viral RNA-Dependent RNA Polymerase. Viruses 2018, 10, 24.

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