Literature DB >> 23408636

Conformational flexibility of the Dengue virus RNA-dependent RNA polymerase revealed by a complex with an inhibitor.

Christian G Noble1, Siew Pheng Lim, Yen-Liang Chen, Chong Wai Liew, Lijian Yap, Julien Lescar, Pei-Yong Shi.   

Abstract

We report a highly reproducible method to crystallize the RNA-dependent RNA polymerase (RdRp) domain of dengue virus serotype 3 (DENV-3), allowing structure refinement to a 1.79-Å resolution and revealing amino acids not seen previously. We also present a DENV-3 polymerase/inhibitor cocrystal structure at a 2.1-Å resolution. The inhibitor binds to the RdRp as a dimer and causes conformational changes in the protein. The improved crystallization conditions and new structural information should accelerate structure-based drug discovery.

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Year:  2013        PMID： 23408636      PMCID： PMC3624333          DOI： 10.1128/JVI.00045-13

Source DB:  PubMed          Journal:  J Virol        ISSN： 0022-538X            Impact factor:   5.103


  12 in total

1.  Comparative mechanistic studies of de novo RNA synthesis by flavivirus RNA-dependent RNA polymerases.

Authors:  Barbara Selisko; Hélène Dutartre; Jean-Claude Guillemot; Claire Debarnot; Delphine Benarroch; Alexander Khromykh; Philippe Desprès; Marie-Pierre Egloff; Bruno Canard
Journal:  Virology       Date:  2006-04-21       Impact factor: 3.616

2.  Crystal structure of the dengue virus RNA-dependent RNA polymerase catalytic domain at 1.85-angstrom resolution.

Authors:  Thai Leong Yap; Ting Xu; Yen-Liang Chen; Helene Malet; Marie-Pierre Egloff; Bruno Canard; Subhash G Vasudevan; Julien Lescar
Journal:  J Virol       Date:  2007-02-14       Impact factor: 5.103

3.  A multi-step strategy to obtain crystals of the dengue virus RNA-dependent RNA polymerase that diffract to high resolution.

Authors:  Thai Leong Yap; Yen Liang Chen; Ting Xu; Daying Wen; Subhash G Vasudevan; Julien Lescar
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2007-01-17

Review 4.  RNA-dependent RNA polymerases from flaviviruses and Picornaviridae.

Authors:  Julien Lescar; Bruno Canard
Journal:  Curr Opin Struct Biol       Date:  2009-11-10       Impact factor: 6.809

5.  A fluorescence-based alkaline phosphatase-coupled polymerase assay for identification of inhibitors of dengue virus RNA-dependent RNA polymerase.

Authors:  Pornwaratt Niyomrattanakit; Siti Nurdiana Abas; Chin Chin Lim; David Beer; Pei-Yong Shi; Yen-Liang Chen
Journal:  J Biomol Screen       Date:  2011-01-10

6.  Inhibition of dengue virus polymerase by blocking of the RNA tunnel.

Authors:  Pornwaratt Niyomrattanakit; Yen-Liang Chen; Hongping Dong; Zheng Yin; Min Qing; J Frasier Glickman; Kai Lin; Dieter Mueller; Hans Voshol; Joanne Y H Lim; Shahul Nilar; Thomas H Keller; Pei-Yong Shi
Journal:  J Virol       Date:  2010-03-17       Impact factor: 5.103

7.  De novo synthesis of RNA by the dengue virus RNA-dependent RNA polymerase exhibits temperature dependence at the initiation but not elongation phase.

Authors:  M Ackermann; R Padmanabhan
Journal:  J Biol Chem       Date:  2001-08-23       Impact factor: 5.157

8.  Crystal structure of the RNA polymerase domain of the West Nile virus non-structural protein 5.

Authors:  Hélène Malet; Marie-Pierre Egloff; Barbara Selisko; Rebecca E Butcher; Peter J Wright; Michael Roberts; Arnaud Gruez; Gerlind Sulzenbacher; Clemens Vonrhein; Gérard Bricogne; Jason M Mackenzie; Alexander A Khromykh; Andrew D Davidson; Bruno Canard
Journal:  J Biol Chem       Date:  2007-02-07       Impact factor: 5.157

Review 9.  Chapter 2. New insights into flavivirus nonstructural protein 5.

Authors:  Andrew D Davidson
Journal:  Adv Virus Res       Date:  2009       Impact factor: 9.937

10.  Construction and characterization of a stable subgenomic dengue virus type 2 replicon system for antiviral compound and siRNA testing.

Authors:  Chuan Young Ng; Feng Gu; Wai Yee Phong; Yen-Liang Chen; Siew Pheng Lim; Andrew Davidson; Subhash G Vasudevan
Journal:  Antiviral Res       Date:  2007-07-26       Impact factor: 5.970
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  35 in total

1.  Identification of a Conserved RNA-dependent RNA Polymerase (RdRp)-RNA Interface Required for Flaviviral Replication.

Authors:  Kenneth Hodge; Chairat Tunghirun; Maliwan Kamkaew; Thawornchai Limjindaporn; Pa-Thai Yenchitsomanus; Sarin Chimnaronk
Journal:  J Biol Chem       Date:  2016-06-22       Impact factor: 5.157

2.  Synergistic suppression of dengue virus replication using a combination of nucleoside analogs and nucleoside synthesis inhibitors.

Authors:  Kim Long Yeo; Yen-Liang Chen; Hao Ying Xu; Hongping Dong; Qing-Yin Wang; Fumiaki Yokokawa; Pei-Yong Shi
Journal:  Antimicrob Agents Chemother       Date:  2015-01-26       Impact factor: 5.191

3.  A Conserved Pocket in the Dengue Virus Polymerase Identified through Fragment-based Screening.

Authors:  Christian G Noble; Siew Pheng Lim; Rishi Arora; Fumiaki Yokokawa; Shahul Nilar; Cheah Chen Seh; S Kirk Wright; Timothy E Benson; Paul W Smith; Pei-Yong Shi
Journal:  J Biol Chem       Date:  2016-02-12       Impact factor: 5.157

4.  Two RNA Tunnel Inhibitors Bind in Highly Conserved Sites in Dengue Virus NS5 Polymerase: Structural and Functional Studies.

Authors:  Rishi Arora; Chong Wai Liew; Tingjin Sherryl Soh; Dorcas Adobea Otoo; Cheah Chen Seh; Kimberley Yue; Shahul Nilar; Gang Wang; Fumiaki Yokokawa; Christian G Noble; Yen Liang Chen; Pei-Yong Shi; Julien Lescar; Thomas M Smith; Timothy E Benson; Siew Pheng Lim
Journal:  J Virol       Date:  2020-11-23       Impact factor: 5.103

5.  Hydrophobic and charged residues in the C-terminal arm of hepatitis C virus RNA-dependent RNA polymerase regulate initiation and elongation.

Authors:  Amy L Cherry; Caitriona A Dennis; Andrew Baron; Leslie E Eisele; Pia A Thommes; Joachim Jaeger
Journal:  J Virol       Date:  2014-11-26       Impact factor: 5.103

6.  NS5 from Dengue Virus Serotype 2 Can Adopt a Conformation Analogous to That of Its Zika Virus and Japanese Encephalitis Virus Homologues.

Authors:  Abbas El Sahili; Tingjin Sherryl Soh; Jonas Schiltz; Aïcha Gharbi-Ayachi; Cheah Chen Seh; Pei-Yong Shi; Siew Pheng Lim; Julien Lescar
Journal:  J Virol       Date:  2019-12-12       Impact factor: 5.103

7.  The crystal structure of Zika virus NS5 reveals conserved drug targets.

Authors:  Wenqian Duan; Hao Song; Haiyuan Wang; Yan Chai; Chao Su; Jianxun Qi; Yi Shi; George F Gao
Journal:  EMBO J       Date:  2017-03-02       Impact factor: 11.598

Review 8.  Regulation of Flavivirus RNA synthesis and replication.

Authors:  Barbara Selisko; Chunling Wang; Eva Harris; Bruno Canard
Journal:  Curr Opin Virol       Date:  2014-10-17       Impact factor: 7.090

9.  Non-nucleoside Inhibitors of Zika Virus RNA-Dependent RNA Polymerase.

Authors:  Aicha Gharbi-Ayachi; Sridhar Santhanakrishnan; Yee Hwa Wong; Kitti W K Chan; Siok Thing Tan; Roderick W Bates; Subhash G Vasudevan; Abbas El Sahili; Julien Lescar
Journal:  J Virol       Date:  2020-10-14       Impact factor: 5.103

10.  MetalS(3), a database-mining tool for the identification of structurally similar metal sites.

Authors:  Yana Valasatava; Antonio Rosato; Gabriele Cavallaro; Claudia Andreini
Journal:  J Biol Inorg Chem       Date:  2014-04-04       Impact factor: 3.358
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