Crystal structure of the coxsackievirus A16 RNA-dependent RNA polymerase elongation complex reveals novel features in motif A dynamics

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Abstract

The RNA-dependent RNA polymerases (RdRPs) encoded by RNA viruses represent a unique class of nucleic acid polymerases. Unlike other classes of single-subunit polymerases, viral RdRPs have evolved a unique conformational change in their palm domain to close the active site during catalysis. The hallmark of this conformational change is the backbone shift of the polymerase motif A from an “open” state to a “closed” state, allowing two universally conserved aspartic acid residues to orient toward each other for divalent metal binding and catalysis. The “closed” motif A conformation was only observed upon the binding of correct NTP in RdRP catalytic complexes or under rare conditions such as induced by a bound lutetium ion or a bound glutamate molecule. By solving the crystal structure of the catalytic elongation complex of the coxsackievirus RdRP, we in this work observed for the first time the “closed” motif A conformation in the absence of an NTP substrate or other conformational-change-inducing factors. This observation emphasizes the intrinsic dynamic features of viral RdRP motif A, and solidifies the structural basis for how this important structural element participates in catalytic events of the RdRPs.

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Crystal structure of the coxsackievirus A16 RNA-dependent RNA polymerase elongation complex reveals novel features in motif A dynamics

References

  1. Gohara DW, Ha CS, Kumar S, et al. 1999. Protein Expr Purif, 17: 128–138.CrossRefPubMedGoogle Scholar
  2. Gong P, Kortus MG, Nix JC, et al. 2013. PLoS One, 8: e60272.CrossRefPubMedPubMedCentralGoogle Scholar
  3. Gong P, Peersen OB. 2010. Proc Natl Acad Sci U S A, 107: 22505–22510.CrossRefPubMedPubMedCentralGoogle Scholar
  4. Li Y, Korolev S, Waksman G. 1998. EMBO J, 17: 7514–7525.PubMedPubMedCentralGoogle Scholar
  5. Mao Q, Wang Y, Yao X, et al. 2014. Hum Vaccin Immunother, 10: 360–367.CrossRefPubMedGoogle Scholar
  6. McDonald S, Block A, Beaucourt S, et al. 2016. J Biol Chem, 291: 13999–14011.CrossRefPubMedPubMedCentralGoogle Scholar
  7. Ng KK, Cherney MM, Vazquez AL, et al. 2002. J Biol Chem, 277: 1381–1387.CrossRefPubMedGoogle Scholar
  8. Pflugrath JW. 1999. Acta Crystallogr D Biol Crystallogr, 55: 1718–1725.CrossRefPubMedGoogle Scholar
  9. Shu B, Gong P. 2016. Proc Natl Acad Sci U S A, 113: E4005–4014.CrossRefPubMedPubMedCentralGoogle Scholar
  10. Solomon T, Lewthwaite P, Perera D, et al. 2010. Lancet Infect Dis, 10: 778–790.CrossRefPubMedGoogle Scholar
  11. Theobald DL, Wuttke DS. 2006. Bioinformatics, 22: 2171–2172.CrossRefPubMedPubMedCentralGoogle Scholar
  12. Vives-Adrian L, Lujan C, Oliva B, et al. 2014. J Virol, 88: 5595–5607.CrossRefPubMedPubMedCentralGoogle Scholar
  13. Yin YW, Steitz TA. 2004. Cell, 116: 393–404.CrossRefPubMedGoogle Scholar
  14. Zamyatkin DF, Parra F, Alonso JM, et al. 2008. J Biol Chem, 283: 7705–7712.CrossRefPubMedGoogle Scholar

Copyright information

© Wuhan Institute of Virology, CAS and Springer Nature Singapore Pte Ltd. 2017

Authors and Affiliations

  1. 1.Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of VirologyChinese Academy of SciencesWuhanChina
  2. 2.University of Chinese Academy of SciencesBeijingChina

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