4C11

Dengue virus RNA dependent RNA polymerase with residues from the NS5 linker region

Summary for 4C11

• Entry DOI: 10.2210/pdb4c11/pdb
• Descriptor: DENGUE VIRUS TYPE 3 RNA DEPENDENT RNA POLYMERASE, ZINC ION, ... (4 entities in total)
• Functional Keywords: transferase, rna dependent rna polymerase
• Biological source: DENGUE VIRUS; More
• Total number of polymer chains: 2
• Total formula weight: 148206.01

Authors

Lim, S.P.,Lescar, J. (deposition date: 2013-08-09, release date: 2013-08-21, Last modification date: 2024-05-08)

Primary citation

Lim, S.P.,Koh, J.H.K.,Seh, C.C.,Liew, C.W.,Davidson, A.D.,Chua, L.S.,Chandrasekaran, R.,Cornvik, T.C.,Shi, P.,Lescar, J.
A Crystal Structure of the Dengue Virus Ns5 Polymerase Delineates Inter-Domain Amino Acids Residues that Enhance its Thermostability and De Novo Initiation Activities.
J.Biol.Chem., 288:31105-, 2013

PubMed Abstract: The dengue virus (DENV) non-structural protein 5 (NS5) comprises an N-terminal methyltransferase and a C-terminal RNA-dependent RNA polymerase (RdRp) domain. Both enzymatic activities form attractive targets for antiviral development. Available crystal structures of NS5 fragments indicate that residues 263-271 (using the DENV serotype 3 numbering) located between the two globular domains of NS5 could be flexible. We observed that the addition of linker residues to the N-terminal end of the DENV RdRp core domain stabilizes DENV1-4 proteins and improves their de novo polymerase initiation activities by enhancing the turnover of the RNA and NTP substrates. Mutation studies of linker residues also indicate their importance for viral replication. We report the structure at 2.6-Å resolution of an RdRp fragment from DENV3 spanning residues 265-900 that has enhanced catalytic properties compared with the RdRp fragment (residues 272-900) reported previously. This new orthorhombic crystal form (space group P21212) comprises two polymerases molecules arranged as a dimer around a non-crystallographic dyad. The enzyme adopts a closed "preinitiation" conformation similar to the one that was captured previously in space group C2221 with one molecule per asymmetric unit. The structure reveals that residues 269-271 interact with the RdRp domain and suggests that residues 263-268 of the NS5 protein from DENV3 are the major contributors to the flexibility between its methyltransferase and RdRp domains. Together, these results should inform the screening and development of antiviral inhibitors directed against the DENV RdRp.

PubMed: 24025331
DOI: 10.1074/JBC.M113.508606

Experimental method

X-RAY DIFFRACTION (2.6 Å)