2XXD

HCV-JFH1 NS5B polymerase structure at 1.9 angstrom

Summary for 2XXD

• Entry DOI: 10.2210/pdb2xxd/pdb
• Related: 3I5K
• Descriptor: RNA-DIRECTED RNA POLYMERASE, PHOSPHATE ION (3 entities in total)
• Functional Keywords: transferase, hepacivirus, nonstructural proteins, replication, de novo initiation, priming
• Biological source: HEPATITIS C VIRUS (HCV)
• Cellular location: Core protein p21: Host endoplasmic reticulum membrane; Single-pass membrane protein (By similarity). Core protein p19: Virion (By similarity). Envelope glycoprotein E1: Virion membrane; Single-pass type I membrane protein (Potential). Envelope glycoprotein E2: Virion membrane; Single-pass type I membrane protein (Potential). p7: Host endoplasmic reticulum membrane; Multi-pass membrane protein. Protease NS2-3: Host endoplasmic reticulum membrane; Multi-pass membrane protein (Potential). Serine protease NS3: Host endoplasmic reticulum membrane; Peripheral membrane protein (Probable). Non-structural protein 4A: Host endoplasmic reticulum membrane; Single-pass type I membrane protein (Potential). Non-structural protein 4B: Host endoplasmic reticulum membrane; Multi-pass membrane protein (By similarity). Non-structural protein 5A: Host endoplasmic reticulum membrane; Peripheral membrane protein (By similarity). RNA-directed RNA polymerase: Host endoplasmic reticulum membrane; Single-pass type I membrane protein (Potential): Q99IB8
• Total number of polymer chains: 1
• Total formula weight: 62971.82

Authors

Caillet-Saguy, C.,Bressanelli, S. (deposition date: 2010-11-10, release date: 2011-01-12, Last modification date: 2024-05-01)

Primary citation

Schmitt, M.,Scrima, N.,Radujkovic, D.,Caillet-Saguy, C.,Simister, P.C.,Friebe, P.,Wicht, O.,Klein, R.,Bartenschlager, R.,Lohmann, V.,Bressanelli, S.
A Comprehensive Structure-Function Comparison of Hepatitis C Virus Strains Jfh1 and J6 Polymerases Reveals a Key Residue Stimulating Replication in Cell Culture Across Genotypes.
J.Virol., 85:2565-, 2011

PubMed Abstract: The hepatitis C virus (HCV) genotype 2a isolate JFH1 represents the only cloned HCV wild-type sequence capable of efficient replication in cell culture as well as in vivo. Previous reports have pointed to NS5B, the viral RNA-dependent RNA polymerase (RdRp), as a major determinant for efficient replication of this isolate. To understand the contribution of the JFH1 NS5B gene at the molecular level, we aimed at conferring JFH1 properties to NS5B from the closely related J6 isolate. We created intragenotypic chimeras in the NS5B regions of JFH1 and J6 and compared replication efficiency in cell culture and RdRp activity of the purified proteins in vitro, revealing more than three independent mechanisms conferring the role of JFH1 NS5B in efficient RNA replication. Most critical was residue I405 in the thumb domain of the polymerase, which strongly stimulated replication in cell culture by enhancing overall de novo RNA synthesis. A structural comparison of JFH1 and J6 at high resolution indicated a clear correlation of a closed-thumb conformation of the RdRp and the efficiency of the enzyme at de novo RNA synthesis, in accordance with the proposal that I405 enhances de novo initiation. In addition, we identified several residues enhancing replication independent of RdRp activity in vitro. The functional properties of JFH1 NS5B could be restored by a few single-nucleotide substitutions to the J6 isolate. Finally, we were able to enhance the replication efficiency of a genotype 1b isolate with the I405 mutation, indicating that this mechanism of action is conserved across genotypes.

PubMed: 21209117
DOI: 10.1128/JVI.02177-10

Experimental method

X-RAY DIFFRACTION (1.881 Å)