4RY5

C-terminal mutant (W550N) of HCV/J4 RNA polymerase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Hydrophobic and Charged Residues in the C-Terminal Arm of Hepatitis C Virus RNA-Dependent RNA Polymerase Regulate Initiation and Elongation.

Cherry, A.L.Dennis, C.A.Baron, A.Eisele, L.E.Thommes, P.A.Jaeger, J.

(2015) J Virol 89: 2052-2063

  • DOI: 10.1128/JVI.01106-14
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The RNA-dependent RNA polymerase (RdRp) of hepatitis C virus (HCV) is essential for viral genome replication. Crystal structures of the HCV RdRp reveal two C-terminal features, a β-loop and a C-terminal arm, suitably located for involvement in positi ...

    The RNA-dependent RNA polymerase (RdRp) of hepatitis C virus (HCV) is essential for viral genome replication. Crystal structures of the HCV RdRp reveal two C-terminal features, a β-loop and a C-terminal arm, suitably located for involvement in positioning components of the initiation complex. Here we show that these two elements intimately regulate template and nucleotide binding, initiation, and elongation. We constructed a series of β-loop and C-terminal arm mutants, which were used for in vitro analysis of RdRp de novo initiation and primer extension activities. All mutants showed a substantial decrease in initiation activities but a marked increase in primer extension activities, indicating an ability to form more stable elongation complexes with long primer-template RNAs. Structural studies of the mutants indicated that these enzyme properties might be attributed to an increased flexibility in the C-terminal features resulting in a more open polymerase cleft, which likely favors the elongation process but hampers the initiation steps. A UTP cocrystal structure of one mutant shows, in contrast to the wild-type protein, several alternate conformations of the substrate, confirming that even subtle changes in the C-terminal arm result in a more loosely organized active site and flexible binding modes of the nucleotide. We used a subgenomic replicon system to assess the effects of the same mutations on viral replication in cells. Even the subtlest mutations either severely impaired or completely abolished the ability of the replicon to replicate, further supporting the concept that the correct positioning of both the β-loop and C-terminal arm plays an essential role during initiation and in HCV replication in general.


    Organizational Affiliation

    Wadsworth Center, New York State Department of Health, Albany, New York, USA Ordway Research, Center for Medical Science, Albany, New York, USA Joachim.Jaeger@health.ny.gov.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HCV J4 RNA polymerase (NS5B)
A, B
570Hepatitis C virus isolate HC-J4Mutation(s): 1 
Gene Names: NS5B
EC: 2.7.7.48 (PDB Primary Data), 3.4.22 (UniProt), 3.4.21.98 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt)
Find proteins for O92972 (Hepatitis C virus genotype 1b (strain HC-J4))
Go to UniProtKB:  O92972
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UTP
Query on UTP

Download CCD File 
A, B
URIDINE 5'-TRIPHOSPHATE
C9 H15 N2 O15 P3
PGAVKCOVUIYSFO-XVFCMESISA-N
 Ligand Interaction
MN
Query on MN

Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.49α = 90
b = 107.946β = 90
c = 133.25γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-31
    Type: Initial release
  • Version 1.1: 2015-02-11
    Changes: Database references