5E4F

The spring alpha-helix coordinates multiple modes of HCV NS3 helicase action

  • Classification: HYDROLASE
  • Organism(s): Hepatitis C virus (isolate Con1)
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2015-10-05 Released: 2016-05-18 
  • Deposition Author(s): Gu, M., Rice, C.M.
  • Funding Organization(s): National Institutes of Health/National Center for Research Resources (NIH/NCRR), US Public health service, Greenberg Medical Research Institute, the Starr Foundation, the Richard Salomon Family Foundation, the Ronald A. Shellow, M.D. Memorial Fund, Paul Nash and the MGM Mirage Voice Foundation, and Gregory F. Lloyd Memorial contributions, Marie-Josee and Henry R. Kravis Fellowship

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

The Spring alpha-Helix Coordinates Multiple Modes of HCV (Hepatitis C Virus) NS3 Helicase Action.

Gu, M.Rice, C.M.

(2016) J Biol Chem 291: 14499-14509

  • DOI: 10.1074/jbc.M115.704379
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Genomic DNA replication requires helicases to processively unwind duplexes. Although helicases encoded by positive-strand RNA viruses are necessary for RNA genome replication, their functions are not well understood. We determined structures of the h ...

    Genomic DNA replication requires helicases to processively unwind duplexes. Although helicases encoded by positive-strand RNA viruses are necessary for RNA genome replication, their functions are not well understood. We determined structures of the hepatitis C virus helicase (NS3h) in complex with the transition state ATP mimic ADP·AlF4 (-) and compared them with the previous nucleic acid-associated ternary complexes. The results suggested that nucleic acid binding promotes a structural change of the spring helix at the transition state, optimizing the interaction network centered on the nucleophilic water. Analysis of ATP hydrolysis with and without conformational restraints on the spring helix further supported the importance of its action for both nucleic acid-stimulated and basal catalysis. We further found that an F238P substitution, predicted to destabilize the helix, diminished viral RNA replication without significantly affecting ATP-dependent duplex unwinding. The stability of the secondary structure, thus, seems critical for additional functions of NS3h. Taken together, the results suggest that the spring helix may be central to the coordination of multiple modes of NS3h action. Further characterization centered on this element may help understand the molecular details of how the viral helicase facilitates RNA replication. This new structural information may also aid efforts to develop specific inhibitors targeting this essential viral enzyme.


    Organizational Affiliation

    From the Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York 10065 ricec@rockefeller.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine protease NS3
A, B
437Hepatitis C virus (isolate Con1)Mutation(s): 0 
EC: 3.4.21.98 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.6.4.13 (PDB Primary Data), 3.4.22 (UniProt), 2.7.7.48 (UniProt)
Find proteins for Q9WMX2 (Hepatitis C virus genotype 1b (isolate Con1))
Go to UniProtKB:  Q9WMX2
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download CCD File 
A, B
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
ALF
Query on ALF

Download CCD File 
A, B
TETRAFLUOROALUMINATE ION
Al F4
UYOMQIYKOOHAMK-UHFFFAOYSA-J
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.214 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.451α = 90
b = 46.104β = 104.05
c = 109.041γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-10-05 
  • Released Date: 2016-05-18 
  • Deposition Author(s): Gu, M., Rice, C.M.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United States1S10RR022321-01, P30-EB-009998
US Public health serviceUnited StatesCA057973
Greenberg Medical Research Institute, the Starr Foundation, the Richard Salomon Family Foundation, the Ronald A. Shellow, M.D. Memorial Fund, Paul Nash and the MGM Mirage Voice Foundation, and Gregory F. Lloyd Memorial contributionsUnited States--
Marie-Josee and Henry R. Kravis FellowshipUnited States--

Revision History 

  • Version 1.0: 2016-05-18
    Type: Initial release
  • Version 1.1: 2016-06-08
    Changes: Database references
  • Version 1.2: 2016-07-27
    Changes: Database references
  • Version 1.3: 2017-09-27
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.4: 2019-12-04
    Changes: Author supporting evidence