3P1G

Crystal Structure of the Xenotropic Murine Leukemia Virus-Related Virus (XMRV) RNase H Domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural and Inhibition Studies of the RNase H Function of Xenotropic Murine Leukemia Virus-Related Virus Reverse Transcriptase.

Kirby, K.A.Marchand, B.Ong, Y.T.Ndongwe, T.P.Hachiya, A.Michailidis, E.Leslie, M.D.Sietsema, D.V.Fetterly, T.L.Dorst, C.A.Singh, K.Wang, Z.Parniak, M.A.Sarafianos, S.G.

(2012) Antimicrob.Agents Chemother. 56: 2048-2061

  • DOI: 10.1128/AAC.06000-11

  • PubMed Abstract: 
  • RNase H inhibitors (RNHIs) have gained attention as potential HIV-1 therapeutics. Although several RNHIs have been studied in the context of HIV-1 reverse transcriptase (RT) RNase H, there is no information on inhibitors that might affect the RNase H ...

    RNase H inhibitors (RNHIs) have gained attention as potential HIV-1 therapeutics. Although several RNHIs have been studied in the context of HIV-1 reverse transcriptase (RT) RNase H, there is no information on inhibitors that might affect the RNase H activity of other RTs. We performed biochemical, virological, crystallographic, and molecular modeling studies to compare the RNase H function and inhibition profiles of the gammaretroviral xenotropic murine leukemia virus-related virus (XMRV) and Moloney murine leukemia virus (MoMLV) RTs to those of HIV-1 RT. The RNase H activity of XMRV RT is significantly lower than that of HIV-1 RT and comparable to that of MoMLV RT. XMRV and MoMLV, but not HIV-1 RT, had optimal RNase H activities in the presence of Mn²⁺ and not Mg²⁺. Using hydroxyl-radical footprinting assays, we demonstrated that the distance between the polymerase and RNase H domains in the MoMLV and XMRV RTs is longer than that in the HIV-1 RT by ∼3.4 Å. We identified one naphthyridinone and one hydroxyisoquinolinedione as potent inhibitors of HIV-1 and XMRV RT RNases H with 50% inhibitory concentrations ranging from ∼0.8 to 0.02 μM. Two acylhydrazones effective against HIV-1 RT RNase H were less potent against the XMRV enzyme. We also solved the crystal structure of an XMRV RNase H fragment at high resolution (1.5 Å) and determined the molecular details of the XMRV RNase H active site, thus providing a framework that would be useful for the design of antivirals that target RNase H.


    Organizational Affiliation

    Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Xenotropic Murine Leukemia Virus-Related Virus (XMRV) RNase H Domain
A
165Xenotropic MuLV-related virus (isolate VP62)Mutation(s): 0 
Gene Names: gag-pol
Find proteins for A1Z651 (Xenotropic MuLV-related virus (isolate VP62))
Go to UniProtKB:  A1Z651
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.161 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 37.530α = 90.00
b = 37.530β = 90.00
c = 100.720γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
d*TREKdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-10-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-02-01
    Type: Database references
  • Version 1.3: 2012-04-04
    Type: Database references