3P1G

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 

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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
  • Primary Citation of Related Structures:  
    3P1G

  • 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 activity of other RTs ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Xenotropic Murine Leukemia Virus-Related Virus (XMRV) RNase H Domain A165Xenotropic MuLV-related virusMutation(s): 0 
EC: 3.4.23 (UniProt), 2.7.7.49 (UniProt), 2.7.7.7 (UniProt), 3.1.26.4 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
Find proteins for A1Z651 (Xenotropic MuLV-related virus (isolate VP62))
Explore A1Z651 
Go to UniProtKB:  A1Z651
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.53α = 90
b = 37.53β = 90
c = 100.72γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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