3V1Q

Crystal structures of the reverse transcriptase-associated ribonuclease H domain of xenotropic murine leukemia-virus related virus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structures of the reverse transcriptase-associated ribonuclease H domain of xenotropic murine leukemia-virus related virus.

Zhou, D.Chung, S.Miller, M.Le Grice, S.F.Wlodawer, A.

(2012) J Struct Biol 177: 638-645

  • DOI: https://doi.org/10.1016/j.jsb.2012.02.006
  • Primary Citation of Related Structures:  
    3V1O, 3V1Q, 3V1R

  • PubMed Abstract: 

    The ribonuclease H (RNase H) domain of retroviral reverse transcriptase (RT) plays a critical role in the life cycle by degrading the RNA strands of DNA/RNA hybrids. In addition, RNase H activity is required to precisely remove the RNA primers from nascent (-) and (+) strand DNA. We report here three crystal structures of the RNase H domain of xenotropic murine leukemia virus-related virus (XMRV) RT, namely (i) the previously identified construct from which helix C was deleted, (ii) the intact domain, and (iii) the intact domain complexed with an active site α-hydroxytropolone inhibitor. Enzymatic assays showed that the intact RNase H domain retained catalytic activity, whereas the variant lacking helix C was only marginally active, corroborating the importance of this helix for enzymatic activity. Modeling of the enzyme-substrate complex elucidated the essential role of helix C in binding a DNA/RNA hybrid and its likely mode of recognition. The crystal structure of the RNase H domain complexed with β-thujaplicinol clearly showed that coordination by two divalent cations mediates recognition of the inhibitor.


  • Organizational Affiliation

    Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute at Frederick, Frederick, MD 21702, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Reverse transcriptase/ribonuclease H p80167Xenotropic MuLV-related virus VP35Mutation(s): 0 
Gene Names: gag-polPOL_XMRV3
EC: 3.1.26.4
UniProt
Find proteins for Q2F7J3 (Xenotropic MuLV-related virus (isolate VP35))
Explore Q2F7J3 
Go to UniProtKB:  Q2F7J3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2F7J3
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.172 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.53α = 90
b = 37.53β = 90
c = 99.91γ = 90
Software Package:
Software NamePurpose
HKL-3000data collection
PHASESphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-03-14
    Type: Initial release
  • Version 1.1: 2012-03-28
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references