4RPT

The 1.35A structure of a viral RNase L antagonist reveals basis for the 2'-5'-oligoadenylate binding and enzyme activity.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for 2'-5'-oligoadenylate binding and enzyme activity of a viral RNase L antagonist.

Ogden, K.M.Hu, L.Jha, B.K.Sankaran, B.Weiss, S.R.Silverman, R.H.Patton, J.T.Prasad, B.V.

(2015) J Virol 89: 6633-6645

  • DOI: 10.1128/JVI.00701-15
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Synthesis of 2'-5'-oligoadenylates (2-5A) by oligoadenylate synthetase (OAS) is an important innate cellular response that limits viral replication by activating the latent cellular RNase, RNase L, to degrade single-stranded RNA. Some rotaviruses and ...

    Synthesis of 2'-5'-oligoadenylates (2-5A) by oligoadenylate synthetase (OAS) is an important innate cellular response that limits viral replication by activating the latent cellular RNase, RNase L, to degrade single-stranded RNA. Some rotaviruses and coronaviruses antagonize the OAS/RNase L pathway through the activity of an encoded 2H phosphoesterase domain that cleaves 2-5A. These viral 2H phosphoesterases are phylogenetically related to the cellular A kinase anchoring protein 7 (AKAP7) and share a core structure and an active site that contains two well-defined HΦ(S/T)Φ (where Φ is a hydrophobic residue) motifs, but their mechanism of substrate binding is unknown. Here, we report the structures of a viral 2H phosphoesterase, the C-terminal domain (CTD) of the group A rotavirus (RVA) VP3 protein, both alone and in complex with 2-5A. The domain forms a compact fold, with a concave β-sheet that contains the catalytic cleft, but it lacks two α-helical regions and two β-strands observed in AKAP7 and other 2H phosphoesterases. The cocrystal structure shows significant conformational changes in the R loop upon ligand binding. Bioinformatics and biochemical analyses reveal that conserved residues and residues required for catalytic activity and substrate binding comprise the catalytic motifs and a region on one side of the binding cleft. We demonstrate that the VP3 CTD of group B rotavirus, but not that of group G, cleaves 2-5A. These findings suggest that the VP3 CTD is a streamlined version of a 2H phosphoesterase with a ligand-binding mechanism that is shared among 2H phosphodiesterases that cleave 2-5A.


    Organizational Affiliation

    Department of Microbiology and Immunology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461-1926, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Capping enzyme protein
A, B
144Rotavirus AMutation(s): 0 
EC: 3.1.4 (UniProt), 2.7.7.50 (UniProt), 2.1.1.56 (UniProt)
Find proteins for B3F2X4 (Rotavirus A (strain RVA/Monkey/United States/RRV/1975/G3P5B[3]))
Go to UniProtKB:  B3F2X4
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MLI
Query on MLI

Download CCD File 
A, B
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A, B
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.24α = 90
b = 68.37β = 106.88
c = 52.42γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SHELXSphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2014-10-31 
  • Released Date: 2015-04-29 
  • Deposition Author(s): Hu, L., Prasad, B.V.V.

Revision History 

  • Version 1.0: 2015-04-29
    Type: Initial release
  • Version 1.1: 2015-08-19
    Changes: Database references