6S2L

FMDV 3D polymerase crystallized in presence of (F)uridylylated VPg peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

(F)uridylylated Peptides Linked to VPg1 of Foot-and- Mouth Disease Virus (FMDV): Design, Synthesis and X-Ray Crystallography of the Complexes with FMDV RNA-Dependent RNA Polymerase.

de Castro, S.Ferrer-Orta, C.Mills, A.Fernandez-Cureses, G.Gago, F.Verdaguer, N.Camarasa, M.J.

(2019) Molecules 24: --

  • DOI: 10.3390/molecules24132360

  • PubMed Abstract: 
  • Foot-and-mouth disease virus (FMDV) is an RNA virus belonging to the <i>Picornaviridae </i> family that contains three small viral proteins (VPgs), named VPg1, VPg2 and VPg3, linked to the 5'-end of the viral genome. These VPg proteins act as primer ...

    Foot-and-mouth disease virus (FMDV) is an RNA virus belonging to the Picornaviridae family that contains three small viral proteins (VPgs), named VPg1, VPg2 and VPg3, linked to the 5'-end of the viral genome. These VPg proteins act as primers for RNA replication, which is initiated by the consecutive binding of two UMP molecules to the hydroxyl group of Tyr3 in VPg. This process, termed uridylylation, is catalyzed by the viral RNA-dependent RNA polymerase named 3D pol . 5-Fluorouridine triphosphate (FUTP) is a potent competitive inhibitor of VPg uridylylation. Peptide analysis showed FUMP covalently linked to the Tyr3 of VPg. This fluorouridylylation prevents further incorporation of the second UMP residue. The molecular basis of how the incorporated FUMP blocks the incorporation of the second UMP is still unknown. To investigate the mechanism of inhibition of VPg uridylylation by FUMP, we have prepared a simplified 15-mer model of VPg1 containing FUMP and studied its x-ray crystal structure in complex with 3D pol . Unfortunately, the fluorouridylylated VPg1 was disordered and not visible in the electron density maps; however, the structure of 3D pol in the presence of VPg1-FUMP showed an 8 Å movement of the β9-α11 loop of the polymerase towards the active site cavity relative to the complex of 3D pol with VPg1-UMP. The conformational rearrangement of this loop preceding the 3D pol B motif seems to block the access of the template nucleotide to the catalytic cavity. This result may be useful in the design of new antivirals against not only FMDV but also other picornaviruses, since all members of this family require the uridylylation of their VPg proteins to initiate the viral RNA synthesis.


    Organizational Affiliation

    Instituto de Química Médica (IQM-CSIC), Juan de la Cierva 3, E-28006 Madrid, Spain.,Instituto de Química Médica (IQM-CSIC), Juan de la Cierva 3, E-28006 Madrid, Spain. sonia@iqm.csic.es.,Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Spain.,Area de Farmacología, Departamento de Ciencias Biomédicas, Unidad Asociada al IQM-CSIC, Universidad de Alcalá, E-28805 Alcalá de Henares, Madrid, Spain.,Instituto de Química Médica (IQM-CSIC), Juan de la Cierva 3, E-28006 Madrid, Spain. mj.camarasa@iqm.csic.es.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Genome polyprotein
A
481Foot-and-mouth disease virus (isolate -/Spain/S8c1SantaPau/1970 serotype C)Mutation(s): 0 
Find proteins for P03311 (Foot-and-mouth disease virus (isolate -/Spain/S8c1SantaPau/1970 serotype C))
Go to UniProtKB:  P03311
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.197 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 93.850α = 90.00
b = 93.850β = 90.00
c = 121.310γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
REFMACphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-07-03
    Type: Initial release
  • Version 1.1: 2019-07-10
    Type: Data collection, Database references