2F8E

Foot and Mouth Disease Virus RNA-dependent RNA polymerase in complex with uridylylated VPg protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The structure of a protein primer-polymerase complex in the initiation of genome replication

Ferrer-Orta, C.Arias, A.Agudo, R.Perez-Luque, R.Escarmis, C.Domingo, E.Verdaguer, N.

(2006) Embo J. 25: 880-888

  • DOI: 10.1038/sj.emboj.7600971
  • Primary Citation of Related Structures:  2D7S
  • Also Cited By: 2E9R, 2E9T, 2EC0

  • PubMed Abstract: 
  • Picornavirus RNA replication is initiated by the covalent attachment of a UMP molecule to the hydroxyl group of a tyrosine in the terminal protein VPg. This reaction is carried out by the viral RNA-dependent RNA polymerase (3D). Here, we report the X ...

    Picornavirus RNA replication is initiated by the covalent attachment of a UMP molecule to the hydroxyl group of a tyrosine in the terminal protein VPg. This reaction is carried out by the viral RNA-dependent RNA polymerase (3D). Here, we report the X-ray structure of two complexes between foot-and-mouth disease virus 3D, VPg1, the substrate UTP and divalent cations, in the absence and in the presence of an oligoadenylate of 10 residues. In both complexes, VPg fits the RNA binding cleft of the polymerase and projects the key residue Tyr3 into the active site of 3D. This is achieved by multiple interactions with residues of motif F and helix alpha8 of the fingers domain and helix alpha13 of the thumb domain of the polymerase. The complex obtained in the presence of the oligoadenylate showed the product of the VPg uridylylation (VPg-UMP). Two metal ions and the catalytic aspartic acids of the polymerase active site, together with the basic residues of motif F, have been identified as participating in the priming reaction.


    Related Citations: 
    • Structure of foot-and-mouth disease virus RNA-dependent RNA polymerase and its complex with a template-primer RNA
      Ferrer-Orta, C.,Arias, A.,Perez-Luque, R.,Escarmis, C.,Domingo, E.,Verdaguer, N.
      (2004) J.Biol.Chem. 279: 47212


    Organizational Affiliation

    Institut de Biologia Molecular de Barcelona (CSIC), Parc Científic de Barcelona, Barcelona, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA-dependent RNA polymerase
X
474Foot-and-mouth disease virus - type CN/A
Find proteins for Q0QEE0 (Foot-and-mouth disease virus - type C)
Go to UniProtKB:  Q0QEE0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
VPg protein
A
23Foot-and-mouth disease virus - type Asia 1N/A
Find proteins for Q9DS05 (Foot-and-mouth disease virus - type Asia 1)
Go to UniProtKB:  Q9DS05
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
U5P
Query on U5P

Download SDF File 
Download CCD File 
A
URIDINE-5'-MONOPHOSPHATE
C9 H13 N2 O9 P
DJJCXFVJDGTHFX-XVFCMESISA-N
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.234 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 94.381α = 90.00
b = 94.381β = 90.00
c = 99.726γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
REFMACrefinement
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-03-28
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance