2D7S

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.277 
  • R-Value Observed: 0.277 

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, 2F8E

  • 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-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 ...

    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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-dependent RNA polymeraseA474Foot-and-mouth disease virus C-S8c1Mutation(s): 0 
EC: 2.7.7.48 (PDB Primary Data), 3.4.22.28 (UniProt), 3.4.22.46 (UniProt), 3.6.1.15 (UniProt)
UniProt
Find proteins for Q9QCE4 (Foot-and-mouth disease virus - type C)
Explore Q9QCE4 
Go to UniProtKB:  Q9QCE4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9QCE4
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
VPg1 proteinB23N/AMutation(s): 0 
EC: 2.7.7.48
UniProt
Find proteins for Q9QCE4 (Foot-and-mouth disease virus - type C)
Explore Q9QCE4 
Go to UniProtKB:  Q9QCE4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9QCE4
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.277 
  • R-Value Observed: 0.277 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.09α = 90
b = 95.09β = 90
c = 100.628γ = 120
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-03-28
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance