4X2B

K20A RNA dependent RNA polymerase mutant from Foot-and-Mouth disease Virus complexed with an RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.94 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Multifunctionality of a picornavirus polymerase domain: nuclear localization signal and nucleotide recognition.

Ferrer-Orta, C.de la Higuera, I.Caridi, F.Sanchez-Aparicio, M.T.Moreno, E.Perales, C.Singh, K.Sarafianos, S.G.Sobrino, F.Domingo, E.Verdaguer, N.

(2015) J Virol 89: 6848-6859

  • DOI: 10.1128/JVI.03283-14
  • Primary Citation of Related Structures:  
    4X2B, 4WYL, 4WZQ, 4WZM, 4WYW

  • PubMed Abstract: 
  • The N-terminal region of the foot-and-mouth disease virus (FMDV) 3D polymerase contains the sequence MRKTKLAPT (residues 16 to 24) that acts as a nuclear localization signal. A previous study showed that substitutions K18E and K20E diminished the transport to the nucleus of 3D and 3CD and severely impaired virus infectivity ...

    The N-terminal region of the foot-and-mouth disease virus (FMDV) 3D polymerase contains the sequence MRKTKLAPT (residues 16 to 24) that acts as a nuclear localization signal. A previous study showed that substitutions K18E and K20E diminished the transport to the nucleus of 3D and 3CD and severely impaired virus infectivity. These residues have also been implicated in template binding, as seen in the crystal structures of different 3D-RNA elongation complexes. Here, we report the biochemical and structural characterization of different mutant polymerases harboring substitutions at residues 18 and 20, in particular, K18E, K18A, K20E, K20A, and the double mutant K18A K20A (KAKA). All mutant enzymes exhibit low RNA binding activity, low processivity, and alterations in nucleotide recognition, including increased incorporation of ribavirin monophosphate (RMP) relative to the incorporation of cognate nucleotides compared with the wild-type enzyme. The structural analysis shows an unprecedented flexibility of the 3D mutant polymerases, including both global rearrangements of the closed-hand architecture and local conformational changes at loop β9-α11 (within the polymerase motif B) and at the template-binding channel. Specifically, in 3D bound to RNA, both K18E and K20E induced the opening of new pockets in the template channel where the downstream templating nucleotide at position +2 binds. The comparisons of free and RNA-bound enzymes suggest that the structural rearrangements may occur in a concerted mode to regulate RNA replication, processivity, and fidelity. Thus, the N-terminal region of FMDV 3D that acts as a nuclear localization signal (NLS) and in template binding is also involved in nucleotide recognition and can affect the incorporation of nucleotide analogues.


    Organizational Affiliation

    Institut de Biologia Molecular de Barcelona, CSIC, Parc Científic de Barcelona, Barcelona, Spain nvmcri@ibmb.csic.es.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RNA dependent RNA polymeraseA481Foot-and-mouth disease virus (strain C1-Santa Pau)Mutation(s): 1 
EC: 2.7.7.48 (PDB Primary Data), 3.4.22.46 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt)
Find proteins for P03311 (Foot-and-mouth disease virus (isolate -/Spain/S8c1SantaPau/1970 serotype C))
Explore P03311 
Go to UniProtKB:  P03311
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    RNA templateB7synthetic construct
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      RNA primerC6synthetic construct
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      MG
      Query on MG

      Download Ideal Coordinates CCD File 
      D [auth A]MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.94 Å
      • R-Value Free: 0.259 
      • R-Value Work: 0.215 
      • R-Value Observed: 0.217 
      • Space Group: P 41 21 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 94.222α = 90
      b = 94.222β = 90
      c = 121.515γ = 90
      Software Package:
      Software NamePurpose
      REFMACrefinement
      XDSdata reduction
      SCALAdata scaling
      REFMACphasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2015-05-06
        Type: Initial release
      • Version 1.1: 2015-05-13
        Changes: Database references
      • Version 1.2: 2015-06-17
        Changes: Database references