5N8X

Trigonal structure of mutant V173I of 3D polymerase from Foot-and-Mouth Disease Virus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.252 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Molecular and Functional Bases of Selection against a Mutation Bias in an RNA Virus.

de la Higuera, I.Ferrer-Orta, C.de Avila, A.I.Perales, C.Sierra, M.Singh, K.Sarafianos, S.G.Dehouck, Y.Bastolla, U.Verdaguer, N.Domingo, E.

(2017) Genome Biol Evol 9: 1212-1228

  • DOI: 10.1093/gbe/evx075
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The selective pressures acting on viruses that replicate under enhanced mutation rates are largely unknown. Here, we describe resistance of foot-and-mouth disease virus to the mutagen 5-fluorouracil (FU) through a single polymerase substitution that ...

    The selective pressures acting on viruses that replicate under enhanced mutation rates are largely unknown. Here, we describe resistance of foot-and-mouth disease virus to the mutagen 5-fluorouracil (FU) through a single polymerase substitution that prevents an excess of A to G and U to C transitions evoked by FU on the wild-type foot-and-mouth disease virus, while maintaining the same level of mutant spectrum complexity. The polymerase substitution inflicts upon the virus a fitness loss during replication in absence of FU but confers a fitness gain in presence of FU. The compensation of mutational bias was documented by in vitro nucleotide incorporation assays, and it was associated with structural modifications at the N-terminal region and motif B of the viral polymerase. Predictions of the effect of mutations that increase the frequency of G and C in the viral genome and encoded polymerase suggest multiple points in the virus life cycle where the mutational bias in favor of G and C may be detrimental. Application of predictive algorithms suggests adverse effects of the FU-directed mutational bias on protein stability. The results reinforce modulation of nucleotide incorporation as a lethal mutagenesis-escape mechanism (that permits eluding virus extinction despite replication in the presence of a mutagenic agent) and suggest that mutational bias can be a target of selection during virus replication.


    Organizational Affiliation

    Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3D polymerase
A
481Foot-and-mouth disease virus (isolate -/Spain/S8c1SantaPau/1970 serotype C)Mutation(s): 1 
Find proteins for P03311 (Foot-and-mouth disease virus (isolate -/Spain/S8c1SantaPau/1970 serotype C))
Go to UniProtKB:  P03311
Small Molecules
Ligands 2 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
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: 2.4 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.252 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 93.506α = 90.00
b = 93.506β = 90.00
c = 99.626γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
REFMACphasing
SCALAdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-05-10
    Type: Initial release
  • Version 1.1: 2017-05-31
    Type: Database references