4OD8

Crystal structure of the vaccinia virus DNA polymerase holoenzyme subunit D4 in complex with the A20 N-terminus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure of the vaccinia virus DNA polymerase holoenzyme subunit d4 in complex with the a20 N-terminal domain.

Contesto-Richefeu, C.Tarbouriech, N.Brazzolotto, X.Betzi, S.Morelli, X.Burmeister, W.P.Iseni, F.

(2014) Plos Pathog. 10: e1003978-e1003978

  • DOI: 10.1371/journal.ppat.1003978
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Vaccinia virus polymerase holoenzyme is composed of the DNA polymerase E9, the uracil-DNA glycosylase D4 and A20, a protein with no known enzymatic activity. The D4/A20 heterodimer is the DNA polymerase co-factor whose function is essential for proce ...

    Vaccinia virus polymerase holoenzyme is composed of the DNA polymerase E9, the uracil-DNA glycosylase D4 and A20, a protein with no known enzymatic activity. The D4/A20 heterodimer is the DNA polymerase co-factor whose function is essential for processive DNA synthesis. Genetic and biochemical data have established that residues located in the N-terminus of A20 are critical for binding to D4. However, no information regarding the residues of D4 involved in A20 binding is yet available. We expressed and purified the complex formed by D4 and the first 50 amino acids of A20 (D4/A20₁₋₅₀). We showed that whereas D4 forms homodimers in solution when expressed alone, D4/A20₁₋₅₀ clearly behaves as a heterodimer. The crystal structure of D4/A20₁₋₅₀ solved at 1.85 Å resolution reveals that the D4/A20 interface (including residues 167 to 180 and 191 to 206 of D4) partially overlaps the previously described D4/D4 dimer interface. A20₁₋₅₀ binding to D4 is mediated by an α-helical domain with important leucine residues located at the very N-terminal end of A20 and a second stretch of residues containing Trp43 involved in stacking interactions with Arg167 and Pro173 of D4. Point mutations of the latter residues disturb D4/A20₁₋₅₀ formation and reduce significantly thermal stability of the complex. Interestingly, small molecule docking with anti-poxvirus inhibitors selected to interfere with D4/A20 binding could reproduce several key features of the D4/A20₁₋₅₀ interaction. Finally, we propose a model of D4/A20₁₋₅₀ in complex with DNA and discuss a number of mutants described in the literature, which affect DNA synthesis. Overall, our data give new insights into the assembly of the poxvirus DNA polymerase cofactor and may be useful for the design and rational improvement of antivirals targeting the D4/A20 interface.


    Organizational Affiliation

    Département de Toxicologie et Risque Chimique, Institut de Recherche Biomédicale des Armées, Brétigny-sur-Orge, France.,Unité de Virologie, Institut de Recherche Biomédicale des Armées, Brétigny-sur-Orge, France.,Université Grenoble Alpes, UVHCI, Grenoble, France; CNRS, UVHCI, Grenoble, France; Unit for Virus Host-Cell Interactions, UMI 3265, Université Grenoble Alpes-EMBL-CNRS, Grenoble, France.,Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS UMR 7258, INSERM U 1068, Institut Paoli-Calmettes & Aix-Marseille Universités, Marseille, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uracil-DNA glycosylase
B, A
232Vaccinia virus (strain Copenhagen)Mutation(s): 0 
Gene Names: UNG
EC: 3.2.2.27
Find proteins for P20536 (Vaccinia virus (strain Copenhagen))
Go to Gene View: UNG
Go to UniProtKB:  P20536
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase processivity factor component A20
D, C
52Vaccinia virus (strain Copenhagen)Mutation(s): 1 
Find proteins for P20995 (Vaccinia virus (strain Copenhagen))
Go to UniProtKB:  P20995
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
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: 1.85 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.175 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 92.620α = 90.00
b = 92.620β = 90.00
c = 145.860γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
DNAdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-26
    Type: Initial release