5JKT

vaccinia virus D4 P173G mutant /A20(1-50)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural analysis of point mutations at the Vaccinia virus A20/D4 interface.

Contesto-Richefeu, C.Tarbouriech, N.Brazzolotto, X.Burmeister, W.P.Peyrefitte, C.N.Iseni, F.

(2016) Acta Crystallogr.,Sect.F 72: 687-691

  • DOI: 10.1107/S2053230X16011778
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The Vaccinia virus polymerase holoenzyme is composed of three subunits: E9, the catalytic DNA polymerase subunit; D4, a uracil-DNA glycosylase; and A20, a protein with no known enzymatic activity. The D4/A20 heterodimer is the DNA polymerase cofactor ...

    The Vaccinia virus polymerase holoenzyme is composed of three subunits: E9, the catalytic DNA polymerase subunit; D4, a uracil-DNA glycosylase; and A20, a protein with no known enzymatic activity. The D4/A20 heterodimer is the DNA polymerase cofactor, the function of which is essential for processive DNA synthesis. The recent crystal structure of D4 bound to the first 50 amino acids of A20 (D4/A201-50) revealed the importance of three residues, forming a cation-π interaction at the dimerization interface, for complex formation. These are Arg167 and Pro173 of D4 and Trp43 of A20. Here, the crystal structures of the three mutants D4-R167A/A201-50, D4-P173G/A201-50 and D4/A201-50-W43A are presented. The D4/A20 interface of the three structures has been analysed for atomic solvation parameters and cation-π interactions. This study confirms previous biochemical data and also points out the importance for stability of the restrained conformational space of Pro173. Moreover, these new structures will be useful for the design and rational improvement of known molecules targeting the D4/A20 interface.


    Organizational Affiliation

    Unité de Virologie, Institut de Recherche Biomédicale des Armées, BP 73, 91223 Brétigny-sur-Orge CEDEX, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uracil-DNA glycosylase
B, A
232Vaccinia virus (strain Copenhagen)Mutation(s): 1 
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): 0 
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
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.183 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 92.980α = 90.00
b = 92.980β = 90.00
c = 145.710γ = 120.00
Software Package:
Software NamePurpose
Aimlessdata scaling
MOLREPphasing
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceanr-13-bsv8-0014
German Research FoundationFrance--

Revision History 

  • Version 1.0: 2016-09-14
    Type: Initial release
  • Version 1.1: 2016-09-28
    Type: Database references
  • Version 1.2: 2017-09-06
    Type: Author supporting evidence