2OWQ

Crystal structure of vaccinia virus uracil-DNA glycosylase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.241 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of vaccinia virus uracil-DNA glycosylase reveals dimeric assembly

Schormann, N.Grigorian, A.Samal, A.Krishnan, R.DeLucas, L.Chattopadhyay, D.

(2007) Bmc Struct.Biol. 7: 45-45

  • DOI: 10.1186/1472-6807-7-45
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Uracil-DNA glycosylases (UDGs) catalyze excision of uracil from DNA. Vaccinia virus, which is the prototype of poxviruses, encodes a UDG (vvUDG) that is significantly different from the UDGs of other organisms in primary, secondary and tertiary struc ...

    Uracil-DNA glycosylases (UDGs) catalyze excision of uracil from DNA. Vaccinia virus, which is the prototype of poxviruses, encodes a UDG (vvUDG) that is significantly different from the UDGs of other organisms in primary, secondary and tertiary structure and characteristic motifs. It adopted a novel catalysis-independent role in DNA replication that involves interaction with a viral protein, A20, to form the processivity factor. UDG:A20 association is essential for assembling of the processive DNA polymerase complex. The structure of the protein must have provisions for such interactions with A20. This paper provides the first glimpse into the structure of a poxvirus UDG.


    Organizational Affiliation

    Center for Biophysical Sciences & Engineering, University of Alabama at Birmingham, Birmingham, AL 35294, USA. nschorm@uab.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uracil-DNA glycosylase
A, B
238Vaccinia virus (strain Western Reserve)Mutation(s): 1 
Gene Names: UNG (TS17)
EC: 3.2.2.27
Find proteins for P04303 (Vaccinia virus (strain Western Reserve))
Go to Gene View: UNG
Go to UniProtKB:  P04303
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
IMD
Query on IMD

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Download CCD File 
A, B
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.241 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 85.197α = 90.00
b = 85.197β = 90.00
c = 139.725γ = 120.00
Software Package:
Software NamePurpose
SHELXSphasing
REFMACrefinement
d*TREKdata scaling
StructureStudiodata collection
d*TREKdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-07-24
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.3: 2016-06-29
    Type: Source and taxonomy