2OWQ

Crystal structure of vaccinia virus uracil-DNA glycosylase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.244 

wwPDB Validation   3D Report Full Report


This is version 1.5 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: https://doi.org/10.1186/1472-6807-7-45
  • Primary Citation of Related Structures:  
    2OWQ

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uracil-DNA glycosylase
A, B
238Vaccinia virus Western ReserveMutation(s): 1 
Gene Names: D4RVACWR109
EC: 3.2.2
UniProt
Find proteins for P04303 (Vaccinia virus (strain Western Reserve))
Explore P04303 
Go to UniProtKB:  P04303
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04303
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
J [auth B],
K [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
IMD
Query on IMD

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
H [auth B]
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.244 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.197α = 90
b = 85.197β = 90
c = 139.725γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
StructureStudiodata collection
d*TREKdata reduction
d*TREKdata scaling
SHELXSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-07-24
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2016-06-29
    Changes: Source and taxonomy
  • Version 1.4: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.5: 2024-02-21
    Changes: Data collection, Refinement description