2BOO

The crystal structure of Uracil-DNA N-Glycosylase (UNG) from Deinococcus radiodurans.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the Uracil-DNA N-Glycosylase (Ung) from Deinococcus Radiodurans.

Leiros, I.Moe, E.Smalas, A.O.Mcsweeney, S.

(2005) Acta Crystallogr.,Sect.D 61: 1049

  • DOI: 10.1107/S090744490501382X

  • PubMed Abstract: 
  • Uracil-DNA glycosylases are DNA-repair enzymes that catalyse the removal of promutagenic uracil from single- and double-stranded DNA, thereby initiating the base-excision repair (BER) pathway. Uracil in DNA can occur by mis-incorporation of dUMP in p ...

    Uracil-DNA glycosylases are DNA-repair enzymes that catalyse the removal of promutagenic uracil from single- and double-stranded DNA, thereby initiating the base-excision repair (BER) pathway. Uracil in DNA can occur by mis-incorporation of dUMP in place of dTMP during DNA synthesis or by deamination of cytosine, resulting in U-A or U-G mispairs. The radiation-resistant bacterium Deinococcus radiodurans has an elevated number of uracil-DNA glycosylases compared with most other organisms. The crystal structure of dr0689 (uracil-DNA N-glycosylase), which has been shown to be the major contributor to the removal of mis-incorporated uracil bases in crude cell extracts of D. radiodurans, is reported.


    Organizational Affiliation

    The European Synchrotron Radiation Facility, 38043 Grenoble CEDEX 9, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
URACIL-DNA GLYCOSYLASE
A
247Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)Mutation(s): 0 
Gene Names: ung
EC: 3.2.2.27
Find proteins for Q9RWH9 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
Go to UniProtKB:  Q9RWH9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NO3
Query on NO3

Download SDF File 
Download CCD File 
A
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.234 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 63.500α = 90.00
b = 85.100β = 90.00
c = 85.900γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
XDSdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-07-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2019-04-03
    Type: Advisory, Data collection, Derived calculations, Experimental preparation, Other