2OYT

Crystal Structure of UNG2/DNA(TM)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Enzymatic capture of an extrahelical thymine in the search for uracil in DNA.

Parker, J.B.Bianchet, M.A.Krosky, D.J.Friedman, J.I.Amzel, L.M.Stivers, J.T.

(2007) Nature 449: 433-437

  • DOI: 10.1038/nature06131
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The enzyme uracil DNA glycosylase (UNG) excises unwanted uracil bases in the genome using an extrahelical base recognition mechanism. Efficient removal of uracil is essential for prevention of C-to-T transition mutations arising from cytosine deamina ...

    The enzyme uracil DNA glycosylase (UNG) excises unwanted uracil bases in the genome using an extrahelical base recognition mechanism. Efficient removal of uracil is essential for prevention of C-to-T transition mutations arising from cytosine deamination, cytotoxic U*A pairs arising from incorporation of dUTP in DNA, and for increasing immunoglobulin gene diversity during the acquired immune response. A central event in all of these UNG-mediated processes is the singling out of rare U*A or U*G base pairs in a background of approximately 10(9) T*A or C*G base pairs in the human genome. Here we establish for the human and Escherichia coli enzymes that discrimination of thymine and uracil is initiated by thermally induced opening of T*A and U*A base pairs and not by active participation of the enzyme. Thus, base-pair dynamics has a critical role in the genome-wide search for uracil, and may be involved in initial damage recognition by other DNA repair glycosylases.


    Organizational Affiliation

    Department of Pharmacology and Molecular Sciences, Johns Hopkins Medical School, 725 North Wolfe Street, Baltimore, Maryland 21205, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uracil-DNA glycosylase
A
223Homo sapiensMutation(s): 0 
Gene Names: UNG (DGU, UNG1, UNG15)
EC: 3.2.2.27
Find proteins for P13051 (Homo sapiens)
Go to Gene View: UNG
Go to UniProtKB:  P13051
Entity ID: 2
MoleculeChainsLengthOrganism
DNA strand1B9N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA strand2C10N/A
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
4MF
Query on 4MF
C
DNA LINKINGC14 H18 N O6 P

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AAB
Query on AAB
B
DNA LINKINGC5 H11 O7 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 48.499α = 90.00
b = 66.318β = 90.00
c = 100.316γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-10-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-07-09
    Type: Non-polymer description
  • Version 1.3: 2018-01-24
    Type: Structure summary