2OXM

Crystal structure of a UNG2/modified DNA complex that represent a stabilized short-lived extrahelical state in ezymatic DNA base flipping


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.328 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.257 

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:  
    2OXM, 2OYT

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Uracil-DNA glycosylaseA223Homo sapiensMutation(s): 0 
Gene Names: UNGDGUUNG1UNG15
EC: 3.2.2.27
Find proteins for P13051 (Homo sapiens)
Explore P13051 
Go to UniProtKB:  P13051
NIH Common Fund Data Resources
PHAROS  P13051
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*TP*GP*TP*TP*AP*TP*CP*TP*T)-3')B9N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*AP*AP*AP*GP*AP*TP*(4MF)P*AP*CP*A)-3')C10N/A
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.50 Å
      • R-Value Free: 0.328 
      • R-Value Work: 0.254 
      • R-Value Observed: 0.257 
      • Space Group: P 21 21 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 48.467α = 90
      b = 65.567β = 90
      c = 98.472γ = 90
      Software Package:
      Software NamePurpose
      DENZOdata reduction
      SCALEPACKdata scaling
      PHASERphasing
      REFMACrefinement
      PDB_EXTRACTdata extraction
      HKL-2000data collection
      HKL-2000data reduction

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2007-10-30
        Type: Initial release
      • Version 1.1: 2011-07-13
        Changes: Version format compliance
      • Version 1.2: 2017-10-18
        Changes: Refinement description
      • Version 1.3: 2018-01-24
        Changes: Structure summary