1SSP

WILD-TYPE URACIL-DNA GLYCOSYLASE BOUND TO URACIL-CONTAINING DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Base excision repair initiation revealed by crystal structures and binding kinetics of human uracil-DNA glycosylase with DNA.

Parikh, S.S.Mol, C.D.Slupphaug, G.Bharati, S.Krokan, H.E.Tainer, J.A.

(1998) EMBO J 17: 5214-5226

  • DOI: 10.1093/emboj/17.17.5214
  • Primary Citation of Related Structures:  
    2SSP, 1AKZ, 1SSP

  • PubMed Abstract: 
  • Three high-resolution crystal structures of DNA complexes with wild-type and mutant human uracil-DNA glycosylase (UDG), coupled kinetic characterizations and comparisons with the refined unbound UDG structure help resolve fundamental issues in the in ...

    Three high-resolution crystal structures of DNA complexes with wild-type and mutant human uracil-DNA glycosylase (UDG), coupled kinetic characterizations and comparisons with the refined unbound UDG structure help resolve fundamental issues in the initiation of DNA base excision repair (BER): damage detection, nucleotide flipping versus extrahelical nucleotide capture, avoidance of apurinic/apyrimidinic (AP) site toxicity and coupling of damage-specific and damage-general BER steps. Structural and kinetic results suggest that UDG binds, kinks and compresses the DNA backbone with a 'Ser-Pro pinch' and scans the minor groove for damage. Concerted shifts in UDG simultaneously form the catalytically competent active site and induce further compression and kinking of the double-stranded DNA backbone only at uracil and AP sites, where these nucleotides can flip at the phosphate-sugar junction into a complementary specificity pocket. Unexpectedly, UDG binds to AP sites more tightly and more rapidly than to uracil-containing DNA, and thus may protect cells sterically from AP site toxicity. Furthermore, AP-endonuclease, which catalyzes the first damage-general step of BER, enhances UDG activity, most likely by inducing UDG release via shared minor groove contacts and flipped AP site binding. Thus, AP site binding may couple damage-specific and damage-general steps of BER without requiring direct protein-protein interactions.


    Related Citations: 
    • A Nucleotide-Flipping Mechanism from the Structure of Human Uracil-DNA Glycosylase Bound to DNA
      Slupphaug, G., Mol, C.D., Kavli, B., Arvai, A.S., Krokan, H.E., Tainer, J.A.
      (1996) Nature 384: 87

    Organizational Affiliation

    The Skaggs Institute for Chemical Biology, Department of Molecular Biology, MB-4, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037-1027, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
URACIL-DNA GLYCOSYLASEE223Homo sapiensMutation(s): 0 
Gene Names: UNGDGUUNG1UNG15
EC: 3.2.2.3 (PDB Primary Data), 3.2.2.27 (UniProt)
Find proteins for P13051 (Homo sapiens)
Explore P13051 
Go to UniProtKB:  P13051
NIH Common Fund Data Resources
PHAROS  P13051
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*CP*TP*GP*TP*(D1P)P*AP*TP*CP*TP*T)-3'A10N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-D(*AP*AP*AP*GP*AP*TP*AP*AP*CP*AP*G)-3'B11N/A
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      URA
      Query on URA

      Download CCD File 
      E
      URACIL
      C4 H4 N2 O2
      ISAKRJDGNUQOIC-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.90 Å
      • R-Value Free: 0.245 
      • R-Value Work: 0.198 
      • R-Value Observed: 0.198 
      • Space Group: P 21 21 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 121.7α = 90
      b = 48.5β = 90
      c = 65γ = 90
      Software Package:
      Software NamePurpose
      DENZOdata reduction
      SCALEPACKdata scaling
      AMoREphasing
      X-PLORrefinement

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 1999-05-06
        Type: Initial release
      • Version 1.1: 2008-04-26
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance