1UGH

CRYSTAL STRUCTURE OF HUMAN URACIL-DNA GLYCOSYLASE IN COMPLEX WITH A PROTEIN INHIBITOR: PROTEIN MIMICRY OF DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of human uracil-DNA glycosylase in complex with a protein inhibitor: protein mimicry of DNA.

Mol, C.D.Arvai, A.S.Sanderson, R.J.Slupphaug, G.Kavli, B.Krokan, H.E.Mosbaugh, D.W.Tainer, J.A.

(1995) Cell 82: 701-708


  • PubMed Abstract: 
  • Uracil-DNA glycosylase inhibitor (Ugi) is a B. subtilis bacteriophage protein that protects the uracil-containing phage DNA by irreversibly inhibiting the key DNA repair enzyme uracil-DNA glycosylase (UDG). The 1.9 A crystal structure of Ugi complexe ...

    Uracil-DNA glycosylase inhibitor (Ugi) is a B. subtilis bacteriophage protein that protects the uracil-containing phage DNA by irreversibly inhibiting the key DNA repair enzyme uracil-DNA glycosylase (UDG). The 1.9 A crystal structure of Ugi complexed to human UDG reveals that the Ugi structure, consisting of a twisted five-stranded antiparallel beta sheet and two alpha helices, binds by inserting a beta strand into the conserved DNA-binding groove of the enzyme without contacting the uracil specificity pocket. The resulting interface, which buries over 1200 A2 on Ugi and involves the entire beta sheet and an alpha helix, is polar and contains 22 water molecules. Ugi binds the sequence-conserved DNA-binding groove of UDG via shape and electrostatic complementarity, specific charged hydrogen bonds, and hydrophobic packing enveloping Leu-272 from a protruding UDG loop. The apparent mimicry by Ugi of DNA interactions with UDG provides both a structural mechanism for UDG binding to DNA, including the enzyme-assisted expulsion of uracil from the DNA helix, and a crystallographic basis for the design of inhibitors with scientific and therapeutic applications.


    Related Citations: 
    • Protein Mimicry of DNA from Crystal Structures of the Uracil-DNA Glycosylase Inhibitor Protein and its Complex with Escherichia Coli Uracil-DNA Glycosylase
      Putnam, C.D.,Shroyer, M.J.N.,Lundquist, A.J.,Mol, C.D.,Arvai, A.S.,Mosbaugh, D.W.,Tainer, J.A.
      (1999) J.Mol.Biol. 287: 331
    • 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
    • Crystal Structure and Mutational Analysis of Human Uracil-DNA Glycosylase: Structural Basis for Specificity and Catalysis
      Mol, C.D.,Arvai, A.S.,Slupphaug, G.,Kavli, B.,Alseth, I.,Krokan, H.E.,Tainer, J.A.
      (1995) Cell 80: 869
    • 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

    Department of Molecular Biology, Scripps Research Institute, La Jolla, California 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (URACIL-DNA GLYCOSYLASE)
E
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
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (URACIL-DNA GLYCOSYLASE INHIBITOR)
I
82Bacillus phage PBS2Mutation(s): 0 
Gene Names: UGI
Find proteins for P14739 (Bacillus phage PBS2)
Go to UniProtKB:  P14739
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 48.320α = 90.00
b = 64.690β = 113.77
c = 55.340γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
SCALEPACKdata scaling
DENZOdata reduction
X-PLORphasing
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-02-16
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance