4SKN

A NUCLEOTIDE-FLIPPING MECHANISM FROM THE STRUCTURE OF HUMAN URACIL-DNA GLYCOSYLASE BOUND TO DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 87-92

  • DOI: 10.1038/384087a0

  • PubMed Abstract: 
  • Any uracil bases in DNA, a result of either misincorporation or deamination of cytosine, are removed by uracil-DNA glycosylase (UDG), one of the most efficient and specific of the base-excision DNA-repair enzymes. Crystal structures of human and vira ...

    Any uracil bases in DNA, a result of either misincorporation or deamination of cytosine, are removed by uracil-DNA glycosylase (UDG), one of the most efficient and specific of the base-excision DNA-repair enzymes. Crystal structures of human and viral UDGs complexed with free uracil have indicated that the enzyme binds an extrahelical uracil. Such binding of undamaged extrahelical bases has been seen in the structures of two bacterial methyltransferases and bacteriophage T4 endonuclease V. Here we characterize the DNA binding and kinetics of several engineered human UDG mutants and present the crystal structure of one of these, which to our knowledge represents the first structure of any eukaryotic DNA repair enzyme in complex with its damaged, target DNA. Electrostatic orientation along the UDG active site, insertion of an amino acid (residue 272) into the DNA through the minor groove, and compression of the DNA backbone flanking the uracil all result in the flipping-out of the damaged base from the DNA major groove, allowing specific recognition of its phosphate, deoxyribose and uracil moieties. Our structure thus provides a view of a productive complex specific for cleavage of uracil from DNA and also reveals the basis for the enzyme-assisted nucleotide flipping by this critical DNA-repair enzyme.


    Organizational Affiliation

    UNIGEN Center for Molecular Biology, The Norwegian University of Science and Technology, Trondheim, Norway.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (URACIL-DNA GLYCOSYLASE)
E
223Homo sapiensMutation(s): 2 
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: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*GP*GP*GP*(D1P)P*GP*GP*CP*TP*T)-3')A10N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*AP*AP*GP*CP*CP*GP*CP*CP*C)-3')B10N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
URA
Query on URA

Download SDF File 
Download CCD File 
E
URACIL
C4 H4 N2 O2
ISAKRJDGNUQOIC-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ORP
Query on ORP
A
SACCHARIDEC5 H11 O7 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 48.830α = 90.00
b = 65.660β = 90.00
c = 97.150γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
AMoREphasing
X-PLORrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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