2RBA

Structure of Human Thymine DNA Glycosylase Bound to Abasic and Undamaged DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of human thymine DNA glycosylase bound to DNA elucidates sequence-specific mismatch recognition.

Maiti, A.Morgan, M.T.Pozharski, E.Drohat, A.C.

(2008) Proc.Natl.Acad.Sci.Usa 105: 8890-8895

  • DOI: 10.1073/pnas.0711061105

  • PubMed Abstract: 
  • Cytosine methylation at CpG dinucleotides produces m(5)CpG, an epigenetic modification that is important for transcriptional regulation and genomic stability in vertebrate cells. However, m(5)C deamination yields mutagenic G.T mispairs, which are imp ...

    Cytosine methylation at CpG dinucleotides produces m(5)CpG, an epigenetic modification that is important for transcriptional regulation and genomic stability in vertebrate cells. However, m(5)C deamination yields mutagenic G.T mispairs, which are implicated in genetic disease, cancer, and aging. Human thymine DNA glycosylase (hTDG) removes T from G.T mispairs, producing an abasic (or AP) site, and follow-on base excision repair proteins restore the G.C pair. hTDG is inactive against normal A.T pairs, and is most effective for G.T mispairs and other damage located in a CpG context. The molecular basis of these important catalytic properties has remained unknown. Here, we report a crystal structure of hTDG (catalytic domain, hTDG(cat)) in complex with abasic DNA, at 2.8 A resolution. Surprisingly, the enzyme crystallized in a 2:1 complex with DNA, one subunit bound at the abasic site, as anticipated, and the other at an undamaged (nonspecific) site. Isothermal titration calorimetry and electrophoretic mobility-shift experiments indicate that hTDG and hTDG(cat) can bind abasic DNA with 1:1 or 2:1 stoichiometry. Kinetics experiments show that the 1:1 complex is sufficient for full catalytic (base excision) activity, suggesting that the 2:1 complex, if adopted in vivo, might be important for some other activity of hTDG, perhaps binding interactions with other proteins. Our structure reveals interactions that promote the stringent specificity for guanine versus adenine as the pairing partner of the target base and interactions that likely confer CpG sequence specificity. We find striking differences between hTDG and its prokaryotic ortholog (MUG), despite the relatively high (32%) sequence identity.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
G/T mismatch-specific thymine DNA glycosylase
A, B
204Homo sapiensMutation(s): 0 
Gene Names: TDG
EC: 3.2.2.29
Find proteins for Q13569 (Homo sapiens)
Go to Gene View: TDG
Go to UniProtKB:  Q13569
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*DCP*DAP*DGP*DCP*DTP*DCP*DTP*DGP*DTP*DAP*DCP*DGP*DTP*DGP*DAP*DGP*DCP*DAP*DGP*DTP*DGP*DGP*DA)-3')C23N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*DCP*DCP*DAP*DCP*DTP*DGP*DCP*DTP*DCP*DAP*(3DR)P*DGP*DTP*DAP*DCP*DAP*DGP*DAP*DGP*DCP*DTP*DGP*DT)-3')D23N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
3DR
Query on 3DR
D
DNA LINKINGC5 H11 O6 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.230 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 162.133α = 90.00
b = 162.133β = 90.00
c = 56.142γ = 120.00
Software Package:
Software NamePurpose
Blu-Icedata collection
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-06-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance