3UOB

Crystal structure of Human Thymine DNA Glycosylase Bound to Substrate Analog 2'-deoxy-2'-beta-fluoro-cytidine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.011 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Thymine DNA glycosylase specifically recognizes 5-carboxylcytosine-modified DNA.

Zhang, L.Lu, X.Lu, J.Liang, H.Dai, Q.Xu, G.L.Luo, C.Jiang, H.He, C.

(2012) Nat.Chem.Biol. 8: 328-330

  • DOI: 10.1038/nchembio.914
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human thymine DNA glycosylase (hTDG) efficiently excises 5-carboxylcytosine (5caC), a key oxidation product of 5-methylcytosine in genomic DNA, in a recently discovered cytosine demethylation pathway. We present here the crystal structures of the hTD ...

    Human thymine DNA glycosylase (hTDG) efficiently excises 5-carboxylcytosine (5caC), a key oxidation product of 5-methylcytosine in genomic DNA, in a recently discovered cytosine demethylation pathway. We present here the crystal structures of the hTDG catalytic domain in complex with duplex DNA containing either 5caC or a fluorinated analog. These structures, together with biochemical and computational analyses, reveal that 5caC is specifically recognized in the active site of hTDG, supporting the role of TDG in mammalian 5-methylcytosine demethylation.


    Organizational Affiliation

    Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
G/T mismatch-specific thymine DNA glycosylase
A, B
201Homo 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
5'-D(*CP*AP*GP*CP*TP*CP*TP*GP*TP*AP*CP*GP*TP*GP*AP*GP*CP*AP*GP*TP*GP*GP*A)-3'C23N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*CP*CP*AP*CP*TP*GP*CP*TP*CP*AP*(1FC)P*GP*TP*AP*CP*AP*GP*AP*GP*CP*TP*GP*T)-3'D23N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
1FC
Query on 1FC
D
DNA LINKINGC10 H13 F N3 O9 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.011 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.219 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 163.418α = 90.00
b = 163.418β = 90.00
c = 54.701γ = 120.00
Software Package:
Software NamePurpose
PHASESphasing
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-11-16 
  • Released Date: 2012-02-15 
  • Deposition Author(s): Zhang, L., He, C.

Revision History 

  • Version 1.0: 2012-02-15
    Type: Initial release
  • Version 1.1: 2015-06-03
    Type: Database references