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: 3.01 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.225 

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:  
    3UOB, 3UO7

  • 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 hTDG catalytic domain in complex with duplex DNA containing either 5caC or a fluorinated analog ...

    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

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
G/T mismatch-specific thymine DNA glycosylase A, B201Homo sapiensMutation(s): 0 
Gene Names: TDG
EC: 3.2.2.29
Find proteins for Q13569 (Homo sapiens)
Explore Q13569 
Go to UniProtKB:  Q13569
NIH Common Fund Data Resources
PHAROS:  Q13569
GTEx:  ENSG00000139372
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
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
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.225 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 163.418α = 90
b = 163.418β = 90
c = 54.701γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHASESphasing
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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