3UOB | pdb_00003uob

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

• PDB DOI: https://doi.org/10.2210/pdb3UOB/pdb
• NAKB: 3UOB

• Classification: HYDROLASE/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.01 Å
• R-Value Free: 
  0.276 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.234 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: experimental

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

• PubMed: 22327402 
• DOI: https://doi.org/10.1038/nchembio.914
• Primary Citation Related Structures: 
  3UO7, 3UOB


• 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. 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.

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Organizational Affiliation: 
• Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 59.73 kDa 
• Atom Count: 3,764 
• Modeled Residue Count: 399 
• Deposited Residue Count: 448 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
G/T mismatch-specific thymine DNA glycosylase	C [auth A], D [auth B]	201	Homo sapiens	Mutation(s): 0  Gene Names: TDG EC: 3.2.2.29
UniProt & NIH Common Fund Data Resources
Find proteins for Q13569 (Homo sapiens) Explore Q13569  Go to UniProtKB:  Q13569
PHAROS:  Q13569 GTEx:  ENSG00000139372

Entity ID: 1
Molecule	Chains	Length	Organism	Image
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'	A [auth C]	23	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
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'	B [auth D]	23	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.01 Å
• R-Value Free:  0.276 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.234 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 163.418	α = 90
b = 163.418	β = 90
c = 54.701	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description