4FNC

Human TDG in a post-reactive complex with 5-hydroxymethyluracil (5hmU)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.493 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Excision of 5-hydroxymethyluracil and 5-carboxylcytosine by the thymine DNA glycosylase domain: its structural basis and implications for active DNA demethylation.

Hashimoto, H.Hong, S.Bhagwat, A.S.Zhang, X.Cheng, X.

(2012) Nucleic Acids Res. 40: 10203-10214

  • DOI: 10.1093/nar/gks845

  • PubMed Abstract: 
  • The mammalian thymine DNA glycosylase (TDG) is implicated in active DNA demethylation via the base excision repair pathway. TDG excises the mismatched base from G:X mismatches, where X is uracil, thymine or 5-hydroxymethyluracil (5hmU). These are, re ...

    The mammalian thymine DNA glycosylase (TDG) is implicated in active DNA demethylation via the base excision repair pathway. TDG excises the mismatched base from G:X mismatches, where X is uracil, thymine or 5-hydroxymethyluracil (5hmU). These are, respectively, the deamination products of cytosine, 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). In addition, TDG excises the Tet protein products 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) but not 5hmC and 5mC, when paired with a guanine. Here we present a post-reactive complex structure of the human TDG domain with a 28-base pair DNA containing a G:5hmU mismatch. TDG flips the target nucleotide from the double-stranded DNA, cleaves the N-glycosidic bond and leaves the C1' hydrolyzed abasic sugar in the flipped state. The cleaved 5hmU base remains in a binding pocket of the enzyme. TDG allows hydrogen-bonding interactions to both T/U-based (5hmU) and C-based (5caC) modifications, thus enabling its activity on a wider range of substrates. We further show that the TDG catalytic domain has higher activity for 5caC at a lower pH (5.5) as compared to the activities at higher pH (7.5 and 8.0) and that the structurally related Escherichia coli mismatch uracil glycosylase can excise 5caC as well. We discuss several possible mechanisms, including the amino-imino tautomerization of the substrate base that may explain how TDG discriminates against 5hmC and 5mC.


    Organizational Affiliation

    Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
G/T mismatch-specific thymine DNA glycosylase
A
204Homo sapiensGene Names: TDG
EC: 3.2.2.29
Find proteins for Q13569 (Homo sapiens)
Go to Gene View: TDG
Go to UniProtKB:  Q13569
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (28-MER)C28N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (29-MER)D29N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HMU
Query on HMU

Download SDF File 
Download CCD File 
A
5-HYDROXYMETHYL URACIL
5-(HYDROXYMETHYL)PYRIMIDINE-2,4(1H,3H)-DIONE
C5 H6 N2 O3
JDBGXEHEIRGOBU-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
AAB
Query on AAB
D
DNA LINKINGC5 H11 O7 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.493 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.224 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 90.960α = 90.00
b = 53.720β = 96.49
c = 81.560γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
PHENIXphasing
HKL-2000data scaling
PHENIXmodel building
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-09-19
    Type: Initial release
  • Version 1.1: 2012-10-17
    Type: Database references
  • Version 1.2: 2012-11-21
    Type: Database references
  • Version 1.3: 2014-07-09
    Type: Non-polymer description