4XEG

Structure of the enzyme-product complex resulting from TDG action on a G/hmU mismatch


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Thymine DNA glycosylase exhibits negligible affinity for nucleobases that it removes from DNA.

Malik, S.S.Coey, C.T.Varney, K.M.Pozharski, E.Drohat, A.C.

(2015) Nucleic Acids Res. 43: 9541-9552

  • DOI: 10.1093/nar/gkv890
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Thymine DNA Glycosylase (TDG) performs essential functions in maintaining genetic integrity and epigenetic regulation. Initiating base excision repair, TDG removes thymine from mutagenic G ·: T mispairs caused by 5-methylcytosine (mC) deamination and ...

    Thymine DNA Glycosylase (TDG) performs essential functions in maintaining genetic integrity and epigenetic regulation. Initiating base excision repair, TDG removes thymine from mutagenic G ·: T mispairs caused by 5-methylcytosine (mC) deamination and other lesions including uracil (U) and 5-hydroxymethyluracil (hmU). In DNA demethylation, TDG excises 5-formylcytosine (fC) and 5-carboxylcytosine (caC), which are generated from mC by Tet (ten-eleven translocation) enzymes. Using improved crystallization conditions, we solved high-resolution (up to 1.45 Å) structures of TDG enzyme-product complexes generated from substrates including G·U, G·T, G·hmU, G·fC and G·caC. The structures reveal many new features, including key water-mediated enzyme-substrate interactions. Together with nuclear magnetic resonance experiments, the structures demonstrate that TDG releases the excised base from its tight product complex with abasic DNA, contrary to previous reports. Moreover, DNA-free TDG exhibits no significant binding to free nucleobases (U, T, hmU), indicating a Kd > 10 mM. The structures reveal a solvent-filled channel to the active site, which might facilitate dissociation of the excised base and enable caC excision, which involves solvent-mediated acid catalysis. Dissociation of the excised base allows TDG to bind the beta rather than the alpha anomer of the abasic sugar, which might stabilize the enzyme-product complex.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA.,Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA University of Maryland Marlene and Stewart Greenebaum Cancer Center, Baltimore, MD 21201, USA Center for Biomolecular Therapeutics, Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA EPozharskiy@som.umaryland.edu.,Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA University of Maryland Marlene and Stewart Greenebaum Cancer Center, Baltimore, MD 21201, USA adrohat@som.umaryland.edu.,Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA University of Maryland Marlene and Stewart Greenebaum Cancer Center, Baltimore, MD 21201, USA Center for Biomolecular Therapeutics, Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
G/T mismatch-specific thymine DNA glycosylase
A
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: 2
MoleculeChainsLengthOrganism
DNA (28-MER)C28unidentified
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (28-MER)D28unidentified
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

Download SDF File 
Download CCD File 
A
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ORP
Query on ORP
D
SACCHARIDEC5 H11 O7 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.188 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 89.199α = 90.00
b = 53.393β = 95.42
c = 82.220γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM072711

Revision History 

  • Version 1.0: 2015-09-09
    Type: Initial release
  • Version 1.1: 2015-09-23
    Type: Database references
  • Version 1.2: 2015-11-11
    Type: Database references
  • Version 1.3: 2017-09-06
    Type: Author supporting evidence, Database references, Derived calculations