4E9F

Structure of the glycosylase domain of MBD4 bound to AP site containing DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Biochemical and structural characterization of the glycosylase domain of MBD4 bound to thymine and 5-hydroxymethyuracil-containing DNA.

Morera, S.Grin, I.Vigouroux, A.Couve, S.Henriot, V.Saparbaev, M.Ishchenko, A.A.

(2012) Nucleic Acids Res 40: 9917-9926

  • DOI: https://doi.org/10.1093/nar/gks714
  • Primary Citation of Related Structures:  
    4E9E, 4E9F, 4E9G, 4E9H, 4EA4, 4EA5

  • PubMed Abstract: 

    Active DNA demethylation in mammals occurs via hydroxylation of 5-methylcytosine to 5-hydroxymethylcytosine (5hmC) by the ten-eleven translocation family of proteins (TETs). 5hmC residues in DNA can be further oxidized by TETs to 5-carboxylcytosines and/or deaminated by the Activation Induced Deaminase/Apolipoprotein B mRNA-editing enzyme complex family proteins to 5-hydromethyluracil (5hmU). Excision and replacement of these intermediates is initiated by DNA glycosylases such as thymine-DNA glycosylase (TDG), methyl-binding domain protein 4 (MBD4) and single-strand specific monofunctional uracil-DNA glycosylase 1 in the base excision repair pathway. Here, we report detailed biochemical and structural characterization of human MBD4 which contains mismatch-specific TDG activity. Full-length as well as catalytic domain (residues 426-580) of human MBD4 (MBD4(cat)) can remove 5hmU when opposite to G with good efficiency. Here, we also report six crystal structures of human MBD4(cat): an unliganded form and five binary complexes with duplex DNA containing a T•G, 5hmU•G or AP•G (apurinic/apyrimidinic) mismatch at the target base pair. These structures reveal that MBD4(cat) uses a base flipping mechanism to specifically recognize thymine and 5hmU. The recognition mechanism of flipped-out 5hmU bases in MBD4(cat) active site supports the potential role of MBD4, together with TDG, in maintenance of genome stability and active DNA demethylation in mammals.


  • Organizational Affiliation

    Laboratoire d'Enzymologie et Biochimie Structurales, CNRS, Gif-sur-Yvette Cedex, F-91198, France. morera@lebs.cnrs-gif.fr


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methyl-CpG-binding domain protein 4161Homo sapiensMutation(s): 0 
Gene Names: MBD4MED1
EC: 3.2.2
UniProt & NIH Common Fund Data Resources
Find proteins for O95243 (Homo sapiens)
Explore O95243 
Go to UniProtKB:  O95243
PHAROS:  O95243
GTEx:  ENSG00000129071 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95243
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*CP*AP*GP*CP*GP*(3DR)P*GP*CP*AP*GP*C)-3')B [auth C]12N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*CP*TP*GP*CP*GP*CP*GP*CP*TP*GP*G)-3')C [auth D]12N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth C]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.07α = 90
b = 55.84β = 90
c = 96.65γ = 90
Software Package:
Software NamePurpose
DNAdata collection
PHASERphasing
BUSTERrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-08
    Type: Initial release
  • Version 1.1: 2012-11-07
    Changes: Database references
  • Version 1.2: 2016-12-28
    Changes: Structure summary
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description