4E9G: Structure Of The Glycosylase Domain Of Mbd4 Bound To Thymine Containing Dna

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.
PDB ID: 4E9GDownload
MMDB ID: 101859
PDB Deposition Date: 2012/3/21
Updated in MMDB: 2012/11
Experimental Method:
x-ray diffraction
Resolution: 2.35  Å
Source Organism:
synthetic construct
Similar Structures:
Biological Unit for 4E9G: trimeric; determined by author and by software (PISA)
Molecular Components in 4E9G
Label Count Molecule
Protein (1 molecule)
Methyl-cpg-binding Domain Protein 4(Gene symbol: MBD4)
Molecule annotation
Nucleotides(2 molecules)
DNA (5'-d(*cp*cp*ap*gp*cp*gp*tp*gp*cp*ap*gp*c)-3')
Molecule annotation
DNA (5'-d(*gp*cp*tp*gp*cp*gp*cp*gp*cp*tp*gp*g)-3')
Molecule annotation
* Click molecule labels to explore molecular sequence information.

Citing MMDB