4E9G

structure of the glycosylase domain of MBD4 bound to thymine containing DNA

Summary for 4E9G

• Entry DOI: 10.2210/pdb4e9g/pdb
• Related: 4E9E 4E9F 4E9H 4EA4 4EAB
• Descriptor: Methyl-CpG-binding domain protein 4, DNA (5'-D(*CP*CP*AP*GP*CP*GP*TP*GP*CP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*CP*GP*CP*GP*CP*TP*GP*G)-3'), ... (4 entities in total)
• Functional Keywords: hhh dna glycosylase family, hydrolase-dna complex, hydrolase/dna
• Biological source: Homo sapiens (human); More
• Cellular location: Nucleus: O95243
• Total number of polymer chains: 3
• Total formula weight: 26716.15

Authors

Morera, S.,Vigouroux, A. (deposition date: 2012-03-21, release date: 2012-08-08, Last modification date: 2023-09-13)

Primary citation

Morera, S.,Grin, I.,Vigouroux, A.,Couve, S.,Henriot, V.,Saparbaev, M.,Ishchenko, A.A.
Biochemical and structural characterization of the glycosylase domain of MBD4 bound to thymine and 5-hydroxymethyuracil-containing DNA.
Nucleic Acids Res., 40:9917-9926, 2012

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.

PubMed: 22848106
DOI: 10.1093/nar/gks714

Experimental method

X-RAY DIFFRACTION (2.35 Å)