2MB7

Solution structure of MBD3 methylcytosine binding domain

2MB7 の概要

• エントリーDOI: 10.2210/pdb2mb7/pdb
• NMR情報: BMRB: 19391
• 分子名称: Methyl-CpG-binding domain protein 3 (1 entity in total)
• 機能のキーワード: mbd3, dna methylation, nurd, chromatin, transcription
• 由来する生物種: Homo sapiens (human)
• 細胞内の位置: Nucleus: O95983
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 8342.52

構造登録者

Williams Jr., D.C.,Scarsdale, J.N. (登録日: 2013-07-26, 公開日: 2013-12-11, 最終更新日: 2024-05-15)

主引用文献

Cramer, J.M.,Scarsdale, J.N.,Walavalkar, N.M.,Buchwald, W.A.,Ginder, G.D.,Williams, D.C.
Probing the Dynamic Distribution of Bound States for Methylcytosine-binding Domains on DNA.
J.Biol.Chem., 289:1294-1302, 2014

PubMed Abstract: Although highly homologous to other methylcytosine-binding domain (MBD) proteins, MBD3 does not selectively bind methylated DNA, and thus the functional role of MBD3 remains in question. To explore the structural basis of its binding properties and potential function, we characterized the solution structure and binding distribution of the MBD3 MBD on hydroxymethylated, methylated, and unmethylated DNA. The overall fold of this domain is very similar to other MBDs, yet a key loop involved in DNA binding is more disordered than previously observed. Specific recognition of methylated DNA constrains the structure of this loop and results in large chemical shift changes in NMR spectra. Based on these spectral changes, we show that MBD3 preferentially localizes to methylated and, to a lesser degree, unmethylated cytosine-guanosine dinucleotides (CpGs), yet does not distinguish between hydroxymethylated and unmethylated sites. Measuring residual dipolar couplings for the different bound states clearly shows that the MBD3 structure does not change between methylation-specific and nonspecific binding modes. Furthermore, residual dipolar couplings measured for MBD3 bound to methylated DNA can be described by a linear combination of those for the methylation and nonspecific binding modes, confirming the preferential localization to methylated sites. The highly homologous MBD2 protein shows similar but much stronger localization to methylated as well as unmethylated CpGs. Together, these data establish the structural basis for the relative distribution of MBD2 and MBD3 on genomic DNA and their observed occupancy at active and inactive CpG-rich promoters.

PubMed: 24307175
DOI: 10.1074/jbc.M113.512236

実験手法

SOLUTION NMR