SNAP-annotated 5mC-DNA-protein interactions: PDB entry 1ig4

PDB-id

1ig4; DSSR-derived features in text and JSON formats; DNAproDB

Class

transcription-DNA

Method

NMR

Summary

Solution structure of the methyl-cpg-binding domain of human mbd1 in complex with methylated DNA

Reference

Ohki I, Shimotake N, Fujita N, Jee J, Ikegami T, Nakao M, Shirakawa M (2001): "Solution structure of the methyl-CpG binding domain of human MBD1 in complex with methylated DNA." Cell(Cambridge,Mass.), 105, 487-497. doi: 10.1016/S0092-8674(01)00324-5.

Abstract

In vertebrates, the biological consequences of DNA methylation are often mediated by protein factors containing conserved methyl-CpG binding domains (MBDs). Mutations in the MBD protein MeCP2 cause the neurodevelopmental disease Rett syndrome. We report here the solution structure of the MBD of the human methylation-dependent transcriptional regulator MBD1 bound to methylated DNA. DNA binding causes a loop in MBD1 to fold into a major and novel DNA binding interface. Recognition of the methyl groups and CG sequence at the methylation site is due to five highly conserved residues that form a hydrophobic patch. The structure indicates how MBD may access nucleosomal DNA without encountering steric interference from core histones, and provides a basis to interpret mutations linked to Rett syndrome in MeCP2.

• The contacts include paired nucleotides (mostly a G in Watson-Crick G-C pairing) and amino-acids within a 4.5-Å distance cutoff to base atoms of 5mC.
• The structure is oriented in the base reference frame of 5mC, allowing for easy comparison and direct superimposition between entries.
• The black sphere (•) denotes the 5-methyl carbon atom in 5mC.