Summary information and primary citation

1ig4; SNAP-derived features in text and JSON formats; DNAproDB
Solution structure of the methyl-cpg-binding domain of human mbd1 in complex with methylated DNA
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.
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.

Cartoon-block schematics in six views (download the tarball)

PyMOL session file Download PDB file View in 3Dmol.js

List of 2 5mC-amino acid contacts

No. 1 B.5CM106: hydrophobic-with-A.VAL20 is-WC-paired is-in-duplex [+]:CcG/cGG
No. 2 C.5CM118: other-contacts is-WC-paired is-in-duplex [-]:cGG/CcG