5mC interactions in PDB entry 3C2I auto-curated with SNAP

Last updated on 2019-09-30 by Xiang-Jun Lu <xiangjun@x3dna.org>. The block schematics were created with DSSR and rendered using PyMOL.

Summary information and primary citation [schematics · contacts · top · homepage · tutorial]

transcription regulator
X-ray (2.5 Å)
The crystal structure of methyl-cpg binding domain of human mecp2 in complex with a methylated DNA sequence from bdnf
List of 2 5mC-amino acid contacts:
  1. B.5CM8: stacking-with-A.ARG111 is-WC-paired is-in-duplex [+]:AcG/cGT
  2. C.5CM33: stacking-with-A.ARG133 is-WC-paired is-in-duplex [-]:cGG/CcG
direct SNAP output · DNAproDB 2.0
Ho, K.L., McNae, I.W., Schmiedeberg, L., Klose, R.J., Bird, A.P., Walkinshaw, M.D.: (2008) "MeCP2 binding to DNA depends upon hydration at methyl-CpG." Mol.Cell, 29, 525-531.
MeCP2 is an essential transcriptional repressor that mediates gene silencing through binding to methylated DNA. Binding specificity has been thought to depend on hydrophobic interactions between cytosine methyl groups and a hydrophobic patch within the methyl-CpG-binding domain (MBD). X-ray analysis of a methylated DNA-MBD cocrystal reveals, however, that the methyl groups make contact with a predominantly hydrophilic surface that includes tightly bound water molecules. This suggests that MeCP2 recognizes hydration of the major groove of methylated DNA rather than cytosine methylation per se. The MeCP2-DNA complex also identifies a unique structural role for T158, the residue most commonly mutated in Rett syndrome.

Base-block schematics in six views [summary · contacts · top · homepage · tutorial]

List of 2 5mC-amino acid contacts [summary · schematics · top · homepage · tutorial]

No. 1 B.5CM8: download PDB file for the 5mC entry
stacking-with-A.ARG111 is-WC-paired is-in-duplex [+]:AcG/cGT
No. 2 C.5CM33: download PDB file for the 5mC entry
stacking-with-A.ARG133 is-WC-paired is-in-duplex [-]:cGG/CcG