6C1T

MBD2 in complex with a partially methylated DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for the ability of MBD domains to bind methyl-CG and TG sites in DNA.

Liu, K.Xu, C.Lei, M.Yang, A.Loppnau, P.Hughes, T.R.Min, J.

(2018) J. Biol. Chem. 293: 7344-7354

  • DOI: 10.1074/jbc.RA118.001785
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cytosine methylation is a well characterized epigenetic mark and occurs at both CG and non-CG sites in DNA. Both methylated CG (mCG)- and mCH (H = A, C, or T)-containing DNAs, especially mCAC-containing DNAs, are recognized by methyl-CpG-binding prot ...

    Cytosine methylation is a well characterized epigenetic mark and occurs at both CG and non-CG sites in DNA. Both methylated CG (mCG)- and mCH (H = A, C, or T)-containing DNAs, especially mCAC-containing DNAs, are recognized by methyl-CpG-binding protein 2 (MeCP2) to regulate gene expression in neuron development. However, the molecular mechanism involved in the binding of methyl-CpG-binding domain (MBD) of MeCP2 to these different DNA motifs is unclear. Here, we systematically characterized the DNA-binding selectivity of the MBDs in MeCP2 and MBD1-4 with isothermal titration calorimetry-based binding assays, mutagenesis studies, and X-ray crystallography. We found that the MBD domains of MeCP2 and MBD1-4
    bind mCG-containing DNAs independently of the sequence outside the mCG dinucleotide. Moreover, some 1 MBDs bound to both methylated and unmethylated CA dinucleotide-
    containing DNAs, with a preference for the CAC sequence motif. We also found that MBD domains bind to mCA or nonmethylated CA DNA by recognizing the complementary TG dinucleotide, which is consistent with an overlooked ligand of MeCP2, i.e., the matrix/scaffold attachment regions (MARs/SARs) with a consensus sequence of 5'-GGTGT-3', which was
    identified in early 1990s. Our results also explain why MeCP2 exhibits similar binding affinity to both mCAand hmCA-containing dsDNAs. In summary, our results suggest that in addition to mCG sites, unmethylated CA or TG sites also serve as DNA-binding sites for MeCP2 and other MBDcontaining proteins. This discovery expands the genome-wide activity of MBD-containing proteins in gene regulation.


    Organizational Affiliation

    University of Toronto, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Methyl-CpG-binding domain protein 2
A, D
79Homo sapiensMutation(s): 0 
Gene Names: MBD2
Find proteins for Q9UBB5 (Homo sapiens)
Go to Gene View: MBD2
Go to UniProtKB:  Q9UBB5
Entity ID: 2
MoleculeChainsLengthOrganism
12-mer DNAB12synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
12-mer DNAC12synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

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Download CCD File 
A, B, C, D
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5CM
Query on 5CM
B
DNA LINKINGC10 H16 N3 O7 PDC
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 71.473α = 90.00
b = 36.933β = 108.25
c = 104.076γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-02-14
    Type: Initial release
  • Version 1.1: 2018-04-18
    Type: Data collection, Database references
  • Version 1.2: 2018-05-23
    Type: Data collection, Database references