6C1A

MBD2 in complex with methylated DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.232 

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:  
    6CNQ, 6CNP, 6C1A, 6C1U, 6C1T, 6C1V

  • 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 protein 2 (MeCP2) to regulate gene expression in neuron development ...

    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 selectivities of the MBD domains 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 identity outside the mCG dinucleotide. Moreover, some MBD domains bound to both methylated and unmethylated CA dinucleotide-containing DNAs, with a preference for the CAC sequence motif. We also found that the 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' that was identified in early 1990s. Our results also explain why MeCP2 exhibits similar binding affinity to both mCA- and 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 MBD-containing proteins. This discovery expands the genome-wide activity of MBD-containing proteins in gene regulation.


    Organizational Affiliation

    the Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Methyl-CpG-binding domain protein 2A, B, E, F79Homo sapiensMutation(s): 0 
Gene Names: MBD2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBB5 (Homo sapiens)
Explore Q9UBB5 
Go to UniProtKB:  Q9UBB5
PHAROS:  Q9UBB5
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    dna strand 1C, G12synthetic construct
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      complement to dna strand 1D, H12synthetic construct
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      UNX
      Query on UNX

      Download Ideal Coordinates CCD File 
      AA [auth B] , AB [auth G] , BA [auth B] , BB [auth G] , CA [auth B] , CB [auth G] , DA [auth C] , DB [auth G] , 
      AA [auth B],  AB [auth G],  BA [auth B],  BB [auth G],  CA [auth B],  CB [auth G],  DA [auth C],  DB [auth G],  EA [auth C],  EB [auth G],  FA [auth C],  FB [auth G],  GA [auth C],  GB [auth H],  HA [auth D],  HB [auth H],  I [auth A],  IA [auth D],  J [auth A],  JA [auth D],  K [auth A],  KA [auth D],  L [auth A],  LA [auth E],  M [auth A],  MA [auth E],  N [auth A],  NA [auth E],  O [auth A],  OA [auth E],  P [auth A],  PA [auth E],  Q [auth A],  QA [auth E],  R [auth A],  RA [auth E],  S [auth A],  SA [auth E],  T [auth A],  TA [auth E],  U [auth B],  UA [auth E],  V [auth B],  VA [auth F],  W [auth B],  WA [auth F],  X [auth B],  XA [auth F],  Y [auth B],  YA [auth F],  Z [auth B],  ZA [auth G]
      UNKNOWN ATOM OR ION
      X
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.05 Å
      • R-Value Free: 0.265 
      • R-Value Work: 0.231 
      • R-Value Observed: 0.232 
      • Space Group: P 1
      • Diffraction Data DOI: 10.18430/M36C1A Protein Diffraction
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 36.533α = 83.97
      b = 39.875β = 85.7
      c = 105.151γ = 62.75
      Software Package:
      Software NamePurpose
      REFMACrefinement
      Aimlessdata scaling
      PDB_EXTRACTdata extraction
      XDSdata reduction
      PHASERphasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

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