3VXV

Crystal structure of methyl CpG Binding Domain of MBD4 in complex with the 5mCG/TG sequence


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis of the versatile DNA recognition ability of the methyl-CpG binding domain of methyl-CpG binding domain protein 4

Otani, J.Arita, K.Kato, T.Kinoshita, M.Kimura, H.Suetake, I.Tajima, S.Ariyoshi, M.Shirakawa, M.

(2013) J.Biol.Chem. 288: 6351-6362

  • DOI: 10.1074/jbc.M112.431098
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The methyl-CpG binding domain (MBD) protein MBD4 participates in DNA repair as a glycosylase that excises mismatched thymine bases in CpG sites and also functions in transcriptional repression. Unlike other MBD proteins, MBD4 recognizes not only meth ...

    The methyl-CpG binding domain (MBD) protein MBD4 participates in DNA repair as a glycosylase that excises mismatched thymine bases in CpG sites and also functions in transcriptional repression. Unlike other MBD proteins, MBD4 recognizes not only methylated CpG dinucleotides ((5m)CG/(5m)CG) but also T/G mismatched sites generated by spontaneous deamination of 5-methylcytosine ((5m)CG/TG). The glycosylase activity of MBD4 is also implicated in active DNA demethylation initiated by the deaminase-catalyzed conversion of 5-methylcytosine to thymine. Here, we report the crystal structures of the MBD of MBD4 (MBDMBD4) complexed with (5m)CG/(5m)CG and (5m)CG/TG. The crystal structures show that the DNA interface of MBD4 has flexible structural features and harbors an extensive water network that supports its dual base specificities. Combined with the results of biochemical analyses, the crystal structure of MBD4 bound to 5-hydroxymethylcytosine further demonstrates that MBDMBD4 is able to recognize a wide range of 5-methylcytosine modifications through the unique water network. The versatile base recognition ability of MBDMBD4 implies multifunctional roles for MBD4 in the regulation of dynamic DNA methylation patterns coupled with deamination and/or oxidation of 5-methylcytosine.


    Organizational Affiliation

    Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Methyl-CpG-binding domain protein 4
A
69Mus musculusMutation(s): 0 
Gene Names: Mbd4
EC: 3.2.2.-
Find proteins for Q9Z2D7 (Mus musculus)
Go to UniProtKB:  Q9Z2D7
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*TP*CP*AP*CP*TP*AP*CP*(5CM)P*GP*GP*AP*CP*A)-3')B14N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*TP*CP*TP*GP*GP*TP*AP*GP*TP*GP*AP*CP*T)-3')C14N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, C
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5CM
Query on 5CM
B
DNA LINKINGC10 H16 N3 O7 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.188 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 89.074α = 90.00
b = 94.989β = 90.00
c = 54.738γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement
SOLVEphasing
HKL-2000data collection

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-16
    Type: Initial release
  • Version 1.1: 2013-08-14
    Type: Database references