4DK9

Crystal Structure of MBD4 Catalytic Domain Bound to Abasic DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.76 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of Human Methyl-Binding Domain IV Glycosylase Bound to Abasic DNA.

Manvilla, B.A.Maiti, A.Begley, M.C.Toth, E.A.Drohat, A.C.

(2012) J.Mol.Biol. 420: 164-175

  • DOI: 10.1016/j.jmb.2012.04.028

  • PubMed Abstract: 
  • The mammalian repair protein MBD4 (methyl-CpG-binding domain IV) excises thymine from mutagenic G·T mispairs generated by deamination of 5-methylcytosine (mC), and downstream base excision repair proteins restore a G·C pair. MBD4 is also implicated i ...

    The mammalian repair protein MBD4 (methyl-CpG-binding domain IV) excises thymine from mutagenic G·T mispairs generated by deamination of 5-methylcytosine (mC), and downstream base excision repair proteins restore a G·C pair. MBD4 is also implicated in active DNA demethylation by initiating base excision repair of G·T mispairs generated by a deaminase enzyme. The question of how mismatch glycosylases attain specificity for excising thymine from G·T, but not A·T, pairs remains largely unresolved. Here, we report a crystal structure of the glycosylase domain of human MBD4 (residues 427-580) bound to DNA containing an abasic nucleotide paired with guanine, providing a glimpse of the enzyme-product complex. The mismatched guanine remains intrahelical, nestled into a recognition pocket. MBD4 provides selective interactions with the mismatched guanine (N1H, N2H(2)) that are not compatible with adenine, which likely confer mismatch specificity. The structure reveals no interactions that would be expected to provide the MBD4 glycosylase domain with specificity for acting at CpG sites. Accordingly, we find modest 1.5- to 2.7-fold reductions in G·T activity upon altering the CpG context. In contrast, 37- to 580-fold effects were observed previously for thymine DNA glycosylase. These findings suggest that specificity of MBD4 for acting at CpG sites depends largely on its methyl-CpG-binding domain, which binds preferably to G·T mispairs in a methylated CpG site. MBD4 glycosylase cannot excise 5-formylcytosine (fC) or 5-carboxylcytosine (caC), intermediates in a Tet (ten eleven translocation)-initiated DNA demethylation pathway. Our structure suggests that MBD4 does not provide the electrostatic interactions needed to excise these oxidized forms of mC.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 North Greene Street, Baltimore, MD 21201, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Methyl-CpG-binding domain protein 4
A
157Homo sapiensMutation(s): 0 
Gene Names: MBD4 (MED1)
EC: 3.2.2.-
Find proteins for O95243 (Homo sapiens)
Go to Gene View: MBD4
Go to UniProtKB:  O95243
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*AP*AP*GP*AP*CP*GP*TP*GP*GP*AP*C)-3'B11N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*TP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*T)-3'C11N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
3DR
Query on 3DR
C
DNA LINKINGC5 H11 O6 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.76 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.234 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 40.999α = 90.00
b = 55.161β = 90.00
c = 122.193γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data reduction
REFMACrefinement
HKL-2000data collection
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-04-25
    Type: Initial release
  • Version 1.1: 2012-05-16
    Type: Database references
  • Version 1.2: 2012-07-25
    Type: Database references