1NGN | pdb_00001ngn

Mismatch repair in methylated DNA. Structure of the mismatch-specific thymine glycosylase domain of methyl-CpG-binding protein MBD4

• PDB DOI: https://doi.org/10.2210/pdb1NGN/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-12-17 Released: 2003-03-18 
• Deposition Author(s): Wu, P., Qiu, C., Sohail, A., Zhang, X., Bhagwat, A.S., Cheng, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.263 (Depositor) 
• R-Value Work: 
  0.213 (Depositor) 

Literature

Mismatch repair in methylated DNA. Structure and activity of the mismatch-specific thymine glycosylase domain of methyl-CpG-binding protein MBD4

Wu, P., Qiu, C., Sohail, A., Zhang, X., Bhagwat, A.S., Cheng, X.

(2003) J Biological Chem 278: 5285-5291

• PubMed: 12456671 
• DOI: https://doi.org/10.1074/jbc.M210884200
• Primary Citation Related Structures: 
  1NGN


• PubMed Abstract: 
  

  MBD4 is a member of the methyl-CpG-binding protein family. It contains two DNA binding domains, an amino-proximal methyl-CpG binding domain (MBD) and a C-terminal mismatch-specific glycosylase domain. Limited in vitro proteolysis of mouse MBD4 yields two stable fragments: a 139-residue fragment including the MBD, and the other 155-residue fragment including the glycosylase domain. Here we show that the latter fragment is active as a glycosylase on a DNA duplex containing a G:T mismatch within a CpG sequence context. The crystal structure confirmed the C-terminal domain is a member of the helix-hairpin-helix DNA glycosylase superfamily. The MBD4 active site is situated in a cleft that likely orients and binds DNA. Modeling studies suggest the mismatched target nucleotide will be flipped out into the active site where candidate residues for catalysis and substrate specificity are present.

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Organizational Affiliation: 
• Department of Biochemistry, Emory University, Atlanta, Georgia 30322, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 18.57 kDa 
• Atom Count: 1,304 
• Modeled Residue Count: 144 
• Deposited Residue Count: 155 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
methyl-CpG binding protein MBD4	A	155	Mus musculus	Mutation(s): 0  Gene Names: Mbd4 EC: 3.2.2
UniProt
Find proteins for Q9Z2D7 (Mus musculus) Explore Q9Z2D7  Go to UniProtKB:  Q9Z2D7

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.263 (Depositor) 
• R-Value Work:  0.213 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.58	α = 90
b = 48.58	β = 90
c = 146.57	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
SOLVE	phasing
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-03-18 
Deposition Author(s): Wu, P., Qiu, C., Sohail, A., Zhang, X., Bhagwat, A.S., Cheng, X.

Revision History  

• Version 1.0: 2003-03-18
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references