1KHC

Crystal Structure of the PWWP Domain of Mammalian DNA Methyltransferase Dnmt3b


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds.

Qiu, C.Sawada, K.Zhang, X.Cheng, X.

(2002) Nat.Struct.Mol.Biol. 9: 217-224

  • DOI: 10.1038/nsb759

  • PubMed Abstract: 
  • The PWWP domain is a weakly conserved sequence motif found in > 60 eukaryotic proteins, including the mammalian DNA methyltransferases Dnmt3a and Dnmt3b. These proteins often contain other chromatin-association domains. A 135-residue PWWP domain from ...

    The PWWP domain is a weakly conserved sequence motif found in > 60 eukaryotic proteins, including the mammalian DNA methyltransferases Dnmt3a and Dnmt3b. These proteins often contain other chromatin-association domains. A 135-residue PWWP domain from mouse Dnmt3b (amino acids 223--357) has been structurally characterized at 1.8 A resolution. The N-terminal half of this domain resembles a barrel-like five-stranded structure, whereas the C-terminal half contains a five-helix bundle. The two halves are packed against each other to form a single structural module that exhibits a prominent positive electrostatic potential. The PWWP domain alone binds DNA in vitro, probably through its basic surface. We also show that recombinant Dnmt3b2 protein (a splice variant of Dnmt3b) and two N-terminal deletion mutants (Delta218 and Delta369) have approximately equal methyl transfer activity on unmethylated and hemimethylated CpG-containing oligonucleotides. The Delta218 protein, which includes the PWWP domain, binds DNA more strongly than Delta369, which lacks the PWWP domain.


    Organizational Affiliation

    Department of Biochemistry, Emory University, 1510 Clifton Road, Atlanta, Georgia 30322, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA cytosine-5 methyltransferase 3B2
A
147Mus musculusGene Names: Dnmt3b
EC: 2.1.1.37
Find proteins for O88509 (Mus musculus)
Go to UniProtKB:  O88509
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UNX
Query on UNX

Download SDF File 
Download CCD File 
A
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.190 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 52.750α = 90.00
b = 52.750β = 90.00
c = 186.860γ = 120.00
Software Package:
Software NamePurpose
SOLVEphasing
X-PLORrefinement
DENZOdata reduction
RESOLVEphasing
RESOLVEmodel building
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-02-27
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-11-16
    Type: Atomic model