Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 16.67 kDa 
• Atom Count: 1,241 
• Modelled Residue Count: 137 
• Deposited Residue Count: 147 
• Unique protein chains: 1

 1KHC

Crystal Structure of the PWWP Domain of Mammalian DNA Methyltransferase Dnmt3b

• PDB DOI: 10.2210/pdb1KHC/pdb

• Classification: TRANSFERASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2001-11-29 Released: 2002-02-27 
• Deposition Author(s): Qiu, C., Sawada, K., Zhang, X., Cheng, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.237 
• R-Value Work: 0.190 

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 Biol 9: 217-224

• PubMed: 11836534 
• DOI: 10.1038/nsb759
• Primary Citation of Related Structures:  
  1KHC


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA cytosine-5 methyltransferase 3B2	A	147	Mus musculus	Mutation(s): 0  Gene Names: Dnmt3b EC: 2.1.1.37
UniProt & NIH Common Fund Data Resources
Find proteins for O88509 (Mus musculus) Explore O88509  Go to UniProtKB:  O88509
IMPC:  MGI:1261819

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UNX	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.237 
• R-Value Work: 0.190 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.75	α = 90
b = 52.75	β = 90
c = 186.86	γ = 120

Software Package:

Software Name	Purpose
SOLVE	phasing
RESOLVE	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-02-27 
Deposition Author(s): Qiu, C., Sawada, K., Zhang, X., Cheng, X.

Revision History  

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