1KHC

Crystal Structure of the PWWP Domain of Mammalian DNA Methyltransferase Dnmt3b

Summary for 1KHC

• Entry DOI: 10.2210/pdb1khc/pdb
• Descriptor: DNA cytosine-5 methyltransferase 3B2, UNKNOWN ATOM OR ION (3 entities in total)
• Functional Keywords: five beta-sheets barrel followed by five-helix bundle, transferase
• Biological source: Mus musculus (house mouse)
• Cellular location: Nucleus: O88509
• Total number of polymer chains: 1
• Total formula weight: 16670.04

Authors

Qiu, C.,Sawada, K.,Zhang, X.,Cheng, X. (deposition date: 2001-11-29, release date: 2002-02-27, Last modification date: 2024-02-14)

Primary citation

Qiu, C.,Sawada, K.,Zhang, X.,Cheng, X.
The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds.
Nat.Struct.Biol., 9:217-224, 2002

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.

PubMed: 11836534

Experimental method

X-RAY DIFFRACTION (1.8 Å)