Nature Structural Biology9, 217 - 224 (2002)
Published online: 11 February 2002; | doi:10.1038/nsb759
The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds
Chen Qiu1, 2, Ken Sawada1, Xing Zhang1
& Xiaodong Cheng1
1
Department of Biochemistry, Emory University, 1510 Clifton Road, Atlanta, Georgia 30322, USA.
2
Department of Chemistry, Emory University, 1510 Clifton Road, Atlanta, Georgia 30322, USA.
Correspondence should be addressed to Xiaodong Cheng xcheng@emory.edu
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 Å 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 (218 and 369) have approximately equal methyl transfer activity on unmethylated and hemimethylated CpG-containing oligonucleotides. The 218 protein, which includes the PWWP domain, binds DNA more strongly than 369, which lacks the PWWP domain.
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