Identification of a second DNA binding site in human DNA methyltransferase 3A by substrate inhibition and domain deletion.
The human DNA methyltransferase 3A (DNMT3A) is essential for establishing DNA methylation patterns. Knowing the key factors involved in the regulation of mammalian DNA methylation is critical to furthering understanding of embryonic development and designing therapeutic approaches targeting epigenetic mechanisms. We observe substrate inhibition for the full length DNMT3A but not for its isolated catalytic domain, demonstrating that DNMT3A has a second binding site for DNA. Deletion of recognized domains of DNMT3A reveals that the conserved PWWP domain is necessary for substrate inhibition and forms at least part of the allosteric DNA binding site. The PWWP domain is demonstrated here to bind DNA in a cooperative manner with muM affinity. No clear sequence preference was observed, similar to previous observations with the isolated PWWP domain of Dnmt3b but with one order of magnitude weaker affinity. Potential roles for a low affinity, low specificity second DNA binding site are discussed.
Purdy
Matthew M
MM
Department of Chemistry and Biochemistry, University of California, Santa Barbara, 93106-9510, USA.
Holz-Schietinger
Celeste
C
Reich
Norbert O
NO
D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D020134:Catalytic Domain; D002417:Cattle; D017124:Conserved Sequence; D004247:DNA / Q000378:metabolism*; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D000090205:DNA Methyltransferase 3A; D004791:Enzyme Inhibitors / Q000494:pharmacology*; D006801:Humans; D007292:Inosine Nucleotides / Q000737:chemistry / Q000494:pharmacology; D007700:Kinetics; D008969:Molecular Sequence Data; D009841:Oligonucleotides / Q000235:genetics / Q000494:pharmacology; D011108:Polymers / Q000737:chemistry; D017434:Protein Structure, Tertiary / Q000235:genetics; D017384:Sequence Deletion
C000717967:DNMT3A protein, human; D004791:Enzyme Inhibitors; D007292:Inosine Nucleotides; D009841:Oligonucleotides; D011108:Polymers; D004247:DNA; D004248:DNA (Cytosine-5-)-Methyltransferases; D000090205:DNA Methyltransferase 3A