Structure of the catalytic domain of human DOT1L, a non-SET domain nucleosomal histone methyltransferase

Cell. 2003 Mar 7;112(5):711-23. doi: 10.1016/s0092-8674(03)00114-4.


Dot1 is an evolutionarily conserved histone methyltransferase that methylates lysine-79 of histone H3 in the core domain. Unlike other histone methyltransferases, Dot1 does not contain a SET domain, and it specifically methylates nucleosomal histone H3. We have solved a 2.5 A resolution structure of the catalytic domain of human Dot1, hDOT1L, in complex with S-adenosyl-L-methionine (SAM). The structure reveals a unique organization of a mainly alpha-helical N-terminal domain and a central open alpha/beta structure, an active site consisting of a SAM binding pocket, and a potential lysine binding channel. We also show that a flexible, positively charged region at the C terminus of the catalytic domain is critical for nucleosome binding and enzymatic activity. These structural and biochemical analyses, combined with molecular modeling, provide mechanistic insights into the catalytic mechanism and nucleosomal specificity of Dot1 proteins.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Sequence / genetics
  • Animals
  • Binding Sites / genetics
  • Catalytic Domain / genetics*
  • Chickens
  • Eukaryotic Cells / metabolism*
  • HeLa Cells
  • Histone Methyltransferases
  • Histone-Lysine N-Methyltransferase*
  • Humans
  • Lysine / genetics
  • Lysine / metabolism
  • Methyltransferases / genetics
  • Methyltransferases / metabolism*
  • Models, Biological
  • Molecular Sequence Data
  • Molecular Structure
  • Nuclear Proteins / genetics
  • Nuclear Proteins / metabolism*
  • Nucleosomes / genetics
  • Nucleosomes / metabolism*
  • Protein Methyltransferases
  • Saccharomyces cerevisiae Proteins / genetics
  • Saccharomyces cerevisiae Proteins / metabolism*


  • Nuclear Proteins
  • Nucleosomes
  • Saccharomyces cerevisiae Proteins
  • DOT1L protein, human
  • Histone Methyltransferases
  • Methyltransferases
  • Protein Methyltransferases
  • Dot1 protein, S cerevisiae
  • Histone-Lysine N-Methyltransferase
  • Lysine

Associated data

  • PDB/1NW3