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.