The methylation of lysine residues of histones plays a pivotal role in the 
regulation of chromatin structure and gene expression. Here, we report two 
crystal structures of SET7/9, a histone methyltransferase (HMTase) that 
transfers methyl groups to Lys4 of histone H3, in complex with 
S-adenosyl-L-methionine (AdoMet) determined at 1.7 and 2.3 A resolution. The 
structures reveal an active site consisting of: (i) a binding pocket between the 
SET domain and a c-SET helix where an AdoMet molecule in an unusual conformation 
binds; (ii) a narrow substrate-specific channel that only unmethylated lysine 
residues can access; and (iii) a catalytic tyrosine residue. The methyl group of 
AdoMet is directed to the narrow channel where a substrate lysine enters from 
the opposite side. We demonstrate that SET7/9 can transfer two but not three 
methyl groups to unmodified Lys4 of H3 without substrate dissociation. The 
unusual features of the SET domain-containing HMTase discriminate between the 
un- and methylated lysine substrate, and the methylation sites for the histone 
H3 tail.