Polycomb gene silencing requires histone methyltransferase activity of Polycomb 
repressive complex 2 (PRC2), which methylates lysine 27 of histone H3. 
Information on how PRC2 works is limited by lack of structural data on the 
catalytic subunit, Enhancer of zeste (E(Z)), and the paucity of E(z) mutant 
alleles that alter its SET domain. Here we analyze missense alleles of 
Drosophila E(z), selected for molecular study because of their dominant genetic 
effects. Four missense alleles identify key E(Z) SET domain residues, and a 
fifth is located in the adjacent CXC domain. Analysis of mutant PRC2 complexes 
in vitro, and H3-K27 methylation in vivo, shows that each SET domain mutation 
disrupts PRC2 histone methyltransferase. Based on known SET domain structures, 
the mutations likely affect either the lysine-substrate binding pocket, the 
binding site for the adenosylmethionine methyl donor, or a critical tyrosine 
predicted to interact with the substrate lysine epsilon-amino group. In 
contrast, the CXC mutant retains catalytic activity, Lys-27 specificity, and 
trimethylation capacity. Deletion analysis also reveals a functional requirement 
for a conserved E(Z) domain N-terminal to CXC and SET. These results identify 
critical SET domain residues needed for PRC2 enzyme function, and they also 
emphasize functional inputs from outside the SET domain.