SET domain genes have been identified in numbers of bacterial genomes based on 
similarity to SET domains of eukaryotic histone methyltransferases. Herein, a 
Chlamydophila pneumoniae SET domain gene was clarified to be coincidently 
expressed with hctA and hctB genes encoding chlamydial histone H1-like proteins, 
Hc1 and Hc2, respectively. The SET domain protein (cpnSET) is localized in 
chlamydial cells and interacts with Hc1 and Hc2 through the C-terminal SET 
domain. As expected from conservation of catalytic sites in cpnSET, it functions 
as a protein methyltransferase to murine histone H3 and Hc1. However, little is 
known about protein methylation in the molecular pathogenesis of chlamydial 
infection. cpnSET may play an important role in chlamydial cell maturation due 
to modification of chlamydial histone H1-like proteins.