Methylation of cytosine in DNA plays a crucial role in development through 
inheritable gene silencing. The DNA methyltransferase Dnmt1 is responsible for 
the propagation of methylation patterns to the next generation via its 
preferential methylation of hemimethylated CpG sites in the genome; however, how 
Dnmt1 maintains methylation patterns is not fully understood. Here we report the 
crystal structure of the large fragment (291-1620) of mouse Dnmt1 and its 
complexes with cofactor S-adenosyl-L-methionine and its product 
S-adenosyl-L-homocystein. Notably, in the absence of DNA, the N-terminal domain 
responsible for targeting Dnmt1 to replication foci is inserted into the 
DNA-binding pocket, indicating that this domain must be removed for methylation 
to occur. Upon binding of S-adenosyl-L-methionine, the catalytic cysteine 
residue undergoes a conformation transition to a catalytically competent 
position. For the recognition of hemimethylated DNA, Dnmt1 is expected to 
utilize a target recognition domain that overhangs the putative DNA-binding 
pocket. Taking into considerations the recent report of a shorter fragment 
structure of Dnmt1 that the CXXC motif positions itself in the catalytic pocket 
and prevents aberrant de novo methylation, we propose that maintenance 
methylation is a multistep process accompanied by structural changes.