The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix

Maintenance methylation of hemimethylated CpG dinucleotides at DNA replication forks is the key to faithful mitotic inheritance of genomic methylation patterns. UHRF1 ( ubiquitin- like, containing PHD and RING finger domains 1) is required for maintenance methylation by interacting with DNA nucleotide methyltransferase 1 ( DNMT1), the maintenance methyltransferase, and with hemi-methylated CpG, the substrate for DNMT1 ( refs 1 and 2). Here we present the crystal structure of the SET and RING- associated ( SRA) domain of mouse UHRF1 in complex with DNA containing a hemimethylated CpGsite. The DNA is contacted in both the major and minor grooves by two loops that penetrate into the middle of the DNA helix. The 5- methylcytosine has flipped completely out of the DNA helix and is positioned in a binding pocket with planar stacking contacts, Watson - Crick polar hydrogen bonds and van der Waals interactions specific for 5- methylcytosine. Hence, UHRF1 contains a previously unknown DNA- binding module and is the first example of a non- enzymatic, sequence- specific DNA- binding protein domain to use the base flipping mechanism to interact with DNA.