2ZO1: Mouse Np95 Sra Domain Dna Specific Complex 2

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 hemimethylated 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 CpG site. 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.
PDB ID: 2ZO1Download
MMDB ID: 66591
PDB Deposition Date: 2008/5/5
Updated in MMDB: 2012/11
Experimental Method:
x-ray diffraction
Resolution: 1.96  Å
Source Organism:
synthetic construct
Similar Structures:
Biological Unit for 2ZO1: trimeric; determined by author and by software (PISA)
Molecular Components in 2ZO1
Label Count Molecule
Protein (1 molecule)
E3 Ubiquitin-protein Ligase Uhrf1(Gene symbol: Uhrf1)
Molecule annotation
Nucleotides(2 molecules)
DNA (5'- D(*dtp*dcp*dcp*dap*dtp*dgp*dcp*dgp*dcp*dtp*dgp*dap*dc)-3')
Molecule annotation
DNA (5'-d(*dgp*dtp*dcp*dap*dgp*(5cm) P*dgp*dcp*dap*dap*dtp*dgp*dg)-3')
Molecule annotation
Chemicals (2 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB