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

Nature volume 455, pages 826–829 (2008)Cite this article

Abstract

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.

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Figure 1: Structure of SRA–DNA complex.
Figure 2: Details of SRA–DNA interactions.
Figure 3: Structure of the SRA–DNA specific ( P 2 1 2 1 2 1 ) and non-specific ( P 6 1 22) complexes.

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Protein Data Bank

Data deposits

The X-ray structures (coordinates and structure factor files) of mouse UHRF1 SRA with bound DNA have been submitted to PDB under accession numbers 2ZO0 (P212121), 2ZO1 (P41212) and 2ZO2 (P6122), respectively.

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Acknowledgements

We thank R. M. Blumenthal for critical comments. The Emory University School of Medicine supported the use of SER-CAT beamlines. This work was supported by grant GM049245 to X.C. from the National Institutes of Health (NIH). Work in the Jacobsen laboratory is funded by the NIH grant GM060398. M.B. is funded by NIH-NSRA Fellowship number CA1263022. S.E.J. is an Investigator of the Howard Hughes Medical Institute and X.C. is a Georgia Research Alliance Eminent Scholar.

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Authors and Affiliations

  1. Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, Georgia 30322, USA,

    Hideharu Hashimoto, John R. Horton, Xing Zhang & Xiaodong Cheng

  2. Department of Molecular Cell and Developmental Biology,,

    Magnolia Bostick & Steven E. Jacobsen

  3. Hughes Medical Institute, University of California, Los Angeles, 621 Charles E. Young Dr. South, Los Angeles, California 90095, USA ,

    Steven E. Jacobsen

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  1. Hideharu Hashimoto
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Correspondence to Xiaodong Cheng.

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Hashimoto, H., Horton, J., Zhang, X. et al. The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix. Nature 455, 826–829 (2008). https://doi.org/10.1038/nature07280

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