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Nat Commun. 2019 Apr 15;10(1):1751. doi: 10.1038/s41467-019-09756-z.

Structural basis of specific H2A K13/K15 ubiquitination by RNF168.

Author information

1
Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA, Leiden, the Netherlands.
2
NMR Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands.
3
Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, P.O. Box 90203, 1006 BE, Amsterdam, the Netherlands.
4
Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, 23 Innovation Walk, Clayton, VIC, 3800, Australia.
5
EMBL-Australia and the ARC Centre of Excellence in Advanced Molecular Imaging, Clayton, VIC, 3800, Australia.
6
Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, P.O. Box 90203, 1006 BE, Amsterdam, the Netherlands. t.sixma@nki.nl.
7
Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA, Leiden, the Netherlands. h.vaningen@uu.nl.
8
NMR Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands. h.vaningen@uu.nl.

Abstract

Ubiquitination of chromatin by modification of histone H2A is a critical step in both regulation of DNA repair and regulation of cell fate. These very different outcomes depend on the selective modification of distinct lysine residues in H2A, each by a specific E3 ligase. While polycomb PRC1 complexes modify K119, resulting in gene silencing, the E3 ligase RNF168 modifies K13/15, which is a key event in the response to DNA double-strand breaks. The molecular origin of ubiquitination site specificity by these related E3 enzymes is one of the open questions in the field. Using a combination of NMR spectroscopy, crosslinking mass-spectrometry, mutagenesis and data-driven modelling, here we show that RNF168 binds the acidic patch on the nucleosome surface, directing the E2 to the target lysine. The structural model highlights the role of E3 and nucleosome in promoting ubiquitination and provides a basis for understanding and engineering of chromatin ubiquitination specificity.

PMID:
30988309
PMCID:
PMC6465349
DOI:
10.1038/s41467-019-09756-z
[Indexed for MEDLINE]
Free PMC Article

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