BRCA1/BARD1 site-specific ubiquitylation of nucleosomal H2A is directed by BARD1

Samuel R Witus; Anika L Burrell; Daniel P Farrell; Jianming Kang; Meiling Wang; Jesse M Hansen; Alex Pravat; Lisa M Tuttle; Mikaela D Stewart; Peter S Brzovic; Champak Chatterjee; Weixing Zhao; Frank DiMaio; Justin M Kollman; Rachel E Klevit

doi:10.1038/s41594-020-00556-4

BRCA1/BARD1 site-specific ubiquitylation of nucleosomal H2A is directed by BARD1

Nat Struct Mol Biol. 2021 Mar;28(3):268-277. doi: 10.1038/s41594-020-00556-4. Epub 2021 Feb 15.

Authors

Samuel R Witus¹, Anika L Burrell¹, Daniel P Farrell^{1

2}, Jianming Kang^{1

3}, Meiling Wang⁴, Jesse M Hansen¹, Alex Pravat¹, Lisa M Tuttle¹, Mikaela D Stewart^{1

5}, Peter S Brzovic¹, Champak Chatterjee³, Weixing Zhao⁴, Frank DiMaio^{1

2}, Justin M Kollman¹, Rachel E Klevit⁶

Affiliations

¹ Department of Biochemistry, University of Washington, Seattle, WA, USA.
² Institute for Protein Design, University of Washington, Seattle, WA, USA.
³ Department of Chemistry, University of Washington, Seattle, WA, USA.
⁴ Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, USA.
⁵ Department of Biology, Texas Christian University, Fort Worth, TX, USA.
⁶ Department of Biochemistry, University of Washington, Seattle, WA, USA. klevit@uw.edu.

Abstract

Mutations in the E3 ubiquitin ligase RING domains of BRCA1/BARD1 predispose carriers to breast and ovarian cancers. We present the structure of the BRCA1/BARD1 RING heterodimer with the E2 enzyme UbcH5c bound to its cellular target, the nucleosome, along with biochemical data that explain how the complex selectively ubiquitylates lysines 125, 127 and 129 in the flexible C-terminal tail of H2A in a fully human system. The structure reveals that a novel BARD1-histone interface couples to a repositioning of UbcH5c compared to the structurally similar PRC1 E3 ligase Ring1b/Bmi1 that ubiquitylates H2A Lys119 in nucleosomes. This interface is sensitive to both H3 Lys79 methylation status and mutations found in individuals with cancer. Furthermore, NMR reveals an unexpected mode of E3-mediated substrate regulation through modulation of dynamics in the C-terminal tail of H2A. Our findings provide insight into how E3 ligases preferentially target nearby lysine residues in nucleosomes by a steric occlusion and distancing mechanism.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

BRCA1 Protein / chemistry*
BRCA1 Protein / metabolism*
BRCA1 Protein / ultrastructure
Binding Sites
Catalytic Domain
Cryoelectron Microscopy
Histones / chemistry
Histones / metabolism*
Histones / ultrastructure
Humans
Lysine / chemistry
Lysine / metabolism
Models, Molecular
Nucleosomes / chemistry*
Nucleosomes / metabolism*
Protein Binding
Reproducibility of Results
Tumor Suppressor Proteins / chemistry*
Tumor Suppressor Proteins / metabolism*
Tumor Suppressor Proteins / ultrastructure
Ubiquitin-Conjugating Enzymes / chemistry
Ubiquitin-Conjugating Enzymes / metabolism
Ubiquitin-Conjugating Enzymes / ultrastructure
Ubiquitin-Protein Ligases / chemistry*
Ubiquitin-Protein Ligases / metabolism*
Ubiquitin-Protein Ligases / ultrastructure
Ubiquitination*

Substances

BRCA1 Protein
BRCA1 protein, human
Histones
Nucleosomes
Tumor Suppressor Proteins
UBE2D3 protein, human
Ubiquitin-Conjugating Enzymes
BARD1 protein, human
Ubiquitin-Protein Ligases
Lysine

Abstract

Publication types

MeSH terms

Substances

Grants and funding