Ubiquitin stimulated reversal of topoisomerase 2 DNA-protein crosslinks by TDP2

Author:

Schellenberg Matthew J1,Appel C Denise1,Riccio Amanda A1,Butler Logan R1,Krahn Juno M1,Liebermann Jenna A2,Cortés-Ledesma Felipe23,Williams R Scott1ORCID

Affiliation:

1. Structural Cell Biology Group, Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, US Department of Health and Human Services, Research Triangle Park, NC 27709, USA

2. Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), CSIC-Universidad de Sevilla Universidad Pablo de Olavide-Junta de Andalucía, 41092 Sevilla, Spain

3. Topology and DNA breaks Group, Spanish National Cancer Centre (CNIO), Madrid 28029, Spain

Abstract

Abstract Tyrosyl-DNA phosphodiesterase 2 (TDP2) reverses Topoisomerase 2 DNA–protein crosslinks (TOP2-DPCs) in a direct-reversal pathway licensed by ZATTZNF451 SUMO2 E3 ligase and SUMOylation of TOP2. TDP2 also binds ubiquitin (Ub), but how Ub regulates TDP2 functions is unknown. Here, we show that TDP2 co-purifies with K63 and K27 poly-Ubiquitinated cellular proteins independently of, and separately from SUMOylated TOP2 complexes. Poly-ubiquitin chains of ≥ Ub3 stimulate TDP2 catalytic activity in nuclear extracts and enhance TDP2 binding of DNA–protein crosslinks in vitro. X-ray crystal structures and small-angle X-ray scattering analysis of TDP2-Ub complexes reveal that the TDP2 UBA domain binds K63-Ub3 in a 1:1 stoichiometric complex that relieves a UBA-regulated autoinhibitory state of TDP2. Our data indicates that that poly-Ub regulates TDP2-catalyzed TOP2-DPC removal, and TDP2 single nucleotide polymorphisms can disrupt the TDP2-Ubiquitin interface.

Funder

National Institutes of Health

National Institute of Environmental Health Sciences

Ministerio de Economía, Industria y Competitividad, Gobierno de España

European Research Council

University of Seville Predoctoral Studentship

Mayo Clinic start-up funds

Center for Biomedical Discovery new investigator funds

U.S. Department of Energy

Biological and Environmental Research

High-End Instrumentation Grant

Publisher

Oxford University Press (OUP)

Subject

Genetics

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