5INN

Mouse Tdp2 D358N protein, apo state with increased disorder amongst variable DNA-binding grasp conformations

Summary for 5INN

• Entry DOI: 10.2210/pdb5inn/pdb
• Related: 4GZ1 5INK 5INL 5INM 5INO 5INP 5INQ
• Descriptor: Tyrosyl-DNA phosphodiesterase 2, SULFATE ION, GLYCEROL, ... (5 entities in total)
• Functional Keywords: hydrolase, dna repair, endonuclease/exonuclease/phosphatase (eep) domain
• Biological source: Mus musculus (Mouse)
• Total number of polymer chains: 5
• Total formula weight: 145068.48

Authors

Schellenberg, M.J.,Appel, C.D.,Williams, R.S. (deposition date: 2016-03-07, release date: 2016-04-27, Last modification date: 2023-09-27)

Primary citation

Schellenberg, M.J.,Perera, L.,Strom, C.N.,Waters, C.A.,Monian, B.,Appel, C.D.,Vilas, C.K.,Williams, J.G.,Ramsden, D.A.,Williams, R.S.
Reversal of DNA damage induced Topoisomerase 2 DNA-protein crosslinks by Tdp2.
Nucleic Acids Res., 44:3829-3844, 2016

PubMed Abstract: Mammalian Tyrosyl-DNA phosphodiesterase 2 (Tdp2) reverses Topoisomerase 2 (Top2) DNA-protein crosslinks triggered by Top2 engagement of DNA damage or poisoning by anticancer drugs. Tdp2 deficiencies are linked to neurological disease and cellular sensitivity to Top2 poisons. Herein, we report X-ray crystal structures of ligand-free Tdp2 and Tdp2-DNA complexes with alkylated and abasic DNA that unveil a dynamic Tdp2 active site lid and deep substrate binding trench well-suited for engaging the diverse DNA damage triggers of abortive Top2 reactions. Modeling of a proposed Tdp2 reaction coordinate, combined with mutagenesis and biochemical studies support a single Mg(2+)-ion mechanism assisted by a phosphotyrosyl-arginine cation-π interface. We further identify a Tdp2 active site SNP that ablates Tdp2 Mg(2+) binding and catalytic activity, impairs Tdp2 mediated NHEJ of tyrosine blocked termini, and renders cells sensitive to the anticancer agent etoposide. Collectively, our results provide a structural mechanism for Tdp2 engagement of heterogeneous DNA damage that causes Top2 poisoning, and indicate that evaluation of Tdp2 status may be an important personalized medicine biomarker informing on individual sensitivities to chemotherapeutic Top2 poisons.

PubMed: 27060144
DOI: 10.1093/nar/gkw228

Experimental method

X-RAY DIFFRACTION (2.8 Å)