Reversal of DNA damage induced Topoisomerase 2 DNA-protein crosslinks by Tdp2

Nucleic Acids Res. 2016 May 5;44(8):3829-44. doi: 10.1093/nar/gkw228. Epub 2016 Apr 8.

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.

MeSH terms

  • Animals
  • Catalytic Domain
  • DNA / chemistry
  • DNA / metabolism
  • DNA Adducts / chemistry
  • DNA Adducts / metabolism
  • DNA Damage*
  • DNA End-Joining Repair
  • DNA Topoisomerases, Type II / chemistry
  • DNA Topoisomerases, Type II / metabolism*
  • Humans
  • Magnesium / chemistry
  • Mice
  • Mice, Knockout
  • Models, Molecular
  • Mutation
  • Nuclear Proteins / chemistry
  • Nuclear Proteins / genetics
  • Nuclear Proteins / metabolism
  • Phosphoric Diester Hydrolases / chemistry*
  • Phosphoric Diester Hydrolases / genetics
  • Phosphoric Diester Hydrolases / metabolism
  • Phosphotyrosine / metabolism
  • Polymorphism, Single Nucleotide
  • Transcription Factors / chemistry
  • Transcription Factors / genetics
  • Transcription Factors / metabolism
  • Tumor Necrosis Factor Receptor-Associated Peptides and Proteins / chemistry*
  • Tumor Necrosis Factor Receptor-Associated Peptides and Proteins / genetics
  • Tumor Necrosis Factor Receptor-Associated Peptides and Proteins / metabolism

Substances

  • DNA Adducts
  • Nuclear Proteins
  • Transcription Factors
  • Tumor Necrosis Factor Receptor-Associated Peptides and Proteins
  • Phosphotyrosine
  • DNA
  • Phosphoric Diester Hydrolases
  • TDP2 protein, human
  • TDP2 protein, mouse
  • DNA Topoisomerases, Type II
  • Magnesium