The mechanism of human tyrosyl-DNA phosphodiesterase 1 in the cleavage of AP site and its synthetic analogs

DNA Repair (Amst). 2013 Dec;12(12):1037-42. doi: 10.1016/j.dnarep.2013.09.008. Epub 2013 Oct 31.


The mechanism of hydrolysis of the apurinic/apyrimidinic (AP) site and its synthetic analogs by using tyrosyl-DNA phosphodiesterase 1 (Tdp1) was analyzed. Tdp1 catalyzes the cleavage of AP site and the synthetic analog of the AP site, 3-hydroxy-2(hydroxymethyl)-tetrahydrofuran (THF), in DNA by hydrolysis of the phosphodiester bond between the substituent and 5' adjacent phosphate. The product of Tdp1 cleavage in the case of the AP site is unstable and is hydrolyzed with the formation of 3'- and 5'-margin phosphates. The following repair demands the ordered action of polynucleotide kinase phosphorylase, with XRCC1, DNA polymerase β, and DNA ligase. In the case of THF, Tdp1 generates break with the 5'-THF and the 3'-phosphate termini. Tdp1 is also able to effectively cleave non-nucleotide insertions in DNA, decanediol and diethyleneglycol moieties by the same mechanism as in the case of THF cleavage. The efficiency of Tdp1 catalyzed hydrolysis of AP-site analog correlates with the DNA helix distortion induced by the substituent. The following repair of 5'-THF and other AP-site analogs can be processed by the long-patch base excision repair pathway.

Keywords: Apurinic/apyrimidinic site; Cleavage mechanism; Tyrosyl-DNA phosphodiesterase 1.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Apurinic Acid / analogs & derivatives
  • Apurinic Acid / metabolism*
  • DNA / chemistry
  • DNA / metabolism*
  • DNA Polymerase beta / metabolism
  • DNA Repair*
  • DNA-Binding Proteins / metabolism
  • Furans / metabolism*
  • Humans
  • Hydrolysis
  • Nucleic Acid Conformation
  • Phosphates / metabolism
  • Phosphoric Diester Hydrolases / metabolism*
  • Polynucleotide 5'-Hydroxyl-Kinase / metabolism
  • Polynucleotides / metabolism*
  • Signal Transduction
  • Substrate Specificity
  • X-ray Repair Cross Complementing Protein 1


  • 3-hydroxy-2-(hydroxymethyl)tetrahydrofuran
  • DNA-Binding Proteins
  • Furans
  • Phosphates
  • Polynucleotides
  • X-ray Repair Cross Complementing Protein 1
  • XRCC1 protein, human
  • apyrimidinic acid
  • Apurinic Acid
  • DNA
  • Polynucleotide 5'-Hydroxyl-Kinase
  • DNA Polymerase beta
  • Phosphoric Diester Hydrolases
  • TDP1 protein, human