Crystal structure of a transition state mimic for Tdp1 assembled from vanadate, DNA, and a topoisomerase I-derived peptide

Chem Biol. 2003 Feb;10(2):139-47. doi: 10.1016/s1074-5521(03)00021-8.


Tyrosyl-DNA phosphodiesterase (Tdp1) is a member of the phospholipase D superfamily and acts as a DNA repair enzyme that removes stalled topoisomerase I- DNA complexes by hydrolyzing the bond between a tyrosine side chain and a DNA 3' phosphate. Despite the complexity of the substrate of this phosphodiesterase, vanadate succeeded in linking human Tdp1, a tyrosine-containing peptide, and a single-stranded DNA oligonucleotide into a quaternary complex that mimics the transition state for the first step of the catalytic reaction. The conformation of the bound substrate mimic gives compelling evidence that the topoisomerase I-DNA complex must undergo extensive modification prior to cleavage by Tdp1. The structure also illustrates that the use of vanadate as the central moiety in high-order complexes has the potential to be a general method for capturing protein-substrate interactions for phosphoryl transfer enzymes, even when the substrates are large, complicated, and unusual.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Crystallization
  • Crystallography, X-Ray
  • DNA / metabolism*
  • DNA Topoisomerases, Type I / chemistry*
  • Humans
  • Hydrogen Bonding
  • Models, Molecular
  • Molecular Mimicry
  • Oligonucleotides / chemistry
  • Phosphoric Diester Hydrolases / chemistry*
  • Protein Conformation
  • Vanadates / chemistry*


  • Oligonucleotides
  • Vanadates
  • DNA
  • Phosphoric Diester Hydrolases
  • TDP1 protein, human
  • tyrosyl-DNA phosphodiesterase
  • DNA Topoisomerases, Type I

Associated data

  • PDB/1NOP