1NOP

Crystal structure of human tyrosyl-DNA phosphodiesterase (Tdp1) in complex with vanadate, DNA and a human topoisomerase I-derived peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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

Davies, D.R.Interthal, H.Champoux, J.J.Hol, W.G.J.

(2003) Chem.Biol. 10: 139-147


  • PubMed Abstract: 
  • 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. Desp ...

    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.


    Related Citations: 
    • The crystal structure of human tyrosyl-DNA phosphodiesterase, Tdp1
      Davies, D.R.,Interthal, H.,Champoux, J.J.,Hol, W.G.J.
      (2002) Structure 10: 237
    • Insights into substrate binding and catalytic mechanism of human tyrosyl-DNA phosphodiesterase (Tdp1) from vanadate- and tungstate-inhibited structures
      Davies, D.R.,Interthal, H.,Champoux, J.J.,Hol, W.G.J.
      (2002) J.Mol.Biol. 324: 917


    Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
tyrosyl-DNA phosphodiesterase 1
A, B
485Homo sapiensGene Names: TDP1
EC: 3.1.4.-
Find proteins for Q9NUW8 (Homo sapiens)
Go to Gene View: TDP1
Go to UniProtKB:  Q9NUW8
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
topoisomerase I-derived peptide
C
8N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*AP*GP*AP*GP*TP*T)-3'D,F6N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VO4
Query on VO4

Download SDF File 
Download CCD File 
A, B
VANADATE ION
O4 V
LSGOVYNHVSXFFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 49.803α = 90.00
b = 104.719β = 90.00
c = 193.924γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
AMoREphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-03-11
    Type: Initial release
  • Version 1.1: 2008-05-02
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance