1RG2

Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide AGTA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Explorations of peptide and oligonucleotide binding sites of tyrosyl-DNA phosphodiesterase using vanadate complexes.

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

(2004) J.Med.Chem. 47: 829-837

  • DOI: 10.1021/jm030487x
  • Primary Citation of Related Structures:  1RFF, 1RFI, 1RG1, 1RGT, 1RGU, 1RH0

  • PubMed Abstract: 
  • Tyrosyl-DNA phosphodiesterase (Tdp1) catalyzes the hydrolysis of a phosphodiester bond between a tyrosine residue and a DNA 3' phosphate and functions as a DNA repair enzyme that cleaves stalled topoisomerase I-DNA complexes. We previously determined ...

    Tyrosyl-DNA phosphodiesterase (Tdp1) catalyzes the hydrolysis of a phosphodiester bond between a tyrosine residue and a DNA 3' phosphate and functions as a DNA repair enzyme that cleaves stalled topoisomerase I-DNA complexes. We previously determined a procedure to crystallize a quaternary complex containing Tdp1, vanadate, a DNA oligonucleotide, and a tyrosine-containing peptide that mimics the transition state for hydrolysis of the Tdp1 substrate. Here, the ability of vanadate to accept a variety of different ligands is exploited to produce several different quaternary complexes with a variety of oligonucleotides, and peptides or a tyrosine analogue, in efforts to explore the binding properties of the Tdp1 DNA and peptide binding clefts. Eight crystal structures of Tdp1 with vanadate, oligonucleotides, and peptides or peptide analogues were determined. These structures demonstrated that Tdp1 is able to bind substituents with limited sequence variation in the polypeptide moiety and also bind oligonucleotides with sequence variation at the 3' end. Additionally, the tyrosine analogue octopamine can replace topoisomerase I derived peptides as the apical ligand to vanadate. The versatility of this system suggests that the formation of quaternary complexes around vanadate could be adapted to become a useful method for structure-based inhibitor design and has the potential to be generally applicable to other enzymes that perform chemistry on phosphate esters.


    Related Citations: 
    • 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
    • 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
    • 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


    Organizational Affiliation

    Department of Biochemistry, P.O. Box 357742, School of Medicine, University of Washington, Seattle, Washington 98195-7242, 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: 1
MoleculeChainsLengthOrganism
5'-D(*AP*GP*TP*A)-3'D,F4N/A
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SPM
Query on SPM

Download SDF File 
Download CCD File 
A
SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
 Ligand Interaction
OTR
Query on OTR

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Download CCD File 
A, B
4-(2R-AMINO-1-HYDROXYETHYL)PHENOL
R-OCTOPAMINE
C8 H11 N O2
QHGUCRYDKWKLMG-QMMMGPOBSA-N
 Ligand Interaction
OTS
Query on OTS

Download SDF File 
Download CCD File 
A, B
4-(2S-AMINO-1-HYDROXYETHYL)PHENOL
S-OCTOPAMINE
C8 H11 N O2
QHGUCRYDKWKLMG-MRVPVSSYSA-N
 Ligand Interaction
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: 2.1 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 49.811α = 90.00
b = 104.688β = 90.00
c = 193.310γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-03-02
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance