5NW9

Crystal structure of the complex of Tdp1 with duplex DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for DNA 3'-end processing by human tyrosyl-DNA phosphodiesterase 1.

Flett, F.J.Ruksenaite, E.Armstrong, L.A.Bharati, S.Carloni, R.Morris, E.R.Mackay, C.L.Interthal, H.Richardson, J.M.

(2018) Nat Commun 9: 24-24

  • DOI: 10.1038/s41467-017-02530-z
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Tyrosyl-DNA phosphodiesterase (Tdp1) is a DNA 3'-end processing enzyme that repairs topoisomerase 1B-induced DNA damage. We use a new tool combining site-specific DNA-protein cross-linking with mass spectrometry to identify Tdp1 interactions with DNA ...

    Tyrosyl-DNA phosphodiesterase (Tdp1) is a DNA 3'-end processing enzyme that repairs topoisomerase 1B-induced DNA damage. We use a new tool combining site-specific DNA-protein cross-linking with mass spectrometry to identify Tdp1 interactions with DNA. A conserved phenylalanine (F259) of Tdp1, required for efficient DNA processing in biochemical assays, cross-links to defined positions in DNA substrates. Crystal structures of Tdp1-DNA complexes capture the DNA repair machinery after 3'-end cleavage; these reveal how Tdp1 coordinates the 3'-phosphorylated product of nucleosidase activity and accommodates duplex DNA. A hydrophobic wedge splits the DNA ends, directing the scissile strand through a channel towards the active site. The F259 side-chain stacks against the -3 base pair, delimiting the junction of duplexed and melted DNA, and fixes the scissile strand in the channel. Our results explain why Tdp1 cleavage is non-processive and provide a molecular basis for DNA 3'-end processing by Tdp1.


    Organizational Affiliation

    Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, The King's Buildings, Roger Land Building, Alexander Crum Brown Road, Edinburgh, EH9 3FF, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosyl-DNA phosphodiesterase 1
A, B
485Homo sapiensMutation(s): 0 
Gene Names: TDP1
EC: 3.1.4.-
Find proteins for Q9NUW8 (Homo sapiens)
Go to Gene View: TDP1
Go to UniProtKB:  Q9NUW8
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(P*TP*GP*CP*GP*CP*AP*GP*TP*A)-3')C9synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.232 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 108.010α = 90.00
b = 195.310β = 90.00
c = 50.830γ = 90.00
Software Package:
Software NamePurpose
xia2data scaling
PHASERphasing
REFMACrefinement
PHASERphasing
xia2data reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBJ000884

Revision History 

  • Version 1.0: 2018-01-10
    Type: Initial release
  • Version 1.1: 2018-01-17
    Type: Database references
  • Version 1.2: 2018-06-27
    Type: Data collection, Derived calculations