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 
  • R-Value Observed: 0.234 

wwPDB Validation   3D Report Full Report


This is version 1.3 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:  
    5NW9, 5NWA

  • 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. A conserved phenylalanine (F259) of Tdp1, required for efficient DNA processing in biochemical assays, cross-links to defined positions in DNA substrates ...

    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 Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, The King's Buildings, Max Born Crescent, Edinburgh, EH9 3BF, UK. julia.richardson@ed.ac.uk.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosyl-DNA phosphodiesterase 1A, B485Homo sapiensMutation(s): 0 
Gene Names: TDP1
EC: 3.1.4
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NUW8 (Homo sapiens)
Explore Q9NUW8 
Go to UniProtKB:  Q9NUW8
PHAROS:  Q9NUW8
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*TP*GP*CP*GP*CP*AP*GP*TP*A)-3')C9synthetic construct
    Protein Feature View
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    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.04 Å
    • R-Value Free: 0.271 
    • R-Value Work: 0.232 
    • R-Value Observed: 0.234 
    • Space Group: P 21 21 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 108.01α = 90
    b = 195.31β = 90
    c = 50.83γ = 90
    Software Package:
    Software NamePurpose
    xia2data scaling
    PHASERphasing
    REFMACrefinement
    PDB_EXTRACTdata extraction
    PHASERphasing
    xia2data reduction

    Structure Validation

    View Full Validation Report




    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    Biotechnology and Biological Sciences Research CouncilUnited KingdomBJ000884

    Revision History  (Full details and data files)

    • Version 1.0: 2018-01-10
      Type: Initial release
    • Version 1.1: 2018-01-17
      Changes: Database references
    • Version 1.2: 2018-06-27
      Changes: Data collection, Derived calculations
    • Version 1.3: 2019-10-16
      Changes: Data collection