4QZC

Mouse Tdt, F405A mutant, in complex with a DSB substrate, C-G base pair


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for a novel mechanism of DNA bridging and alignment in eukaryotic DSB DNA repair.

Gouge, J.Rosario, S.Romain, F.Poitevin, F.Beguin, P.Delarue, M.

(2015) EMBO J 34: 1126-1142

  • DOI: 10.15252/embj.201489643
  • Primary Citation of Related Structures:  
    4QZ8, 4QZ9, 4QZE, 4QZF, 4QZG, 4QZH, 4QZI, 4QZA, 4QZB, 4QZC

  • PubMed Abstract: 
  • Eukaryotic DNA polymerase mu of the PolX family can promote the association of the two 3'-protruding ends of a DNA double-strand break (DSB) being repaired (DNA synapsis) even in the absence of the core non-homologous end-joining (NHEJ) machinery. Here, we show that terminal deoxynucleotidyltransferase (TdT), a closely related PolX involved in V(D)J recombination, has the same property ...

    Eukaryotic DNA polymerase mu of the PolX family can promote the association of the two 3'-protruding ends of a DNA double-strand break (DSB) being repaired (DNA synapsis) even in the absence of the core non-homologous end-joining (NHEJ) machinery. Here, we show that terminal deoxynucleotidyltransferase (TdT), a closely related PolX involved in V(D)J recombination, has the same property. We solved its crystal structure with an annealed DNA synapsis containing one micro-homology (MH) base pair and one nascent base pair. This structure reveals how the N-terminal domain and Loop 1 of Tdt cooperate for bridging the two DNA ends, providing a templating base in trans and limiting the MH search region to only two base pairs. A network of ordered water molecules is proposed to assist the incorporation of any nucleotide independently of the in trans templating base. These data are consistent with a recent model that explains the statistics of sequences synthesized in vivo by Tdt based solely on this dinucleotide step. Site-directed mutagenesis and functional tests suggest that this structural model is also valid for Pol mu during NHEJ.


    Organizational Affiliation

    Unité de Dynamique Structurale des Macromolécules, Institut Pasteur, UMR 3528 du C.N.R.S., Paris, France marc.delarue@pasteur.fr.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA nucleotidylexotransferaseA400Mus musculusMutation(s): 1 
Gene Names: DnttTdt
EC: 2.7.7.31 (PDB Primary Data), 3.1.11 (UniProt)
Find proteins for P09838 (Mus musculus)
Explore P09838 
Go to UniProtKB:  P09838
NIH Common Fund Data Resources
IMPC:  MGI:98659
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-D(*AP*AP*AP*AP*AP*C)-3'B [auth D], D [auth U]6N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      5'-D(*TP*TP*TP*TP*TP*GP*G)-3'C [auth T]7N/A
      Small Molecules
      Ligands 3 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      DCT
      Query on DCT

      Download Ideal Coordinates CCD File 
      H [auth A]2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE
      C9 H16 N3 O12 P3
      ARLKCWCREKRROD-POYBYMJQSA-N
       Ligand Interaction
      MG
      Query on MG

      Download Ideal Coordinates CCD File 
      E [auth A], F [auth A]MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N
       Ligand Interaction
      NA
      Query on NA

      Download Ideal Coordinates CCD File 
      G [auth A]SODIUM ION
      Na
      FKNQFGJONOIPTF-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.75 Å
      • R-Value Free: 0.214 
      • R-Value Work: 0.188 
      • R-Value Observed: 0.189 
      • Space Group: C 1 2 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 56.397α = 90
      b = 75.178β = 99.05
      c = 125.943γ = 90
      Software Package:
      Software NamePurpose
      DNAdata collection
      PHASERphasing
      BUSTERrefinement
      XDSdata reduction
      SCALAdata scaling

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      • Deposited Date: 2014-07-27 
      • Released Date: 2015-06-10 
      • Deposition Author(s): Gouge, J., Delarue, M.

      Revision History  (Full details and data files)

      • Version 1.0: 2015-06-10
        Type: Initial release
      • Version 1.1: 2017-07-26
        Changes: Refinement description, Source and taxonomy