4QZD

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.200 

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:  

  • 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. He ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA nucleotidylexotransferase
A
400Mus musculusMutation(s): 1 
Gene Names: Dntt (Tdt)
EC: 2.7.7.31, 3.1.11.-
Find proteins for P09838 (Mus musculus)
Go to UniProtKB:  P09838
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*AP*AP*AP*AP*AP*C)-3'D,U6N/A
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*TP*TP*TP*TP*TP*GP*C)-3'T7N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
DCT
Query on DCT

Download SDF File 
Download CCD File 
A
2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE
C9 H16 N3 O12 P3
ARLKCWCREKRROD-POYBYMJQSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.200 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 55.933α = 90.00
b = 74.920β = 98.43
c = 125.633γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
SCALAdata scaling
PHASERphasing
BUSTERrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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

Revision History 

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