4I2I

Binary complex of mouse TdT with AP5A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structures of Intermediates along the Catalytic Cycle of Terminal Deoxynucleotidyltransferase: Dynamical Aspects of the Two-Metal Ion Mechanism.

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

(2013) J.Mol.Biol. 425: 4334-4352

  • DOI: 10.1016/j.jmb.2013.07.009
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Terminal deoxynucleotidyltransferase (Tdt) is a non-templated eukaryotic DNA polymerase of the polX family that is responsible for the random addition of nucleotides at the V(D)J junctions of immunoglobulins and T-cell receptors. Here we describe a s ...

    Terminal deoxynucleotidyltransferase (Tdt) is a non-templated eukaryotic DNA polymerase of the polX family that is responsible for the random addition of nucleotides at the V(D)J junctions of immunoglobulins and T-cell receptors. Here we describe a series of high-resolution X-ray structures that mimic the pre-catalytic state, the post-catalytic state and a competent state that can be transformed into the two other ones in crystallo via the addition of dAMPcPP and Zn(2+), respectively. We examined the effect of Mn(2+), Co(2+) and Zn(2+) because they all have a marked influence on the kinetics of the reaction. We demonstrate a dynamic role of divalent transition metal ions bound to site A: (i) Zn(2+) (or Co(2+)) in Metal A site changes coordination from octahedral to tetrahedral after the chemical step, which explains the known higher affinity of Tdt for the primer strand when these ions are present, and (ii) metal A has to leave to allow the translocation of the primer strand and to clear the active site, a typical feature for a ratchet-like mechanism. Except for Zn(2+), the sugar puckering of the primer strand 3' terminus changes from C2'-endo to C3'-endo during catalysis. In addition, our data are compatible with a scheme where metal A is the last component that binds to the active site to complete its productive assembly, as already inferred in human pol beta. The new structures have potential implications for modeling pol mu, a closely related polX implicated in the repair of DNA double-strand breaks, in a complex with a DNA synapsis.


    Organizational Affiliation

    Unité de Dynamique Structurale des Macromolécules, Institut Pasteur, UMR 3528 du CNRS, 25 rue du Dr Roux, 75015 Paris, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA nucleotidylexotransferase
A
400Mus musculusMutation(s): 0 
Gene Names: Dntt (Tdt)
EC: 2.7.7.31, 3.1.11.-
Find proteins for P09838 (Mus musculus)
Go to UniProtKB:  P09838
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
AP5
Query on AP5

Download SDF File 
Download CCD File 
A
BIS(ADENOSINE)-5'-PENTAPHOSPHATE
C20 H29 N10 O22 P5
OIMACDRJUANHTJ-XPWFQUROSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 46.750α = 90.00
b = 84.100β = 90.00
c = 103.890γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
XDSdata reduction
PHASERphasing
BUSTERrefinement
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-11-21 
  • Released Date: 2013-07-24 
  • Deposition Author(s): Gouge, J., Delarue, M.

Revision History 

  • Version 1.0: 2013-07-24
    Type: Initial release
  • Version 1.1: 2013-07-31
    Type: Database references
  • Version 1.2: 2013-11-13
    Type: Database references
  • Version 1.3: 2017-07-26
    Type: Refinement description, Source and taxonomy