Binary complex of mouse TdT with ssDNA

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


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: https://doi.org/10.1016/j.jmb.2013.07.009
  • Primary Citation of Related Structures:  
    4I27, 4I28, 4I29, 4I2A, 4I2B, 4I2C, 4I2D, 4I2E, 4I2F, 4I2G, 4I2H, 4I2I, 4I2J

  • 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 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.


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA nucleotidylexotransferase400Mus musculusMutation(s): 0 
Gene Names: DnttTdt
UniProt & NIH Common Fund Data Resources
Find proteins for P09838 (Mus musculus)
Explore P09838 
Go to UniProtKB:  P09838
IMPC:  MGI:98659
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09838
Sequence Annotations
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
5'-D(P*AP*AP*AP*AP*A)-3'B [auth C]5N/A
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.826α = 90
b = 84.636β = 90
c = 115.85γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-24
    Type: Initial release
  • Version 1.1: 2013-07-31
    Changes: Database references
  • Version 1.2: 2013-11-13
    Changes: Database references
  • Version 1.3: 2017-07-26
    Changes: Refinement description, Source and taxonomy
  • Version 1.4: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description