4I27

Ternary complex of mouse TdT with ssDNA and incoming nucleotide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.174 

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:  
    4I27, 4I28, 4I29, 4I2E, 4I2F, 4I2G, 4I2H, 4I2I, 4I2J, 4I2A

  • 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 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA nucleotidylexotransferaseA400Mus musculusMutation(s): 0 
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*T)-3'B [auth C]6N/A
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    D3T
    Query on D3T

    Download Ideal Coordinates CCD File 
    D [auth A]2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE
    C10 H17 N2 O13 P3
    URGJWIFLBWJRMF-JGVFFNPUSA-N
     Ligand Interaction
    MG
    Query on MG

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

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

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.60 Å
    • R-Value Free: 0.233 
    • R-Value Work: 0.171 
    • R-Value Observed: 0.174 
    • Space Group: P 1 21 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 46.94α = 90
    b = 95.9β = 107.75
    c = 47.23γ = 90
    Software Package:
    Software NamePurpose
    ADSCdata collection
    PHASERphasing
    BUSTERrefinement
    XDSdata reduction
    SCALAdata scaling

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

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

    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