1JMS

Crystal Structure of the Catalytic Core of Murine Terminal Deoxynucleotidyl Transferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structures of a template-independent DNA polymerase: murine terminal deoxynucleotidyltransferase.

Delarue, M.Boule, J.B.Lescar, J.Expert-Bezancon, N.Jourdan, N.Sukumar, N.Rougeon, F.Papanicolaou, C.

(2002) EMBO J 21: 427-439

  • DOI: 10.1093/emboj/21.3.427
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The crystal structure of the catalytic core of murine terminal deoxynucleotidyltransferase (TdT) at 2.35 A resolution reveals a typical DNA polymerase beta-like fold locked in a closed form. In addition, the structures of two different binary complex ...

    The crystal structure of the catalytic core of murine terminal deoxynucleotidyltransferase (TdT) at 2.35 A resolution reveals a typical DNA polymerase beta-like fold locked in a closed form. In addition, the structures of two different binary complexes, one with an oligonucleotide primer and the other with an incoming ddATP-Co(2+) complex, show that the substrates and the two divalent ions in the catalytic site are positioned in TdT in a manner similar to that described for the human DNA polymerase beta ternary complex, suggesting a common two metal ions mechanism of nucleotidyl transfer in these two proteins. The inability of TdT to accommodate a template strand can be explained by steric hindrance at the catalytic site caused by a long lariat-like loop, which is absent in DNA polymerase beta. However, displacement of this discriminating loop would be sufficient to unmask a number of evolutionarily conserved residues, which could then interact with a template DNA strand. The present structure can be used to model the recently discovered human polymerase mu, with which it shares 43% sequence identity.


    Related Citations: 
    • Crystallization of the Catalytic Domain of Murine Deoxynucleotidyl Transferase
      Sukumar, N., Boule, J.B., Expert-Bezancon, N., Jourdan, N., Lescar, J., Rougeon, F., Papanicolaou, C., Delarue, M.
      (2000) Acta Crystallogr D Biol Crystallogr 56: 1662

    Organizational Affiliation

    Unité de Biochimie Structurale, URA 2185 du CNRS, Institut Pasteur, 25 rue du Dr Roux, 75015 Paris France. delarue@pasteur.fr



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TERMINAL DEOXYNUCLEOTIDYLTRANSFERASEA381Mus musculusMutation(s): 0 
Gene Names: TdtDntt
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
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

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

Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.1α = 90
b = 85.2β = 90
c = 111.7γ = 90
Software Package:
Software NamePurpose
MLPHAREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-01-23
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance