Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 43.65 kDa 
• Atom Count: 3,125 
• Modelled Residue Count: 360 
• Deposited Residue Count: 381 
• Unique protein chains: 1

 1JMS

Crystal Structure of the Catalytic Core of Murine Terminal Deoxynucleotidyl Transferase

• PDB DOI:  https://doi.org/10.2210/pdb1JMS/pdb

• Classification: TRANSFERASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2001-07-19 Released: 2002-01-23 
• Deposition Author(s): Delarue, M., Boule, J.B., Lescar, J., Expert-Bezancon, N., Sukumar, N., Jourdan, N., Rougeon, F., Papanicolaou, C.

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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 

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

• PubMed: 11823435 
• DOI: https://doi.org/10.1093/emboj/21.3.427
• Primary Citation of Related Structures:  
  1JMS, 1KDH, 1KEJ


• 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 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.

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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

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Organizational Affiliation: 

Unité de Biochimie Structurale, URA 2185 du CNRS, Institut Pasteur, 25 rue du Dr Roux, 75015 Paris France. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TERMINAL DEOXYNUCLEOTIDYLTRANSFERASE	A	381	Mus musculus	Mutation(s): 0  Gene Names: Tdt, Dntt EC: 2.7.7.31 (PDB Primary Data), 3.1.11 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P09838 (Mus musculus) Explore P09838  Go to UniProtKB:  P09838
IMPC:  MGI:98659

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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 = 47.1	α = 90
b = 85.2	β = 90
c = 111.7	γ = 90

Software Package:

Software Name	Purpose
MLPHARE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-01-23 
Deposition Author(s): Delarue, M., Boule, J.B., Lescar, J., Expert-Bezancon, N., Sukumar, N., Jourdan, N., Rougeon, F., Papanicolaou, C.

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