Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 45.85 kDa 
• Atom Count: 3015 
• Modelled Residue Count: 343 
• Deposited Residue Count: 401 
• Unique protein chains: 1

6GO3

TdT chimera (Loop1 of pol mu) - apoenzyme

• PDB DOI: 10.2210/pdb6GO3/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-06-01 Released: 2019-06-05 
• Deposition Author(s): Loc'h, J., Gerodimos, C.A., Rosario, S., Lieber, M.R., Delarue, M.
• Funding Organization(s): Fondation ARC

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.251 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 

Literature

Structural evidence for an intransbase selection mechanism involving Loop1 in polymerase mu at an NHEJ double-strand break junction.

Loc'h, J., Gerodimos, C.A., Rosario, S., Tekpinar, M., Lieber, M.R., Delarue, M.

(2019) J Biol Chem 294: 10579-10595

• PubMed: 31138645 
• DOI: 10.1074/jbc.RA119.008739
• Primary Citation of Related Structures:  
  6GO3, 6GO4, 6GO5, 6GO6, 6GO7


• PubMed Abstract: 
  

Eukaryotic DNA polymerase (Pol) X family members such as Pol μ and terminal deoxynucleotidyl transferase (TdT) are important components for the nonhomologous DNA end-joining (NHEJ) pathway. TdT participates in a specialized version of NHEJ, V(D)J recombination. It has primarily nontemplated polymerase activity but can take instructions across strands from the downstream dsDNA, and both activities are highly dependent on a structural element called Loop1. However, it is unclear whether Pol μ follows the same mechanism, because the structure of its Loop1 is disordered in available structures. Here, we used a chimeric TdT harboring Loop1 of Pol μ that recapitulated the functional properties of Pol μ in ligation experiments. We solved three crystal structures of this TdT chimera bound to several DNA substrates at 1.96-2.55 Å resolutions, including a full DNA double-strand break (DSB) synapsis. We then modeled the full Pol μ sequence in the context of one these complexes. The atomic structure of an NHEJ junction with a Pol X construct that mimics Pol μ in a reconstituted system explained the distinctive properties of Pol μ compared with TdT. The structure suggested a mechanism of base selection relying on Loop1 and taking instructions via the in trans templating base independently of the primer strand. We conclude that our atomic-level structural observations represent a paradigm shift for the mechanism of base selection in the Pol X family of DNA polymerases.

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Organizational Affiliation: 

From the Unité de Dynamique Structurale des Macromolécules, Institut Pasteur, UMR 3528 du CNRS, 25 Rue du Dr. Roux, 75015 Paris, France and [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA nucleotidylexotransferase,DNA-directed DNA/RNA polymerase mu,DNA nucleotidylexotransferase	A	401	Mus musculus	Mutation(s): 0  Gene Names: Dntt, Tdt, Polm, polmu EC: 2.7.7.31 (PDB Primary Data), 2.7.7.7 (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
Find proteins for Q9JIW4 (Mus musculus) Explore Q9JIW4  Go to UniProtKB:  Q9JIW4
UniProt Groups	Q9JIW4P09838

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.251 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.87	α = 90
b = 85.28	β = 90
c = 119.71	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-06-01 
• Released Date: 2019-06-05 
Deposition Author(s): Loc'h, J., Gerodimos, C.A., Rosario, S., Lieber, M.R., Delarue, M.

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Funding Organization	Location	Grant Number
Fondation ARC	France	Fondation ARC pour la recherche sur le cancer

Revision History  

• Version 1.0: 2019-06-05
  Type: Initial release
  
• Version 1.1: 2019-12-25
  Changes: Database references