4QZB

Mouse Tdt in complex with a DSB substrate, C-T base pair

Summary for 4QZB

• Entry DOI: 10.2210/pdb4qzb/pdb
• Related: 1JMS 4I27 4QZ8 4QZ9 4QZA 4QZC 4QZD 4QZE 4QZF 4QZG 4QZH 4QZI
• Descriptor: DNA nucleotidylexotransferase, 5'-D(*AP*AP*AP*AP*AP*C)-3', 5'-D(*TP*TP*TP*TP*TP*GP*T)-3', ... (7 entities in total)
• Functional Keywords: terminal deoxynucleotidyltransferase, nucleus, transferase-dna complex, transferase/dna
• Biological source: Mus musculus (mouse); More
• Cellular location: Isoform TDT-S: Nucleus. Isoform TDT-L: Cytoplasm. Nucleus : P09838
• Total number of polymer chains: 4
• Total formula weight: 51932.38

Authors

Gouge, J.,Delarue, M. (deposition date: 2014-07-27, release date: 2015-06-10, Last modification date: 2023-09-20)

Primary citation

Gouge, J.,Rosario, S.,Romain, F.,Poitevin, F.,Beguin, P.,Delarue, M.
Structural basis for a novel mechanism of DNA bridging and alignment in eukaryotic DSB DNA repair.
Embo J., 34:1126-1142, 2015

PubMed Abstract: Eukaryotic DNA polymerase mu of the PolX family can promote the association of the two 3'-protruding ends of a DNA double-strand break (DSB) being repaired (DNA synapsis) even in the absence of the core non-homologous end-joining (NHEJ) machinery. Here, we show that terminal deoxynucleotidyltransferase (TdT), a closely related PolX involved in V(D)J recombination, has the same property. We solved its crystal structure with an annealed DNA synapsis containing one micro-homology (MH) base pair and one nascent base pair. This structure reveals how the N-terminal domain and Loop 1 of Tdt cooperate for bridging the two DNA ends, providing a templating base in trans and limiting the MH search region to only two base pairs. A network of ordered water molecules is proposed to assist the incorporation of any nucleotide independently of the in trans templating base. These data are consistent with a recent model that explains the statistics of sequences synthesized in vivo by Tdt based solely on this dinucleotide step. Site-directed mutagenesis and functional tests suggest that this structural model is also valid for Pol mu during NHEJ.

PubMed: 25762590
DOI: 10.15252/embj.201489643

Experimental method

X-RAY DIFFRACTION (2.15 Å)