4QZ8: Mouse Tdt In Complex With A Dsb Substrate, C-g Base Pair

Citation:
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.
PDB ID: 4QZ8Download
MMDB ID: 129894
PDB Deposition Date: 2014/7/27
Updated in MMDB: 2017/07
Experimental Method:
x-ray diffraction
Resolution: 2.7  Å
Source Organism:
Mus musculus
Similar Structures:
Biological Unit for 4QZ8: tetrameric; determined by author and by software (PISA)
Molecular Components in 4QZ8
Label Count Molecule
Protein (1 molecule)
1
DNA Nucleotidylexotransferase(Gene symbol: Dntt)
Molecule annotation
Nucleotides(2 molecules)
2
5'-d(*ap*ap*ap*ap*ap*c)-3'
Molecule annotation
1
5'-d(*tp*tp*tp*tp*tp*gp*g)-3'
Molecule annotation
Chemicals (3 molecules)
1
1
2
1
3
1
* Click molecule labels to explore molecular sequence information.

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