4qzd

From Proteopedia

(Difference between revisions)

Revision as of 05:50, 16 November 2017

Mouse Tdt, F405A mutant, in complex with a DSB substrate, C-C base pair

Structural highlights

4qzd is a 4 chain structure with sequence from Lk3 transgenic mice. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Related:	4i27, 1jms, 4qz8, 4qz9, 4qza, 4qzb, 4qzc, 4qze, 4qzf, 4qzg, 4qzh, 4qzi
Gene:	Dntt, Tdt (LK3 transgenic mice)
Activity:	DNA nucleotidylexotransferase, with EC number 2.7.7.31
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[TDT_MOUSE] Template-independent DNA polymerase which catalyzes the random addition of deoxynucleoside 5'-triphosphate to the 3'-end of a DNA initiator. One of the in vivo functions of this enzyme is the addition of nucleotides at the junction (N region) of rearranged Ig heavy chain and T-cell receptor gene segments during the maturation of B- and T-cells.

Publication Abstract from PubMed

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.

Structural basis for a novel mechanism of DNA bridging and alignment in eukaryotic DSB DNA repair.,Gouge J, Rosario S, Romain F, Poitevin F, Beguin P, Delarue M EMBO J. 2015 Apr 15;34(8):1126-42. doi: 10.15252/embj.201489643. Epub 2015 Mar, 11. PMID:25762590^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ 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. 2015 Apr 15;34(8):1126-42. doi: 10.15252/embj.201489643. Epub 2015 Mar, 11. PMID:25762590 doi:http://dx.doi.org/10.15252/embj.201489643

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4qzd"

@@ Line 3: / Line 3: @@
 <StructureSection load='4qzd' size='340' side='right' caption='[[4qzd]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4qzd]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QZD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QZD FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4qzd]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QZD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QZD FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DCT:2,3-DIDEOXYCYTIDINE+5-TRIPHOSPHATE'>DCT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4i27|4i27]], [[1jms|1jms]], [[4qz8|4qz8]], [[4qz9|4qz9]], [[4qza|4qza]], [[4qzb|4qzb]], [[4qzc|4qzc]], [[4qze|4qze]], [[4qzf|4qzf]], [[4qzg|4qzg]], [[4qzh|4qzh]], [[4qzi|4qzi]]</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Dntt, Tdt ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_nucleotidylexotransferase DNA nucleotidylexotransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.31 2.7.7.31] </span></td></tr>
 <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4qzd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qzd OCA], [http://pdbe.org/4qzd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4qzd RCSB], [http://www.ebi.ac.uk/pdbsum/4qzd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4qzd ProSAT]</span></td></tr>
@@ Line 25: / Line 26: @@
 </StructureSection>
 [[Category: DNA nucleotidylexotransferase]]
+[[Category: Lk3 transgenic mice]]
 [[Category: Delarue, M]]
 [[Category: Gouge, J]]

4qzd

From Proteopedia

Revision as of 05:50, 16 November 2017

Mouse Tdt, F405A mutant, in complex with a DSB substrate, C-C base pair

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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