6go3: Difference between revisions
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<StructureSection load='6go3' size='340' side='right'caption='[[6go3]], [[Resolution|resolution]] 2.20Å' scene=''> | <StructureSection load='6go3' size='340' side='right'caption='[[6go3]], [[Resolution|resolution]] 2.20Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[6go3]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6GO3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6GO3 FirstGlance]. <br> | <table><tr><td colspan='2'>[[6go3]] is a 1 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=6GO3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6GO3 FirstGlance]. <br> | ||
</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=6go3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6go3 OCA], [http://pdbe.org/6go3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6go3 RCSB], [http://www.ebi.ac.uk/pdbsum/6go3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6go3 ProSAT]</span></td></tr> | </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='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=6go3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6go3 OCA], [http://pdbe.org/6go3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6go3 RCSB], [http://www.ebi.ac.uk/pdbsum/6go3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6go3 ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | == Function == | ||
[[http://www.uniprot.org/uniprot/TDT_MOUSE 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. | [[http://www.uniprot.org/uniprot/TDT_MOUSE 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. | ||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Eukaryotic DNA polymerase (Pol) X family members such as Pol mu 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 mu 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 mu that recapitulated the functional properties of Pol mu in ligation experiments. We solved three crystal structures of this TdT chimera bound to several DNA substrates at 1.96-2.55 A resolutions, including a full DNA double-strand break (DSB) synapsis. We then modeled the full Pol mu sequence in the context of one these complexes. The atomic structure of an NHEJ junction with a Pol X construct that mimics Pol mu in a reconstituted system explained the distinctive properties of Pol mu 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. | |||
Structural evidence for an in trans base selection mechanism involving Loop1 in polymerase mu at an NHEJ double-strand break junction.,Loc'h J, Gerodimos CA, Rosario S, Tekpinar M, Lieber MR, Delarue M J Biol Chem. 2019 Jul 5;294(27):10579-10595. doi: 10.1074/jbc.RA119.008739. Epub , 2019 May 28. PMID:31138645<ref>PMID:31138645</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 6go3" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Lk3 transgenic mice]] | |||
[[Category: Delarue, M]] | [[Category: Delarue, M]] | ||
[[Category: Gerodimos, C A]] | [[Category: Gerodimos, C A]] | ||
Latest revision as of 15:55, 25 December 2019
TdT chimera (Loop1 of pol mu) - apoenzymeTdT chimera (Loop1 of pol mu) - apoenzyme
Structural highlights
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 PubMedEukaryotic DNA polymerase (Pol) X family members such as Pol mu 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 mu 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 mu that recapitulated the functional properties of Pol mu in ligation experiments. We solved three crystal structures of this TdT chimera bound to several DNA substrates at 1.96-2.55 A resolutions, including a full DNA double-strand break (DSB) synapsis. We then modeled the full Pol mu sequence in the context of one these complexes. The atomic structure of an NHEJ junction with a Pol X construct that mimics Pol mu in a reconstituted system explained the distinctive properties of Pol mu 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. Structural evidence for an in trans base selection mechanism involving Loop1 in polymerase mu at an NHEJ double-strand break junction.,Loc'h J, Gerodimos CA, Rosario S, Tekpinar M, Lieber MR, Delarue M J Biol Chem. 2019 Jul 5;294(27):10579-10595. doi: 10.1074/jbc.RA119.008739. Epub , 2019 May 28. PMID:31138645[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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