6fi8: Difference between revisions
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<StructureSection load='6fi8' size='340' side='right' caption='[[6fi8]], [[Resolution|resolution]] 2.60Å' scene=''> | <StructureSection load='6fi8' size='340' side='right' caption='[[6fi8]], [[Resolution|resolution]] 2.60Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[6fi8]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6FI8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6FI8 FirstGlance]. <br> | <table><tr><td colspan='2'>[[6fi8]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43504 Atcc 43504]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6FI8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6FI8 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BB387_02765, BB390_06935, BB392_05440, BB394_07800, BB413_07925, BB437_07715, BB438_04880, BB447_07970, BB453_04885, BB461_01775, BB469_00740, BFR58_04045, BFR58_04080, BFR58_04135, BFR58_07690, BFR58_08055, BGL67_05025, BGL76_01750, BGL76_01790, BGL76_01830, BGL76_03945, BGL76_04370, BGL76_05875, BGL76_06710, BGL85_00790 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=210 ATCC 43504])</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=6fi8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6fi8 OCA], [http://pdbe.org/6fi8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6fi8 RCSB], [http://www.ebi.ac.uk/pdbsum/6fi8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6fi8 ProSAT]</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=6fi8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6fi8 OCA], [http://pdbe.org/6fi8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6fi8 RCSB], [http://www.ebi.ac.uk/pdbsum/6fi8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6fi8 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Transposable elements are efficient DNA carriers and thus important tools for transgenesis and insertional mutagenesis. However, their poor target sequence specificity constitutes an important limitation for site-directed applications. The insertion sequence IS608 from Helicobacter pylori recognizes a specific tetranucleotide sequence by base pairing, and its target choice can be re-programmed by changes in the transposon DNA. Here, we present the crystal structure of the IS608 target capture complex in an active conformation, providing a complete picture of the molecular interactions between transposon and target DNA prior to integration. Based on this, we engineered IS608 variants to direct their integration specifically to various 12/17-nt long target sites by extending the base pair interaction network between the transposon and the target DNA. We demonstrate in vitro that the engineered transposons efficiently select their intended target sites. Our data further elucidate how the distinct secondary structure of the single-stranded transposon intermediate prevents extended target specificity in the wild-type transposon, allowing it to move between diverse genomic sites. Our strategy enables efficient targeting of unique DNA sequences with high specificity in an easily programmable manner, opening possibilities for the use of the IS608 system for site-specific gene insertions. | |||
Targeting IS608 transposon integration to highly specific sequences by structure-based transposon engineering.,Morero NR, Zuliani C, Kumar B, Bebel A, Okamoto S, Guynet C, Hickman AB, Chandler M, Dyda F, Barabas O Nucleic Acids Res. 2018 Apr 9. pii: 4964819. doi: 10.1093/nar/gky235. PMID:29635476<ref>PMID:29635476</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 6fi8" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Atcc 43504]] | |||
[[Category: Barabas, O]] | [[Category: Barabas, O]] | ||
[[Category: Morero, N R]] | [[Category: Morero, N R]] | ||
Latest revision as of 09:48, 18 April 2018
Crystal structure of the IS608 transposase in complex with left end 29-mer DNA hairpin and a 6-mer DNA representing the intact target site: pre-cleavage target capture complexCrystal structure of the IS608 transposase in complex with left end 29-mer DNA hairpin and a 6-mer DNA representing the intact target site: pre-cleavage target capture complex
Structural highlights
Publication Abstract from PubMedTransposable elements are efficient DNA carriers and thus important tools for transgenesis and insertional mutagenesis. However, their poor target sequence specificity constitutes an important limitation for site-directed applications. The insertion sequence IS608 from Helicobacter pylori recognizes a specific tetranucleotide sequence by base pairing, and its target choice can be re-programmed by changes in the transposon DNA. Here, we present the crystal structure of the IS608 target capture complex in an active conformation, providing a complete picture of the molecular interactions between transposon and target DNA prior to integration. Based on this, we engineered IS608 variants to direct their integration specifically to various 12/17-nt long target sites by extending the base pair interaction network between the transposon and the target DNA. We demonstrate in vitro that the engineered transposons efficiently select their intended target sites. Our data further elucidate how the distinct secondary structure of the single-stranded transposon intermediate prevents extended target specificity in the wild-type transposon, allowing it to move between diverse genomic sites. Our strategy enables efficient targeting of unique DNA sequences with high specificity in an easily programmable manner, opening possibilities for the use of the IS608 system for site-specific gene insertions. Targeting IS608 transposon integration to highly specific sequences by structure-based transposon engineering.,Morero NR, Zuliani C, Kumar B, Bebel A, Okamoto S, Guynet C, Hickman AB, Chandler M, Dyda F, Barabas O Nucleic Acids Res. 2018 Apr 9. pii: 4964819. doi: 10.1093/nar/gky235. PMID:29635476[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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