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5tgx

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==Restriction/modification system-Type II R-SwaI complexed with partially cleaved DNA==
==Restriction/modification system-Type II R-SwaI complexed with partially cleaved DNA==
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<StructureSection load='5tgx' size='340' side='right' caption='[[5tgx]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
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<StructureSection load='5tgx' size='340' side='right'caption='[[5tgx]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5tgx]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TGX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TGX FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5tgx]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_warneri Staphylococcus warneri] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TGX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5TGX FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
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<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5tgq|5tgq]], [[5th3|5th3]]</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5tgx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tgx OCA], [https://pdbe.org/5tgx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5tgx RCSB], [https://www.ebi.ac.uk/pdbsum/5tgx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5tgx ProSAT]</span></td></tr>
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<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=5tgx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tgx OCA], [http://pdbe.org/5tgx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tgx RCSB], [http://www.ebi.ac.uk/pdbsum/5tgx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tgx ProSAT]</span></td></tr>
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</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/A0A1S4NYF7_STAWA A0A1S4NYF7_STAWA]
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R.SwaI, a Type IIP restriction endonuclease, recognizes a palindromic eight base pair (bp) symmetric sequence, 5-ATTTAAAT-3, and cleaves that target at its center to generate blunt-ended DNA fragments. Here, we report three crystal structures of SwaI: unbound enzyme, a DNA-bound complex with calcium ions; and a DNA-bound, fully cleaved complex with magnesium ions. We compare these structures to two structurally similar 'PD-D/ExK' restriction endonucleases (EcoRV and HincII) that also generate blunt-ended products, and to a structurally distinct enzyme (the HNH endonuclease PacI) that also recognizes an 8-bp target site consisting solely of A:T base pairs. Binding by SwaI induces an extreme bend in the target sequence accompanied by un-pairing and re-ordering of its central A:T base pairs. This result is reminiscent of a more dramatic target deformation previously described for PacI, implying that long A:T-rich target sites might display structural or dynamic behaviors that play a significant role in endonuclease recognition and cleavage.
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DNA recognition by the SwaI restriction endonuclease involves unusual distortion of an 8 base pair A:T-rich target.,Shen BW, Heiter DF, Lunnen KD, Wilson GG, Stoddard BL Nucleic Acids Res. 2017 Feb 17;45(3):1516-1528. doi: 10.1093/nar/gkw1200. PMID:28180307<ref>PMID:28180307</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 5tgx" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Shen, B W]]
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[[Category: Large Structures]]
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[[Category: Stoddard, B L]]
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[[Category: Staphylococcus warneri]]
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[[Category: Dna binding protein]]
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[[Category: Synthetic construct]]
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[[Category: R-swai]]
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[[Category: Shen BW]]
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[[Category: R/m system]]
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[[Category: Stoddard BL]]
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[[Category: Rare cutter]]
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[[Category: Uncleaved dna complex]]
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Current revision

Restriction/modification system-Type II R-SwaI complexed with partially cleaved DNA

PDB ID 5tgx

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