5th3: Difference between revisions

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<StructureSection load='5th3' size='340' side='right'caption='[[5th3]], [[Resolution|resolution]] 2.33&Aring;' scene=''>
<StructureSection load='5th3' size='340' side='right'caption='[[5th3]], [[Resolution|resolution]] 2.33&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[5th3]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_27836 Atcc 27836]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TH3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TH3 FirstGlance]. <br>
<table><tr><td colspan='2'>[[5th3]] is a 12 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=5TH3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5TH3 FirstGlance]. <br>
</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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.33&#8491;</td></tr>
<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>
<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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5tgq|5tgq]], [[5tgx|5tgx]]</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5th3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5th3 OCA], [https://pdbe.org/5th3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5th3 RCSB], [https://www.ebi.ac.uk/pdbsum/5th3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5th3 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=5th3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5th3 OCA], [http://pdbe.org/5th3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5th3 RCSB], [http://www.ebi.ac.uk/pdbsum/5th3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5th3 ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/A0A1S4NYF7_STAWA A0A1S4NYF7_STAWA]
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.
 
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>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5th3" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Atcc 27836]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Shen, B W]]
[[Category: Staphylococcus warneri]]
[[Category: Stoddard, B L]]
[[Category: Synthetic construct]]
[[Category: Cleaved dna complex]]
[[Category: Shen BW]]
[[Category: Dna binding protein]]
[[Category: Stoddard BL]]
[[Category: I-swai]]
[[Category: R/m system]]
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