1wtd

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<StructureSection load='1wtd' size='340' side='right'caption='[[1wtd]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
<StructureSection load='1wtd' size='340' side='right'caption='[[1wtd]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[1wtd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WTD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WTD FirstGlance]. <br>
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<table><tr><td colspan='2'>[[1wtd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WTD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WTD FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 2.401&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1wte|1wte]]</div></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=GOL:GLYCEROL'>GOL</scene></td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Type_II_site-specific_deoxyribonuclease Type II site-specific deoxyribonuclease], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.4 3.1.21.4] </span></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=1wtd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wtd OCA], [https://pdbe.org/1wtd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wtd RCSB], [https://www.ebi.ac.uk/pdbsum/1wtd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wtd ProSAT]</span></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=1wtd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wtd OCA], [https://pdbe.org/1wtd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wtd RCSB], [https://www.ebi.ac.uk/pdbsum/1wtd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wtd ProSAT]</span></td></tr>
</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/Q9RPJ3_ECOLX Q9RPJ3_ECOLX]
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EcoO109I is a type II restriction endonuclease that recognizes the DNA sequence of RGGNCCY. Here we describe the crystal structures of EcoO109I and its complex with DNA. A comparison of the two structures shows that the catalytic domain moves drastically to capture the DNA. One metal ion and two water molecules are observed near the active site of the DNA complex. The metal ion is a Lewis acid that stabilizes the pentavalent phosphorus atom in the transition state. One water molecule, activated by Lys-126, attacks the phosphorus atom in an S(N)2 mechanism, whereas the other water interacts with the 3'-leaving oxygen to donate a proton to the oxygen. EcoO109I is similar to EcoRI family enzymes in terms of its DNA cleavage pattern and folding topology of the common motif in the catalytic domain, but it differs in the manner of DNA recognition. Our findings propose a novel classification of the type II restriction endonucleases and lead to the suggestion that EcoO109I represents a new subclass of the EcoRI family.
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Crystal structures of type II restriction endonuclease EcoO109I and its complex with cognate DNA.,Hashimoto H, Shimizu T, Imasaki T, Kato M, Shichijo N, Kita K, Sato M J Biol Chem. 2005 Feb 18;280(7):5605-10. Epub 2004 Dec 7. PMID:15590682<ref>PMID:15590682</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 1wtd" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
*[[Endonuclease 3D structures|Endonuclease 3D structures]]
*[[Endonuclease 3D structures|Endonuclease 3D structures]]
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== References ==
 
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<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Bacillus coli migula 1895]]
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[[Category: Escherichia coli]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Type II site-specific deoxyribonuclease]]
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[[Category: Hashimoto H]]
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[[Category: Hashimoto, H]]
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[[Category: Imasaki T]]
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[[Category: Imasaki, T]]
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[[Category: Kato M]]
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[[Category: Kato, M]]
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[[Category: Kita K]]
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[[Category: Kita, K]]
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[[Category: Sato M]]
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[[Category: Sato, M]]
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[[Category: Shichijo N]]
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[[Category: Shichijo, N]]
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[[Category: Shimizu T]]
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[[Category: Shimizu, T]]
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[[Category: Dna-free from]]
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[[Category: Hydrolase]]
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[[Category: Restriction endonuclease]]
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Current revision

Crystal structure of type II restrcition endonuclease, EcoO109I DNA-free form

PDB ID 1wtd

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