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1wtd

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[[Image:1wtd.jpg|left|200px]]<br /><applet load="1wtd" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1wtd, resolution 2.401&Aring;" />
 
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'''Crystal structure of type II restrcition endonuclease, EcoO109I DNA-free form'''<br />
 
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==Overview==
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==Crystal structure of type II restrcition endonuclease, EcoO109I DNA-free form==
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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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<StructureSection load='1wtd' size='340' side='right'caption='[[1wtd]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
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== 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/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='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='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='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>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/Q9RPJ3_ECOLX Q9RPJ3_ECOLX]
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==About this Structure==
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==See Also==
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1WTD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=GOL:'>GOL</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Type_II_site-specific_deoxyribonuclease Type II site-specific deoxyribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.4 3.1.21.4] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WTD OCA].
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*[[Endonuclease 3D structures|Endonuclease 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15590682 15590682]
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[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Single protein]]
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[[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: GOL]]
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[[Category: dna-free from]]
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[[Category: restriction endonuclease]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:47:54 2008''
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Current revision

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

PDB ID 1wtd

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