2vs7: Difference between revisions

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-[[Image:2vs7.png|left|200px]]
-{{STRUCTURE_2vs7|  PDB=2vs7  |  SCENE=  }}
+==The crystal structure of I-DmoI in complex with DNA and Ca==
+<StructureSection load='2vs7' size='340' side='right'caption='[[2vs7]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2vs7]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfurococcus_mucosus Desulfurococcus mucosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VS7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VS7 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.05&#8491;</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=CA:CALCIUM+ION'>CA</scene></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=2vs7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vs7 OCA], [https://pdbe.org/2vs7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vs7 RCSB], [https://www.ebi.ac.uk/pdbsum/2vs7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vs7 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DMO1_DESMO DMO1_DESMO] Endonuclease involved in intron homing. Recognizes a recognizes up to 20 bp of DNA in the 23S rRNA gene intron. It has a slow turnover rate and cuts the coding strand with a slight preference over the non-coding strand.
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vs/2vs7_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2vs7 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Homing endonucleases, also known as meganucleases, are sequence-specific enzymes with large DNA recognition sites. These enzymes can be used to induce efficient homologous gene targeting in cells and plants, opening perspectives for genome engineering with applications in a wide series of fields, ranging from biotechnology to gene therapy. Here, we report the crystal structures at 2.0 and 2.1 A resolution of the I-DmoI meganuclease in complex with its substrate DNA before and after cleavage, providing snapshots of the catalytic process. Our study suggests that I-DmoI requires only 2 cations instead of 3 for DNA cleavage. The structure sheds light onto the basis of DNA binding, indicating key residues responsible for nonpalindromic target DNA recognition. In silico and in vivo analysis of the I-DmoI DNA cleavage specificity suggests that despite the relatively few protein-base contacts, I-DmoI is highly specific when compared with other meganucleases. Our data open the door toward the generation of custom endonucleases for targeted genome engineering using the monomeric I-DmoI scaffold.
-===THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH DNA AND CA===
+Crystal structure of I-DmoI in complex with its target DNA provides new insights into meganuclease engineering.,Marcaida MJ, Prieto J, Redondo P, Nadra AD, Alibes A, Serrano L, Grizot S, Duchateau P, Paques F, Blanco FJ, Montoya G Proc Natl Acad Sci U S A. 2008 Nov 4;105(44):16888-93. Epub 2008 Oct 30. PMID:18974222<ref>PMID:18974222</ref>
-{{ABSTRACT_PUBMED_18974222}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 2vs7" style="background-color:#fffaf0;"></div>
-[[2vs7]] is a 9 chain structure of [[Endonuclease]] with sequence from [http://en.wikipedia.org/wiki/Desulfurococcus_mobilis Desulfurococcus mobilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VS7 OCA].
 ==See Also==
-*[[Endonuclease|Endonuclease]]
+*[[Endonuclease 3D structures|Endonuclease 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:018974222</ref><references group="xtra"/>
+__TOC__
-[[Category: Desulfurococcus mobilis]]
+</StructureSection>
-[[Category: Alibes, A.]]
+[[Category: Desulfurococcus mucosus]]
-[[Category: Blanco, F J.]]
+[[Category: Large Structures]]
-[[Category: Duchateau, P.]]
+[[Category: Alibes A]]
-[[Category: Grizot, S.]]
+[[Category: Blanco FJ]]
-[[Category: Marcaida, M J.]]
+[[Category: Duchateau P]]
-[[Category: Montoya, G.]]
+[[Category: Grizot S]]
-[[Category: Nadra, A D.]]
+[[Category: Marcaida MJ]]
-[[Category: Paques, F.]]
+[[Category: Montoya G]]
-[[Category: Prieto, J.]]
+[[Category: Nadra AD]]
-[[Category: Redondo, P.]]
+[[Category: Paques F]]
-[[Category: Serrano, L.]]
+[[Category: Prieto J]]
-[[Category: Dna-binding protein]]
+[[Category: Redondo P]]
-[[Category: Endonuclease]]
+[[Category: Serrano L]]
-[[Category: Gene therapy]]
-[[Category: Genome engineering]]
-[[Category: Hydrolase]]
-[[Category: Intron homing]]
-[[Category: Magnesium]]
-[[Category: Meganuclease]]
-[[Category: Nuclease]]
-[[Category: Protein/nucleic acid crystallography]]