1g9y: Difference between revisions

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-{{Seed}}
-[[Image:1g9y.png|left|200px]]
-<!--
+==HOMING ENDONUCLEASE I-CREI / DNA SUBSTRATE COMPLEX WITH CALCIUM==
-The line below this paragraph, containing "STRUCTURE_1g9y", creates the "Structure Box" on the page.
+<StructureSection load='1g9y' size='340' side='right'caption='[[1g9y]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1g9y]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Chlamydomonas_reinhardtii Chlamydomonas reinhardtii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1G9Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1G9Y FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</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=CA:CALCIUM+ION'>CA</scene></td></tr>
-{{STRUCTURE_1g9y|  PDB=1g9y  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1g9y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g9y OCA], [https://pdbe.org/1g9y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1g9y RCSB], [https://www.ebi.ac.uk/pdbsum/1g9y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1g9y ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DNE1_CHLRE DNE1_CHLRE] Endonuclease involved in group I intron homing. Recognizes and cleaves a 19-24 bp palindromic DNA site.
+== 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/g9/1g9y_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=1g9y ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Homing endonucleases, like restriction enzymes, cleave double-stranded DNA at specific target sites. The cleavage mechanism(s) utilized by LAGLIDADG endonucleases have been difficult to elucidate; their active sites are divergent, and only one low resolution cocrystal structure has been determined. Here we report two high resolution structures of the dimeric I-CreI homing endonuclease bound to DNA: a substrate complex with calcium and a product complex with magnesium. The bound metals in both complexes are verified by manganese anomalous difference maps. The active sites are positioned close together to facilitate cleavage across the DNA minor groove; each contains one metal ion bound between a conserved aspartate (Asp 20) and a single scissile phosphate. A third metal ion bridges the two active sites. This divalent cation is bound between aspartate residues from the active site of each subunit and is in simultaneous contact with the scissile phosphates of both DNA strands. A metal-bound water molecule acts as the nucleophile and is part of an extensive network of ordered water molecules that are positioned by enzyme side chains. These structures illustrate a unique variant of a two-metal endonuclease mechanism is employed by the highly divergent LAGLIDADG enzyme family.
-===HOMING ENDONUCLEASE I-CREI / DNA SUBSTRATE COMPLEX WITH CALCIUM===
+The homing endonuclease I-CreI uses three metals, one of which is shared between the two active sites.,Chevalier BS, Monnat RJ Jr, Stoddard BL Nat Struct Biol. 2001 Apr;8(4):312-6. PMID:11276249<ref>PMID:11276249</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1g9y" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_11276249}}, adds the Publication Abstract to the page
+*[[Endonuclease 3D structures|Endonuclease 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 11276249 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_11276249}}
+__TOC__
+</StructureSection>
-==About this Structure==
-G9Y is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Chlamydomonas_reinhardtii Chlamydomonas reinhardtii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1G9Y OCA].
-==Reference==
-The homing endonuclease I-CreI uses three metals, one of which is shared between the two active sites., Chevalier BS, Monnat RJ Jr, Stoddard BL, Nat Struct Biol. 2001 Apr;8(4):312-6. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11276249 11276249]
 [[Category: Chlamydomonas reinhardtii]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Chevalier, B.]]
+[[Category: Chevalier B]]
-[[Category: Monnat, R J.]]
+[[Category: Monnat RJ]]
-[[Category: Stoddard, B L.]]
+[[Category: Stoddard BL]]
-[[Category: Group i intron]]
-[[Category: Homing endonuclease]]
-[[Category: Laglidadg]]
-[[Category: Nuclease mechanism]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul  1 04:58:09 2008''