1r7m: Difference between revisions

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

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-[[Image:1r7m.gif|left|200px]]<br /><applet load="1r7m" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1r7m, resolution 2.25&Aring;" />
-'''The homing endonuclease I-SceI bound to its DNA recognition region'''<br />
-==Overview==
+==The homing endonuclease I-SceI bound to its DNA recognition region==
-The I-SceI homing endonuclease enhances gene targeting by introducing, double-strand breaks at specific chromosomal loci, thereby increasing the, recombination frequency. Here, we report the crystal structure of the, enzyme complexed to its DNA substrate and Ca(2+) determined at 2.25A, resolution. The structure shows the prototypical beta-saddle of LAGLIDADG, homing endonucleases that is contributed by two pseudo-symmetric domains., The high specificity of I-SceI is explained by the large number of, protein-DNA contacts, many that are made by a long beta-hairpin loop that, reaches into the major groove of the DNA. The DNA minor groove is, compressed at the catalytic center, bringing the two scissile, phosphodiester bonds into close proximity. The protein-Ca(2+)-DNA, structure shows the protein bound to its DNA substrate in a pre-reactive, state that is defined by the presence of two asymmetric active sites, one, of which appears poised to first cleave the DNA bottom strand.
+<StructureSection load='1r7m' size='340' side='right'caption='[[1r7m]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1r7m]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1R7M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1R7M 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]] 2.25&#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>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1r7m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r7m OCA], [https://pdbe.org/1r7m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1r7m RCSB], [https://www.ebi.ac.uk/pdbsum/1r7m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1r7m ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SCE1_YEAST SCE1_YEAST] Mitochondrial DNA endonuclease involved in intron homing. It introduces a specific double-strand break in the DNA of the 21S rRNA gene and thus mediates the insertion of an intron, containing its own coding sequence (group I intron), into an intronless gene. Specifically recognizes and cleaves the sequence 5'-TAGGGATAACAGGGTAAT-3'.
+== 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/r7/1r7m_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=1r7m ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-R7M is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] with CA as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1R7M OCA].
+*[[Endonuclease 3D structures|Endonuclease 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-The crystal structure of the gene targeting homing endonuclease I-SceI reveals the origins of its target site specificity., Moure CM, Gimble FS, Quiocho FA, J Mol Biol. 2003 Dec 5;334(4):685-95. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=14636596 14636596]
+[[Category: Large Structures]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Single protein]]
+[[Category: Gimble FS]]
-[[Category: Gimble, F.S.]]
+[[Category: Moure CM]]
-[[Category: Moure, C.M.]]
+[[Category: Quiocho FA]]
-[[Category: Quiocho, F.A.]]
-[[Category: CA]]
-[[Category: beta-saddle]]
-[[Category: endonuclease]]
-[[Category: laglidadg]]
-[[Category: protein-dna complex]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 01:19:59 2007''