1n3f: Difference between revisions

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OCA

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-[[Image:1n3f.gif|left|200px]]<br /><applet load="1n3f" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1n3f, resolution 2.00&Aring;" />
-'''Crystal structure of I-CreI bound to a palindromic DNA sequence II (palindrome of right side of wildtype DNA target sequence)'''<br />
-==Overview==
+==Crystal structure of I-CreI bound to a palindromic DNA sequence II (palindrome of right side of wildtype DNA target sequence)==
-Homing endonucleases are highly specific catalysts of DNA strand breaks, that induce the transposition of mobile intervening sequences containing, the endonuclease open reading frame. These enzymes recognize long DNA, targets while tolerating individual sequence polymorphisms within those, sites. Sequences of the homing endonucleases themselves diversify to a, great extent after founding intron invasion events, generating highly, divergent enzymes that recognize similar target sequences. Here, we, visualize the mechanism of flexible DNA recognition and the pattern of, structural divergence displayed by two homing endonuclease isoschizomers., We determined structures of I-CreI bound to two DNA target sites that, differ at eight of 22 base-pairs, and the structure of an isoschizomer, I-MsoI, bound to a nearly identical DNA target site. This study, illustrates several principles governing promiscuous base-pair recognition, by DNA-binding proteins, and demonstrates that the isoschizomers display, strikingly different protein/DNA contacts. The structures allow us to, determine the information content at individual positions in the binding, site as a function of the distribution of direct and water-mediated, contacts to nucleotide bases, and provide an evolutionary snapshot of, endonucleases at an early stage of divergence in their target specificity.
+<StructureSection load='1n3f' size='340' side='right'caption='[[1n3f]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1n3f]] is a 12 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=1N3F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1N3F 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&#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=1n3f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n3f OCA], [https://pdbe.org/1n3f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1n3f RCSB], [https://www.ebi.ac.uk/pdbsum/1n3f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1n3f 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/n3/1n3f_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=1n3f ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-N3F is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Chlamydomonas_reinhardtii Chlamydomonas reinhardtii] 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=1N3F OCA].
+*[[Endonuclease 3D structures|Endonuclease 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-Flexible DNA target site recognition by divergent homing endonuclease isoschizomers I-CreI and I-MsoI., Chevalier B, Turmel M, Lemieux C, Monnat RJ Jr, Stoddard BL, J Mol Biol. 2003 May 30;329(2):253-69. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12758074 12758074]
 [[Category: Chlamydomonas reinhardtii]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Chevalier, B.]]
+[[Category: Chevalier B]]
-[[Category: Lemieux, C.]]
+[[Category: Lemieux C]]
-[[Category: Monnat, R.J.]]
+[[Category: Monnat RJ]]
-[[Category: Stoddard, B.L.]]
+[[Category: Stoddard BL]]
-[[Category: Turmel, M.]]
+[[Category: Turmel M]]
-[[Category: CA]]
-[[Category: dna recognition]]
-[[Category: endonuclease]]
-[[Category: homing]]
-[[Category: laglidadg]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 21:55:47 2007''