2ivk: Difference between revisions

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-[[Image:2ivk.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_2ivk", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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-{{STRUCTURE_2ivk|  PDB=2ivk  |  SCENE=  }}
-'''CRYSTAL STRUCTURE OF THE PERIPLASMIC ENDONUCLEASE VVN COMPLEXED WITH A 16-BP DNA'''
+==Crystal structure of the periplasmic endonuclease Vvn complexed with a 16-bp DNA==
+<StructureSection load='2ivk' size='340' side='right'caption='[[2ivk]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2ivk]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_vulnificus Vibrio vulnificus] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IVK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IVK 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]] 2.9&#8491;</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=2ivk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ivk OCA], [https://pdbe.org/2ivk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ivk RCSB], [https://www.ebi.ac.uk/pdbsum/2ivk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ivk ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q7MHK3_VIBVY Q7MHK3_VIBVY]
+== 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/iv/2ivk_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=2ivk ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Nonspecific endonucleases hydrolyze DNA without sequence specificity but with sequence preference, however the structural basis for cleavage preference remains elusive. We show here that the nonspecific endonuclease ColE7 cleaves DNA with a preference for making nicks after (at 3'O-side) thymine bases but the periplasmic nuclease Vvn cleaves DNA more evenly with little sequence preference. The crystal structure of the 'preferred complex' of the nuclease domain of ColE7 bound to an 18 bp DNA with a thymine before the scissile phosphate had a more distorted DNA phosphate backbone than the backbones in the non-preferred complexes, so that the scissile phosphate was compositionally closer to the endonuclease active site resulting in more efficient DNA cleavage. On the other hand, in the crystal structure of Vvn in complex with a 16 bp DNA, the DNA phosphate backbone was similar and not distorted in comparison with that of a previously reported complex of Vvn with a different DNA sequence. Taken together these results suggest a general structural basis for the sequence-dependent DNA cleavage catalyzed by nonspecific endonucleases, indicating that nonspecific nucleases could induce DNA to deform to distinctive levels depending on the local sequence leading to different cleavage rates along the DNA chain.
-==Overview==
+Structural basis for sequence-dependent DNA cleavage by nonspecific endonucleases.,Wang YT, Yang WJ, Li CL, Doudeva LG, Yuan HS Nucleic Acids Res. 2007;35(2):584-94. Epub 2006 Dec 15. PMID:17175542<ref>PMID:17175542</ref>
-Nonspecific endonucleases hydrolyze DNA without sequence specificity but with sequence preference, however the structural basis for cleavage preference remains elusive. We show here that the nonspecific endonuclease ColE7 cleaves DNA with a preference for making nicks after (at 3'O-side) thymine bases but the periplasmic nuclease Vvn cleaves DNA more evenly with little sequence preference. The crystal structure of the 'preferred complex' of the nuclease domain of ColE7 bound to an 18 bp DNA with a thymine before the scissile phosphate had a more distorted DNA phosphate backbone than the backbones in the non-preferred complexes, so that the scissile phosphate was compositionally closer to the endonuclease active site resulting in more efficient DNA cleavage. On the other hand, in the crystal structure of Vvn in complex with a 16 bp DNA, the DNA phosphate backbone was similar and not distorted in comparison with that of a previously reported complex of Vvn with a different DNA sequence. Taken together these results suggest a general structural basis for the sequence-dependent DNA cleavage catalyzed by nonspecific endonucleases, indicating that nonspecific nucleases could induce DNA to deform to distinctive levels depending on the local sequence leading to different cleavage rates along the DNA chain.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-IVK is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Vibrio_vulnificus Vibrio vulnificus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IVK OCA].
+</div>
+<div class="pdbe-citations 2ivk" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Structural basis for sequence-dependent DNA cleavage by nonspecific endonucleases., Wang YT, Yang WJ, Li CL, Doudeva LG, Yuan HS, Nucleic Acids Res. 2007;35(2):584-94. Epub 2006 Dec 15. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17175542 17175542]
+*[[Endonuclease 3D structures|Endonuclease 3D structures]]
-[[Category: Protein complex]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Synthetic construct]]
 [[Category: Vibrio vulnificus]]
-[[Category: Doudeva, L G.]]
+[[Category: Doudeva LG]]
-[[Category: Li, C L.]]
+[[Category: Li CL]]
-[[Category: Wang, Y T.]]
+[[Category: Wang YT]]
-[[Category: Yang, W J.]]
+[[Category: Yang WJ]]
-[[Category: Yuan, H S.]]
+[[Category: Yuan HS]]
-[[Category: Dna cleavage preference]]
-[[Category: Dna hydrolysis]]
-[[Category: Dnase]]
-[[Category: Endonuclease]]
-[[Category: Hydrolase]]
-[[Category: Protein nucleic acid interaction]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 07:56:25 2008''