2vic: Difference between revisions

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-[[Image:2vic.jpg|left|200px]]
- {{Structure
+==CRYSTAL STRUCTURE OF THE ISHP608 TRANSPOSASE IN COMPLEX with Left end 26- mer DNA and manganese==
-|PDB= 2vic |SIZE=350|CAPTION= <scene name='initialview01'>2vic</scene>, resolution 2.35&Aring;
+<StructureSection load='2vic' size='340' side='right'caption='[[2vic]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
-|SITE= <scene name='pdbsite=AC1:Mn+Binding+Site+For+Chain+A'>AC1</scene> and <scene name='pdbsite=AC2:Mn+Binding+Site+For+Chain+D'>AC2</scene>
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>
+<table><tr><td colspan='2'>[[2vic]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori Helicobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VIC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VIC FirstGlance]. <br>
-|ACTIVITY=
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.35&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-|DOMAIN=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2vic FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vic OCA], [https://pdbe.org/2vic PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vic RCSB], [https://www.ebi.ac.uk/pdbsum/2vic PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vic ProSAT]</span></td></tr>
-|RELATEDENTRY=[[2a6m|2A6M]], [[2a6o|2A6O]], [[2vju|2VJU]], [[2vjv|2VJV]], [[2vhg|2VHG]], [[2vih|2VIH]]
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2vic FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vic OCA], [http://www.ebi.ac.uk/pdbsum/2vic PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2vic RCSB]</span>
+== Function ==
-}}
+[https://www.uniprot.org/uniprot/Q933Z0_HELPX Q933Z0_HELPX]
+== 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/vi/2vic_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=2vic ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The smallest known DNA transposases are those from the IS200/IS605 family. Here we show how the interplay of protein and DNA activates TnpA, the Helicobacter pylori IS608 transposase, for catalysis. First, transposon end binding causes a conformational change that aligns catalytically important protein residues within the active site. Subsequent precise cleavage at the left and right ends, the steps that liberate the transposon from its donor site, does not involve a site-specific DNA-binding domain. Rather, cleavage site recognition occurs by complementary base pairing with a TnpA-bound subterminal transposon DNA segment. Thus, the enzyme active site is constructed from elements of both protein and DNA, reminiscent of the interdependence of protein and RNA in the ribosome. Our structural results explain why the transposon ends are asymmetric and how the transposon selects a target site for integration, and they allow us to propose a molecular model for the entire transposition reaction.
-'''CRYSTAL STRUCTURE OF THE ISHP608 TRANSPOSASE IN COMPLEX WITH LEFT END 26-MER DNA AND MANGANESE'''
+Mechanism of IS200/IS605 family DNA transposases: activation and transposon-directed target site selection.,Barabas O, Ronning DR, Guynet C, Hickman AB, Ton-Hoang B, Chandler M, Dyda F Cell. 2008 Jan 25;132(2):208-20. PMID:18243097<ref>PMID:18243097</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2vic" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-The smallest known DNA transposases are those from the IS200/IS605 family. Here we show how the interplay of protein and DNA activates TnpA, the Helicobacter pylori IS608 transposase, for catalysis. First, transposon end binding causes a conformational change that aligns catalytically important protein residues within the active site. Subsequent precise cleavage at the left and right ends, the steps that liberate the transposon from its donor site, does not involve a site-specific DNA-binding domain. Rather, cleavage site recognition occurs by complementary base pairing with a TnpA-bound subterminal transposon DNA segment. Thus, the enzyme active site is constructed from elements of both protein and DNA, reminiscent of the interdependence of protein and RNA in the ribosome. Our structural results explain why the transposon ends are asymmetric and how the transposon selects a target site for integration, and they allow us to propose a molecular model for the entire transposition reaction.
+*[[Transposase 3D structures|Transposase 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-VIC is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Helicobacter_pylori Helicobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VIC OCA].
+__TOC__
+</StructureSection>
-==Reference==
-Mechanism of IS200/IS605 Family DNA Transposases: Activation and Transposon-Directed Target Site Selection., Barabas O, Ronning DR, Guynet C, Hickman AB, Ton-Hoang B, Chandler M, Dyda F, Cell. 2008 Jan 25;132(2):208-20. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18243097 18243097]
 [[Category: Helicobacter pylori]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Barabas, O.]]
+[[Category: Barabas O]]
-[[Category: Chandler, M.]]
+[[Category: Chandler M]]
-[[Category: Dyda, F.]]
+[[Category: Dyda F]]
-[[Category: Guynet, C.]]
+[[Category: Guynet C]]
-[[Category: Hickman, A B.]]
+[[Category: Hickman AB]]
-[[Category: Ronning, D R.]]
+[[Category: Ronning DR]]
-[[Category: Ton-Hoang, B.]]
+[[Category: Ton-Hoang B]]
-[[Category: dna stem loop]]
-[[Category: dna-binding protein]]
-[[Category: huh motif]]
-[[Category: protein-dna complex]]
-[[Category: transposition]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:12:40 2008''