2vhg: Difference between revisions

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-{{Seed}}
-[[Image:2vhg.png|left|200px]]
-<!--
+==Crystal Structure of the ISHp608 Transposase in Complex with Right End 31-mer DNA==
-The line below this paragraph, containing "STRUCTURE_2vhg", creates the "Structure Box" on the page.
+<StructureSection load='2vhg' size='340' side='right'caption='[[2vhg]], [[Resolution|resolution]] 2.90&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'>[[2vhg]] 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=2VHG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VHG 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]] 2.9&#8491;</td></tr>
--->
+<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>
-{{STRUCTURE_2vhg|  PDB=2vhg  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2vhg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vhg OCA], [https://pdbe.org/2vhg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vhg RCSB], [https://www.ebi.ac.uk/pdbsum/2vhg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vhg ProSAT]</span></td></tr>
+</table>
+== 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/vh/2vhg_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=2vhg 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 RIGHT END 31-MER DNA===
+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 2vhg" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18243097}}, adds the Publication Abstract to the page
+*[[Transposase 3D structures|Transposase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18243097 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18243097}}
+__TOC__
+</StructureSection>
-==About this Structure==
-VHG is a 4 chains structure of sequences 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=2VHG OCA].
-==Reference==
-<ref group="xtra">PMID:18243097</ref><references group="xtra"/>
 [[Category: Helicobacter pylori]]
-[[Category: Barabas, O.]]
+[[Category: Large Structures]]
-[[Category: Chandler, M.]]
+[[Category: Barabas O]]
-[[Category: Dyda, F.]]
+[[Category: Chandler M]]
-[[Category: Guynet, C.]]
+[[Category: Dyda F]]
-[[Category: Hickman, A B.]]
+[[Category: Guynet C]]
-[[Category: Ronning, D R.]]
+[[Category: Hickman AB]]
-[[Category: Ton-Hoang, B.]]
+[[Category: Ronning DR]]
-[[Category: Dna stem loop]]
+[[Category: Ton-Hoang B]]
-[[Category: Dna-binding protein]]
-[[Category: Huh motif]]
-[[Category: Protein-dna comlpex]]
-[[Category: Transposition]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 10:31:01 2009''