2qnf: Difference between revisions

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-{{Seed}}
-[[Image:2qnf.png|left|200px]]
-<!--
+==Crystal structure of T4 Endonuclease VII H43N mutant in complex with heteroduplex DNA containing base mismatches==
-The line below this paragraph, containing "STRUCTURE_2qnf", creates the "Structure Box" on the page.
+<StructureSection load='2qnf' size='340' side='right'caption='[[2qnf]], [[Resolution|resolution]] 3.00&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'>[[2qnf]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_T4 Escherichia virus T4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QNF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QNF 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]] 3&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_2qnf|  PDB=2qnf  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2qnf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qnf OCA], [https://pdbe.org/2qnf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qnf RCSB], [https://www.ebi.ac.uk/pdbsum/2qnf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qnf ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/END7_BPT4 END7_BPT4] Cleaves DNA cruciform and Y-structures as well as heteroduplex loops. Resolves Holliday junctions, recognizes a broad spectrum of DNA substrates ranging from branched DNAs to single base mismatches.
+== 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/qn/2qnf_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=2qnf ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Holliday proposed a four-way DNA junction as an intermediate in homologous recombination, and such Holliday junctions have since been identified as a central component in DNA recombination and repair. Phage T4 endonuclease VII (endo VII) was the first enzyme shown to resolve Holliday junctions into duplex DNAs by introducing symmetrical nicks in equivalent strands. Several Holliday junction resolvases have since been characterized, but an atomic structure of a resolvase complex with a Holliday junction remained elusive. Here we report the crystal structure of an inactive T4 endo VII(N62D) complexed with an immobile four-way junction with alternating arm lengths of 10 and 14 base pairs. The junction is a hybrid of the conventional square-planar and stacked-X conformation. Endo VII protrudes into the junction point from the minor groove side, opening it to a 14 A x 32 A parallelogram. This interaction interrupts the coaxial stacking, yet every base pair surrounding the junction remains intact. Additional interactions involve the positively charged protein and DNA phosphate backbones. Each scissile phosphate that is two base pairs from the crossover interacts with a Mg2+ ion in the active site. The similar overall shape and surface charge potential of the Holliday junction resolvases endo VII, RuvC, Ydc2, Hjc and RecU, despite having different folds, active site composition and DNA sequence preference, suggest a conserved binding mode for Holliday junctions.
-===Crystal structure of T4 Endonuclease VII H43N mutant in complex with heteroduplex DNA containing base mismatches===
+Crystal structure of T4 endonuclease VII resolving a Holliday junction.,Biertumpfel C, Yang W, Suck D Nature. 2007 Oct 4;449(7162):616-20. Epub 2007 Sep 16. PMID:17873859<ref>PMID:17873859</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2qnf" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_17873859}}, adds the Publication Abstract to the page
+*[[Endonuclease 3D structures|Endonuclease 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 17873859 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17873859}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Escherichia virus T4]]
-QNF is a 6 chains structure of sequences from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QNF OCA].
+[[Category: Large Structures]]
+[[Category: Biertumpfel C]]
-==Reference==
+[[Category: Suck D]]
-<ref group="xtra">PMID:17873859</ref><references group="xtra"/>
+[[Category: Yang W]]
-[[Category: Crossover junction endodeoxyribonuclease]]
-[[Category: Enterobacteria phage t4]]
-[[Category: Biertumpfel, C.]]
-[[Category: Suck, D.]]
-[[Category: Yang, W.]]
-[[Category: Alternative initiation]]
-[[Category: Calcium]]
-[[Category: Dna mismatch]]
-[[Category: Endo vii]]
-[[Category: Hydrolase]]
-[[Category: Hydrolase/dna complex]]
-[[Category: Metal-binding]]
-[[Category: Resolvase]]
-[[Category: Resolving-enzyme]]
-[[Category: T4 endonuclease vii]]
-[[Category: Zinc]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 15:38:22 2009''