2x7v: Difference between revisions

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-[[Image:2x7v.png|left|200px]]
-<!--
+==Crystal structure of Thermotoga maritima endonuclease IV in the presence of zinc==
-The line below this paragraph, containing "STRUCTURE_2x7v", creates the "Structure Box" on the page.
+<StructureSection load='2x7v' size='340' side='right'caption='[[2x7v]], [[Resolution|resolution]] 2.30&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'>[[2x7v]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima_MSB8 Thermotoga maritima MSB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2X7V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2X7V 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]] 2.3&#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_2x7v|  PDB=2x7v  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2x7v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2x7v OCA], [https://pdbe.org/2x7v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2x7v RCSB], [https://www.ebi.ac.uk/pdbsum/2x7v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2x7v ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/END4_THEMA END4_THEMA] Endonuclease IV plays a role in DNA repair. It cleaves phosphodiester bonds at apurinic or apyrimidinic sites (AP sites) to produce new 5'-ends that are base-free deoxyribose 5-phosphate residues. It preferentially attacks modified AP sites created by bleomycin and neocarzinostatin (By similarity).
+== 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/x7/2x7v_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=2x7v ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The most frequent lesion in DNA is at apurinic/apyrimidinic (AP) sites resulting from DNA-base losses. These AP-site lesions can stall DNA replication and lead to genome instability if left unrepaired. The AP endonucleases are an important class of enzymes that are involved in the repair of AP-site intermediates during damage-general DNA base-excision repair pathways. These enzymes hydrolytically cleave the 5'-phosphodiester bond at an AP site to generate a free 3'-hydroxyl group and a 5'-terminal sugar phosphate using their AP nuclease activity. Specifically, Thermotoga maritima endonuclease IV is a member of the second conserved AP endonuclease family that includes Escherichia coli endonuclease IV, which is the archetype of the AP endonuclease superfamily. In order to more fully characterize the AP endonuclease family of enzymes, two X-ray crystal structures of the T. maritima endonuclease IV homologue were determined in the presence of divalent metal ions bound in the active-site region. These structures of the T. maritima endonuclease IV homologue further revealed the use of the TIM-barrel fold and the trinuclear metal binding site as important highly conserved structural elements that are involved in DNA-binding and AP-site repair processes in the AP endonuclease superfamily.
-===Crystal structure of Thermotoga maritima endonuclease IV in the presence of zinc===
+Structure of the endonuclease IV homologue from Thermotoga maritima in the presence of active-site divalent metal ions.,Tomanicek SJ, Hughes RC, Ng JD, Coates L Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Sep 1;66(Pt, 9):1003-12. Epub 2010 Aug 21. PMID:20823514<ref>PMID:20823514</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2x7v" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_20823514}}, adds the Publication Abstract to the page
+*[[Endonuclease 3D structures|Endonuclease 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 20823514 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_20823514}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-[[2x7v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima_msb8 Thermotoga maritima msb8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2X7V OCA].
+[[Category: Thermotoga maritima MSB8]]
+[[Category: Coates L]]
-==Reference==
+[[Category: Hughes RC]]
-<ref group="xtra">PMID:020823514</ref><references group="xtra"/>
+[[Category: Ng JD]]
-[[Category: Thermotoga maritima msb8]]
+[[Category: Tomanicek SJ]]
-[[Category: Coates, L.]]
-[[Category: Hughes, R C.]]
-[[Category: Ng, J D.]]
-[[Category: Tomanicek, S J.]]
-[[Category: Dna damage]]
-[[Category: Dna repair]]
-[[Category: Dna repair protein]]
-[[Category: Hydrolase]]
-[[Category: Metal-binding]]