3tal: Difference between revisions

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-[[Image:3tal.jpg|left|200px]]
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+==Crystal structure of NurA with manganese==
-The line below this paragraph, containing "STRUCTURE_3tal", creates the "Structure Box" on the page.
+<StructureSection load='3tal' size='340' side='right'caption='[[3tal]], [[Resolution|resolution]] 3.15&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'>[[3tal]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus_DSM_3638 Pyrococcus furiosus DSM 3638]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TAL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TAL 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]] 3.15&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-{{STRUCTURE_3tal|  PDB=3tal  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3tal FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tal OCA], [https://pdbe.org/3tal PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tal RCSB], [https://www.ebi.ac.uk/pdbsum/3tal PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tal ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/NURA_PYRFU NURA_PYRFU] Involved in DNA double-strand break (DSB) repair (PubMed:18957200). Acts probably with HerA to stimulate resection of the 5' strand and produce the long 3' single-strand that is required for RadA loading (PubMed:18957200). Exhibits 5' endonuclease activity and both 5' and 3' exonuclease activities (PubMed:22064858).<ref>PMID:18957200</ref> <ref>PMID:22064858</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Generation of the 3' overhang is a critical event during homologous recombination (HR) repair of DNA double strand breaks. A 5'-3' nuclease, NurA, plays an important role in generating 3' single-stranded DNA during archaeal HR, together with Mre11-Rad50 and HerA. We have determined the crystal structures of apo- and dAMP-Mn(2)(+)-bound NurA from Pyrococcus furiousus (Pf NurA) to provide the basis for its cleavage mechanism. Pf NurA forms a pyramid-shaped dimer containing a large central channel on one side, which becomes narrower towards the peak of the pyramid. The structure contains a PIWI domain with high similarity to argonaute, endoV nuclease and RNase H. The two active sites, each of which contains Mn(2)(+) ion(s) and dAMP, are at the corners of the elliptical channel near the flat face of the dimer. The 3' OH group of the ribose ring is directed toward the channel entrance, explaining the 5'-3' nuclease activity of Pf NurA. We provide a DNA binding and cleavage model for Pf NurA.
-===Crystal structure of NurA with manganese===
+Crystal structure of the NurA-dAMP-Mn2+ complex.,Chae J, Kim YC, Cho Y Nucleic Acids Res. 2011 Nov 7. PMID:22064858<ref>PMID:22064858</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_22064858}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 3tal" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 22064858 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_22064858}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-[[3tal]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TAL OCA].
+[[Category: Pyrococcus furiosus DSM 3638]]
+[[Category: Chae J]]
-==Reference==
+[[Category: Cho Y]]
-<ref group="xtra">PMID:022064858</ref><references group="xtra"/>
+[[Category: Kim YC]]
-[[Category: Pyrococcus furiosus]]
-[[Category: Chae, J.]]
-[[Category: Cho, Y.]]
-[[Category: Kim, Y C.]]
-[[Category: Hydrolase]]
-[[Category: Recombination]]