2w9m: Difference between revisions

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-{{Seed}}
-[[Image:2w9m.png|left|200px]]
-<!--
+==Structure of family X DNA polymerase from Deinococcus radiodurans==
-The line below this paragraph, containing "STRUCTURE_2w9m", creates the "Structure Box" on the page.
+<StructureSection load='2w9m' size='340' side='right'caption='[[2w9m]], [[Resolution|resolution]] 2.46&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'>[[2w9m]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2W9M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2W9M 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]] 2.46&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_2w9m|  PDB=2w9m  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2w9m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w9m OCA], [https://pdbe.org/2w9m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2w9m RCSB], [https://www.ebi.ac.uk/pdbsum/2w9m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2w9m ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q9RX48_DEIRA Q9RX48_DEIRA]
+== 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/w9/2w9m_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=2w9m ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Deinococcus radiodurans is an extraordinarily radioresistant bacterium which is able to repair hundreds of radiation-induced double-stranded DNA breaks. One of the players in this pathway is an X family DNA polymerase (PolXDr). Deletion of PolXDr has been shown to decrease the rate of repair of double-stranded DNA breaks and increase cell sensitivity to gamma-rays. A 3'5' exonuclease activity that stops cutting close to DNA loops has also been demonstrated. The present crystal structure of PolXDr solved at 2.46 A resolution reveals that PolXDr has a novel extended conformation in stark contrast to the closed "right hand" conformation commonly observed for DNA polymerases. This extended conformation is stabilized by the C-terminal PHP domain, whose putative nuclease active site is obstructed by its interaction with the polymerase domain. The overall conformation and the presence of non standard residues in the active site of the polymerase X domain makes PolXDr the founding member of a novel class of polymerases involved in DNA repair but whose detailed mode of action still remains enigmatic.
-===STRUCTURE OF FAMILY X DNA POLYMERASE FROM DEINOCOCCUS RADIODURANS===
+The family X DNA polymerase from deinococcus radiodurans adopts a non-standard extended conformation.,Leulliot N, Cladiere L, Lecointe F, Durand D, Hubscher U, van Tilbeurgh H J Biol Chem. 2009 Feb 26. PMID:19251692<ref>PMID:19251692</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2w9m" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-W9M is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2W9M OCA].
+*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Deinococcus radiodurans]]
-[[Category: Cladiere, L.]]
+[[Category: Large Structures]]
-[[Category: Durand, D.]]
+[[Category: Cladiere L]]
-[[Category: Hubscher, U.]]
+[[Category: Durand D]]
-[[Category: Lecointe, F.]]
+[[Category: Hubscher U]]
-[[Category: Leulliot, N.]]
+[[Category: Lecointe F]]
-[[Category: Vantilbeurgh, H.]]
+[[Category: Leulliot N]]
-[[Category: Dna polymerase]]
+[[Category: Van Tilbeurgh H]]
-[[Category: Dna repair]]
-[[Category: Dna replication]]
-[[Category: Sax]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 18 20:14:26 2009''