2j6v: Difference between revisions

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-{{Seed}}
-[[Image:2j6v.png|left|200px]]
-<!--
+==Crystal structure of the DNA repair enzyme UV Damage Endonuclease==
-The line below this paragraph, containing "STRUCTURE_2j6v", creates the "Structure Box" on the page.
+<StructureSection load='2j6v' size='340' side='right'caption='[[2j6v]], [[Resolution|resolution]] 1.55&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'>[[2j6v]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2J6V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2J6V 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]] 1.55&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ALY:N(6)-ACETYLLYSINE'>ALY</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-{{STRUCTURE_2j6v|  PDB=2j6v  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2j6v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2j6v OCA], [https://pdbe.org/2j6v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2j6v RCSB], [https://www.ebi.ac.uk/pdbsum/2j6v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2j6v ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q746K1_THET2 Q746K1_THET2]
+== 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/j6/2j6v_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2j6v ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The ultraviolet damage endonuclease (UVDE) performs the initial step in an alternative excision repair pathway of UV-induced DNA damage, nicking immediately adjacent to the 5' phosphate of the damaged nucleotides. Unique for a single-protein DNA repair endonuclease, it can detect different types of damage. Here we show that Thermus thermophilus UVDE shares some essential structural features with Endo IV, an enzyme from the base excision repair pathway that exclusively nicks at abasic sites. A comparison between the structures indicates how DNA is bound by UVDE, how UVDE may recognize damage, and which of its residues are involved in catalysis. Furthermore, the comparison suggests an elegant explanation of UVDE's potential to recognize different types of damage. Incision assays including point mutants of UVDE confirmed the relevance of these conclusions.
-===CRYSTAL STRUCTURE OF THE DNA REPAIR ENZYME UV DAMAGE ENDONUC===
+Crystal structure of the DNA repair enzyme ultraviolet damage endonuclease.,Paspaleva K, Thomassen E, Pannu NS, Iwai S, Moolenaar GF, Goosen N, Abrahams JP Structure. 2007 Oct;15(10):1316-24. PMID:17937920<ref>PMID:17937920</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2j6v" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_17937920}}, adds the Publication Abstract to the page
+*[[Endonuclease 3D structures|Endonuclease 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 17937920 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17937920}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-J6V is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2J6V OCA].
-==Reference==
-Crystal structure of the DNA repair enzyme ultraviolet damage endonuclease., Paspaleva K, Thomassen E, Pannu NS, Iwai S, Moolenaar GF, Goosen N, Abrahams JP, Structure. 2007 Oct;15(10):1316-24. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17937920 17937920]
-[[Category: Single protein]]
 [[Category: Thermus thermophilus]]
-[[Category: Abrahams, J P.]]
+[[Category: Abrahams JP]]
-[[Category: Goossen, N.]]
+[[Category: Goossen N]]
-[[Category: Pannu, N S.]]
+[[Category: Pannu NS]]
-[[Category: Paspaleva, K.]]
+[[Category: Paspaleva K]]
-[[Category: Thomassen, E A.J.]]
+[[Category: Thomassen EAJ]]
-[[Category: Dna binding protein]]
-[[Category: Dna repair]]
-[[Category: Endonuclease]]
-[[Category: Lyase]]
-[[Category: Plasmid]]
-[[Category: Tim barrel]]
-[[Category: Uvde]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 12:54:04 2008''