2d3y: Difference between revisions

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-{{Seed}}
-[[Image:2d3y.png|left|200px]]
-<!--
+==Crystal structure of uracil-DNA glycosylase from Thermus Thermophilus HB8==
-The line below this paragraph, containing "STRUCTURE_2d3y", creates the "Structure Box" on the page.
+<StructureSection load='2d3y' size='340' side='right'caption='[[2d3y]], [[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'>[[2d3y]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D3Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D3Y 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=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=DU:2-DEOXYURIDINE-5-MONOPHOSPHATE'>DU</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
-{{STRUCTURE_2d3y|  PDB=2d3y  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2d3y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d3y OCA], [https://pdbe.org/2d3y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d3y RCSB], [https://www.ebi.ac.uk/pdbsum/2d3y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d3y ProSAT], [https://www.topsan.org/Proteins/RSGI/2d3y TOPSAN]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/UDGB_THET8 UDGB_THET8] DNA glycosylase with broad substrate specificity. Can remove uracil from double-stranded DNA containing either a U/G, U/A, U/C or U/T base pair (PubMed:12000829, PubMed:17870091, PubMed:24838246). Can also excise hypoxanthine from double-stranded DNA containing G/I, T/I, and A/I base pairs, xanthine from both double-stranded and single stranded DNA, thymine from G/T mismatched DNA, 5'-hydroxymethyluracil and 5'-fluorouracil (PubMed:17870091, PubMed:24838246).<ref>PMID:12000829</ref> <ref>PMID:17870091</ref> <ref>PMID:24838246</ref>
+== 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/d3/2d3y_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=2d3y ConSurf].
+<div style="clear:both"></div>
-===Crystal structure of uracil-DNA glycosylase from Thermus Thermophilus HB8===
+==See Also==
+*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-D3Y 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=2D3Y OCA].
+__TOC__
-[[Category: Single protein]]
+</StructureSection>
-[[Category: Thermus thermophilus]]
+[[Category: Large Structures]]
-[[Category: Kosaka, H.]]
+[[Category: Thermus thermophilus HB8]]
-[[Category: Kuramitsu, S.]]
+[[Category: Kosaka H]]
-[[Category: Masui, R.]]
+[[Category: Kuramitsu S]]
-[[Category: Nakagawa, N.]]
+[[Category: Masui R]]
-[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
+[[Category: Nakagawa N]]
-[[Category: Base excision repair]]
-[[Category: Iron/sulfer cluster]]
-[[Category: National project on protein structural and functional analyse]]
-[[Category: Nppsfa]]
-[[Category: Riken structural genomics/proteomics initiative]]
-[[Category: Rsgi]]
-[[Category: Structural genomic]]
-[[Category: Thermophile]]
-[[Category: Uracil-dna glycosylase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Sep 29 06:51:29 2008''