2dem: Difference between revisions

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-[[Image:2dem.png|left|200px]]
-{{STRUCTURE_2dem|  PDB=2dem  |  SCENE=  }}
+==Crystal structure of Uracil-DNA glycosylase in complex with AP:A containing DNA==
+<StructureSection load='2dem' size='340' side='right'caption='[[2dem]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2dem]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DEM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DEM FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.95&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2HP:DIHYDROGENPHOSPHATE+ION'>2HP</scene>, <scene name='pdbligand=EOH:ETHANOL'>EOH</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ORP:2-DEOXY-5-PHOSPHONO-RIBOSE'>ORP</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2dem FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dem OCA], [https://pdbe.org/2dem PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dem RCSB], [https://www.ebi.ac.uk/pdbsum/2dem PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dem ProSAT], [https://www.topsan.org/Proteins/RSGI/2dem 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/de/2dem_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=2dem ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Uracil-DNA glycosylase (UDG) removes uracil generated by the deamination of cytosine or misincorporation of deoxyuridine monophosphate. Within the UDG superfamily, a fifth UDG family lacks a polar residue in the active-site motif, which mediates the hydrolysis of the glycosidic bond by activation of a water molecule in UDG families 1-4. We have determined the crystal structure of a novel family 5 UDG from Thermus thermophilus HB8 complexed with DNA containing an abasic site. The active-site structure suggests this enzyme uses both steric force and water activation for its excision reaction. A conserved asparagine residue acts as a ligand to the catalytic water molecule. The structure also implies that another water molecule acts as a barrier during substrate recognition. Based on no significant open-closed conformational change upon binding to DNA, we propose a "slide-in" mechanism for initial damage recognition.
-===Crystal structure of Uracil-DNA glycosylase in complex with AP:A containing DNA===
+Crystal structure of family 5 uracil-DNA glycosylase bound to DNA.,Kosaka H, Hoseki J, Nakagawa N, Kuramitsu S, Masui R J Mol Biol. 2007 Nov 2;373(4):839-50. Epub 2007 Aug 21. PMID:17870091<ref>PMID:17870091</ref>
-{{ABSTRACT_PUBMED_17870091}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 2dem" style="background-color:#fffaf0;"></div>
-[[2dem]] is a 3 chain structure with sequence from [http://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=2DEM OCA].
 ==See Also==
-*[[DNA glycosylate|DNA glycosylate]]
+*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:017870091</ref><references group="xtra"/>
+__TOC__
-[[Category: Thermus thermophilus hb8]]
+</StructureSection>
-[[Category: Hoseki, J.]]
+[[Category: Large Structures]]
-[[Category: Kosaka, H.]]
+[[Category: Synthetic construct]]
-[[Category: Kuramitsu, S.]]
+[[Category: Thermus thermophilus HB8]]
-[[Category: Masui, R.]]
+[[Category: Hoseki J]]
-[[Category: Nakagawa, N.]]
+[[Category: Kosaka H]]
-[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
+[[Category: Kuramitsu S]]
-[[Category: Base excision repair]]
+[[Category: Masui R]]
-[[Category: Hydrolase-dna complex]]
+[[Category: Nakagawa N]]
-[[Category: Iron/sulfur 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]]