2ddg: Difference between revisions

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-[[Image:2ddg.png|left|200px]]
+==Crystal structure of uracil-DNA glycosylase in complex with AP:G containing DNA==
+<StructureSection load='2ddg' size='340' side='right' caption='[[2ddg]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2ddg]] 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=2DDG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DDG FirstGlance]. <br>
+</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2HP:DIHYDROGENPHOSPHATE+ION'>2HP</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EOH:ETHANOL'>EOH</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=ORP:2-DEOXY-5-PHOSPHONO-RIBOSE'>ORP</scene><br>
+<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2d3y|2d3y]]</td></tr>
+<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ttUDGB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 Thermus thermophilus HB8])</td></tr>
+<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ddg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ddg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ddg RCSB], [http://www.ebi.ac.uk/pdbsum/2ddg PDBsum], [http://www.topsan.org/Proteins/RSGI/2ddg TOPSAN]</span></td></tr>
+<table>
+== 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/dd/2ddg_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/chain_selection.php?pdb_ID=2ata 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.
-{{STRUCTURE_2ddg|  PDB=2ddg  |  SCENE=  }}
+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>
-===Crystal structure of uracil-DNA glycosylase in complex with AP:G containing DNA===
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-{{ABSTRACT_PUBMED_17870091}}
-==About this Structure==
-[[2ddg]] 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=2DDG OCA].
 ==See Also==
-*[[DNA glycosylate|DNA glycosylate]]
+*[[DNA glycosylase|DNA glycosylase]]
+*[[Uracil-DNA glycosylase|Uracil-DNA glycosylase]]
-==Reference==
+== References ==
-<ref group="xtra">PMID:017870091</ref><references group="xtra"/>
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Thermus thermophilus hb8]]
 [[Category: Hoseki, J.]]