1ui1: Difference between revisions

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-{{Seed}}
-[[Image:1ui1.png|left|200px]]
-<!--
+==Crystal Structure Of Uracil-DNA Glycosylase From Thermus Thermophilus HB8==
-The line below this paragraph, containing "STRUCTURE_1ui1", creates the "Structure Box" on the page.
+<StructureSection load='1ui1' size='340' side='right'caption='[[1ui1]], [[Resolution|resolution]] 2.80&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'>[[1ui1]] is a 1 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=1UI1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UI1 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]] 2.8&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-{{STRUCTURE_1ui1|  PDB=1ui1  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ui1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ui1 OCA], [https://pdbe.org/1ui1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ui1 RCSB], [https://www.ebi.ac.uk/pdbsum/1ui1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ui1 ProSAT], [https://www.topsan.org/Proteins/RSGI/1ui1 TOPSAN]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/UDGA_THET8 UDGA_THET8] Removes uracil bases that are present in DNA as a result of either deamination of cytosine or misincorporation of dUMP instead of dTMP. Can remove uracil from double-stranded DNA containing either a U/G, U/A, U/C or U/T base pair as well as from single-stranded DNA (PubMed:12000829, PubMed:14556741). Specifically recognizes uracil that is flipped out from double-stranded DNA (PubMed:14556741).<ref>PMID:12000829</ref> <ref>PMID:14556741</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/ui/1ui1_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=1ui1 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Uracil-DNA glycosylase (UDG; EC 3.2.2.-) removes uracil from DNA to initiate DNA base excision repair. Since hydrolytic deamination of cytosine to uracil is one of the most frequent DNA-damaging events in all cells, UDG is an essential enzyme for maintaining the integrity of genomic information. For the first time, we report the crystal structure of a family 4 UDG from Thermus thermophilus HB8 (TthUDG) complexed with uracil, solved at 1.5 angstroms resolution. As opposed to UDG enzymes in its other families, TthUDG possesses a [4Fe-4S] cluster. This iron-sulfur cluster, which is distant from the active site, interacts with loop structures and has been suggested to be unessential to the activity but necessary for stabilizing the loop structures. In addition to the iron-sulfur cluster, salt-bridges and ion pairs on the molecular surface and the presence of proline on loops and turns is thought to contribute to the enzyme's thermostability. Despite very low levels of sequence identity with Escherichia coli and human UDGs (family 1) and E.coli G:T/U mismatch-specific DNA glycosylase (MUG) (family 2), the topology and order of secondary structures of TthUDG are similar to those of these distant relatives. Furthermore, the coordinates of the core structure formed by beta-strands are almost the same. Positive charge is distributed over the active-site groove, where TthUDG would bind DNA strands, as do UDG enzymes in other families. TthUDG recognizes uracil specifically in the same manner as does human UDG (family 1), rather than guanine in the complementary strand DNA, as does E.coli MUG (family 2). These results suggest that the mechanism by which family 4 UDGs remove uracils from DNA is similar to that of family 1 enzymes.
-===Crystal Structure Of Uracil-DNA Glycosylase From Thermus Thermophilus HB8===
+Crystal structure of a family 4 uracil-DNA glycosylase from Thermus thermophilus HB8.,Hoseki J, Okamoto A, Masui R, Shibata T, Inoue Y, Yokoyama S, Kuramitsu S J Mol Biol. 2003 Oct 24;333(3):515-26. PMID:14556741<ref>PMID:14556741</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1ui1" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_14556741}}, adds the Publication Abstract to the page
+*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 14556741 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_14556741}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-UI1 is a 1 chain 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=1UI1 OCA].
-==Reference==
-Crystal structure of a family 4 uracil-DNA glycosylase from Thermus thermophilus HB8., Hoseki J, Okamoto A, Masui R, Shibata T, Inoue Y, Yokoyama S, Kuramitsu S, J Mol Biol. 2003 Oct 24;333(3):515-26. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14556741 14556741]
 [[Category: Thermus thermophilus]]
-[[Category: Hoseki, J.]]
+[[Category: Hoseki J]]
-[[Category: Inoue, Y.]]
+[[Category: Inoue Y]]
-[[Category: Kuramitsu, S.]]
+[[Category: Kuramitsu S]]
-[[Category: Masui, R.]]
+[[Category: Masui R]]
-[[Category: Okamoto, A.]]
+[[Category: Okamoto A]]
-[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
+[[Category: Shibata T]]
-[[Category: Shibata, T.]]
+[[Category: Yokoyama S]]
-[[Category: Yokoyama, S.]]
-[[Category: Base excision repair]]
-[[Category: Iron/sulfer cluster]]
-[[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 Sun Nov 16 14:01:54 2008''