1oe6: Difference between revisions

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-[[Image:1oe6.gif|left|200px]]<br /><applet load="1oe6" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="1oe6, resolution 2.65&Aring;" />
-'''XENOPUS SMUG1, AN ANTI-MUTATOR URACIL-DNA GLYCOSYLASE'''<br />
-==Overview==
+==Xenopus SMUG1, an anti-mutator uracil-DNA Glycosylase==
-Cytosine deamination is a major promutagenic process, generating G:U, mismatches that can cause transition mutations if not repaired. Uracil is, also introduced into DNA via nonmutagenic incorporation of dUTP during, replication. In bacteria, uracil is excised by uracil-DNA glycosylases, (UDG) related to E. coli UNG, and UNG homologs are found in mammals and, viruses. Ung knockout mice display no increase in mutation frequency due, to a second UDG activity, SMUG1, which is specialized for antimutational, uracil excision in mammalian cells. Remarkably, SMUG1 also excises the, oxidation-damage product 5-hydroxymethyluracil (HmU), but like UNG is, inactive against thymine (5-methyluracil), a chemical substructure of HmU., We have solved the crystal structure of SMUG1 complexed with DNA and, base-excision products. This structure indicates a more invasive, interaction with dsDNA than observed with other UDGs and reveals an, elegant water displacement/replacement mechanism that allows SMUG1 to, exclude thymine from its active site while accepting HmU.
+<StructureSection load='1oe6' size='340' side='right'caption='[[1oe6]], [[Resolution|resolution]] 2.65&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1oe6]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Xenopus_laevis Xenopus laevis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OE6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OE6 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]] 2.65&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HMU:5-HYDROXYMETHYL+URACIL'>HMU</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</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=1oe6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oe6 OCA], [https://pdbe.org/1oe6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1oe6 RCSB], [https://www.ebi.ac.uk/pdbsum/1oe6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1oe6 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SMUG1_XENLA SMUG1_XENLA] Responsible for recognizing base lesions in the genome and initiating base excision DNA repair. Acts as a monofunctional DNA glycosylase specific for uracil (U) residues in DNA and has a preference for single-stranded DNA substrates. No enzymatic activity towards G/T mismatches.
+== 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/oe/1oe6_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=1oe6 ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-OE6 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Xenopus_laevis Xenopus laevis] with <scene name='pdbligand=HMU:'>HMU</scene>, <scene name='pdbligand=GOL:'>GOL</scene> and <scene name='pdbligand=IPA:'>IPA</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Known structural/functional Site: <scene name='pdbsite=AC1:Ipa+Binding+Site+For+Chain+A'>AC1</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OE6 OCA].
+*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-Structure and specificity of the vertebrate anti-mutator uracil-DNA glycosylase SMUG1., Wibley JE, Waters TR, Haushalter K, Verdine GL, Pearl LH, Mol Cell. 2003 Jun;11(6):1647-59. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12820976 12820976]
+[[Category: Large Structures]]
-[[Category: Protein complex]]
 [[Category: Xenopus laevis]]
-[[Category: Pearl, L.H.]]
+[[Category: Pearl LH]]
-[[Category: Wibley, J.E.A.]]
+[[Category: Wibley JEA]]
-[[Category: GOL]]
-[[Category: HMU]]
-[[Category: IPA]]
-[[Category: dna glycosylase]]
-[[Category: single stranded]]
-[[Category: smug1]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Feb  3 09:56:52 2008''