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1oe5

From Proteopedia

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[[Image:1oe5.gif|left|200px]]
 
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{{Structure
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==Xenopus SMUG1, an anti-mutator uracil-DNA Glycosylase==
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|PDB= 1oe5 |SIZE=350|CAPTION= <scene name='initialview01'>1oe5</scene>, resolution 2.30&Aring;
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<StructureSection load='1oe5' size='340' side='right'caption='[[1oe5]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
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|SITE= <scene name='pdbsite=AC1:Epe+Binding+Site+For+Chain+B'>AC1</scene>
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=URA:URACIL'>URA</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=DUR:2'-DEOXYURIDINE'>DUR</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene> and <scene name='pdbligand=IPA:ISOPROPYL ALCOHOL'>IPA</scene>
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<table><tr><td colspan='2'>[[1oe5]] 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=1OE5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OE5 FirstGlance]. <br>
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|ACTIVITY=
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
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|GENE=
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<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=DUR:2-DEOXYURIDINE'>DUR</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=URA:URACIL'>URA</scene></td></tr>
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}}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1oe5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oe5 OCA], [https://pdbe.org/1oe5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1oe5 RCSB], [https://www.ebi.ac.uk/pdbsum/1oe5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1oe5 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[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.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/oe/1oe5_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1oe5 ConSurf].
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<div style="clear:both"></div>
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'''XENOPUS SMUG1, AN ANTI-MUTATOR URACIL-DNA GLYCOSYLASE'''
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==See Also==
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*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
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__TOC__
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==Overview==
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</StructureSection>
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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.
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[[Category: Large Structures]]
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==About this Structure==
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1OE5 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Xenopus_laevis Xenopus laevis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OE5 OCA].
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==Reference==
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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://www.ncbi.nlm.nih.gov/pubmed/12820976 12820976]
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[[Category: Protein complex]]
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[[Category: Xenopus laevis]]
[[Category: Xenopus laevis]]
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[[Category: Pearl, L H.]]
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[[Category: Pearl LH]]
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[[Category: Wibley, J E.A.]]
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[[Category: Wibley JEA]]
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[[Category: DUR]]
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[[Category: EPE]]
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[[Category: GOL]]
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[[Category: IPA]]
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[[Category: URA]]
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[[Category: dna glycosylase]]
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[[Category: single stranded]]
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[[Category: smug1]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 13:09:45 2008''
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Current revision

Xenopus SMUG1, an anti-mutator uracil-DNA Glycosylase

PDB ID 1oe5

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