1oe5: Difference between revisions

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[[Image:1oe5.gif|left|200px]]<br />
<applet load="1oe5" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1oe5, resolution 2.30&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, ... [[http://ispc.weizmann.ac.il/pmbin/getpm?12820976 (full description)]]
<StructureSection load='1oe5' size='340' side='right'caption='[[1oe5]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
== Structural highlights ==
<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>
</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>
<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>
<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>
</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/1oe5_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=1oe5 ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1OE5 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 URA, EPE, DUR, GOL and IPA as [[http://en.wikipedia.org/wiki/ligands ligands]]. Structure known Active Site: AC1. Full crystallographic information is available from [[http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1OE5 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: Xenopus laevis]]
[[Category: Pearl, L.H.]]
[[Category: Pearl LH]]
[[Category: Wibley, J.E.A.]]
[[Category: Wibley JEA]]
[[Category: DUR]]
[[Category: EPE]]
[[Category: GOL]]
[[Category: IPA]]
[[Category: URA]]
[[Category: dna glycosylase]]
[[Category: single stranded]]
[[Category: smug1]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Oct 30 11:43:54 2007''
Retrieved from "https://proteopedia.org/1oe5"