1oe6: Difference between revisions

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==Xenopus SMUG1, an anti-mutator uracil-DNA Glycosylase==
==Xenopus SMUG1, an anti-mutator uracil-DNA Glycosylase==
<StructureSection load='1oe6' size='340' side='right' caption='[[1oe6]], [[Resolution|resolution]] 2.65&Aring;' scene=''>
<StructureSection load='1oe6' size='340' side='right'caption='[[1oe6]], [[Resolution|resolution]] 2.65&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1oe6]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/African_clawed_frog African clawed frog]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1OE6 FirstGlance]. <br>
<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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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>
</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='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene></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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1oe4|1oe4]], [[1oe5|1oe5]]</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>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1oe6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oe6 OCA], [http://pdbe.org/1oe6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1oe6 RCSB], [http://www.ebi.ac.uk/pdbsum/1oe6 PDBsum]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://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.  
[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 ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/oe/1oe6_consurf.spt"</scriptWhenChecked>
     <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>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
Line 20: Line 20:
</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].
</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>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.
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:12820976<ref>PMID:12820976</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1oe6" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[DNA glycosylase|DNA glycosylase]]
*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
*[[Uracil-DNA glycosylase|Uracil-DNA glycosylase]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: African clawed frog]]
[[Category: Large Structures]]
[[Category: Pearl, L H]]
[[Category: Xenopus laevis]]
[[Category: Wibley, J E.A]]
[[Category: Pearl LH]]
[[Category: Dna glycosylase]]
[[Category: Wibley JEA]]
[[Category: Hydrolase]]
[[Category: Hydrolase-dna complex]]
[[Category: Single stranded]]

Latest revision as of 08:46, 17 April 2024

Xenopus SMUG1, an anti-mutator uracil-DNA GlycosylaseXenopus SMUG1, an anti-mutator uracil-DNA Glycosylase

Structural highlights

1oe6 is a 4 chain structure with sequence from Xenopus laevis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.65Å
Ligands:, , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1oe6, resolution 2.65Å

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OCA
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