2d3y: Difference between revisions

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==Crystal structure of uracil-DNA glycosylase from Thermus Thermophilus HB8==
==Crystal structure of uracil-DNA glycosylase from Thermus Thermophilus HB8==
<StructureSection load='2d3y' size='340' side='right' caption='[[2d3y]], [[Resolution|resolution]] 1.55&Aring;' scene=''>
<StructureSection load='2d3y' size='340' side='right'caption='[[2d3y]], [[Resolution|resolution]] 1.55&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2d3y]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thet8 Thet8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D3Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D3Y FirstGlance]. <br>
<table><tr><td colspan='2'>[[2d3y]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D3Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D3Y FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=DU:2-DEOXYURIDINE-5-MONOPHOSPHATE'>DU</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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]] 1.55&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ttUDGB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=DU:2-DEOXYURIDINE-5-MONOPHOSPHATE'>DU</scene></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=2d3y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d3y OCA], [http://pdbe.org/2d3y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2d3y RCSB], [http://www.ebi.ac.uk/pdbsum/2d3y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2d3y ProSAT], [http://www.topsan.org/Proteins/RSGI/2d3y TOPSAN]</span></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=2d3y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d3y OCA], [https://pdbe.org/2d3y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d3y RCSB], [https://www.ebi.ac.uk/pdbsum/2d3y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d3y ProSAT], [https://www.topsan.org/Proteins/RSGI/2d3y TOPSAN]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/UDGB_THET8 UDGB_THET8] DNA glycosylase with broad substrate specificity. Can remove uracil from double-stranded DNA containing either a U/G, U/A, U/C or U/T base pair (PubMed:12000829, PubMed:17870091, PubMed:24838246). Can also excise hypoxanthine from double-stranded DNA containing G/I, T/I, and A/I base pairs, xanthine from both double-stranded and single stranded DNA, thymine from G/T mismatched DNA, 5'-hydroxymethyluracil and 5'-fluorouracil (PubMed:17870091, PubMed:24838246).<ref>PMID:12000829</ref> <ref>PMID:17870091</ref> <ref>PMID:24838246</ref>
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d3/2d3y_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d3/2d3y_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
   </jmolCheckbox>
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==See Also==
==See Also==
*[[DNA glycosylase|DNA glycosylase]]
*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Thet8]]
[[Category: Large Structures]]
[[Category: Kosaka, H]]
[[Category: Thermus thermophilus HB8]]
[[Category: Kuramitsu, S]]
[[Category: Kosaka H]]
[[Category: Masui, R]]
[[Category: Kuramitsu S]]
[[Category: Nakagawa, N]]
[[Category: Masui R]]
[[Category: Structural genomic]]
[[Category: Nakagawa N]]
[[Category: Base excision repair]]
[[Category: Hydrolase]]
[[Category: Iron/sulfer cluster]]
[[Category: National project on protein structural and functional analyse]]
[[Category: Nppsfa]]
[[Category: Rsgi]]
[[Category: Thermophile]]
[[Category: Uracil-dna glycosylase]]
Retrieved from "https://proteopedia.org/2d3y"