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2dem

From Proteopedia

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Current revision (08:26, 25 October 2023) (edit) (undo)
 
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<StructureSection load='2dem' size='340' side='right'caption='[[2dem]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
<StructureSection load='2dem' size='340' side='right'caption='[[2dem]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[2dem]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thet8 Thet8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DEM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DEM FirstGlance]. <br>
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<table><tr><td colspan='2'>[[2dem]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DEM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DEM FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2HP:DIHYDROGENPHOSPHATE+ION'>2HP</scene>, <scene name='pdbligand=EOH:ETHANOL'>EOH</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=ORP:2-DEOXY-5-PHOSPHONO-RIBOSE'>ORP</scene></td></tr>
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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]] 1.95&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2d3y|2d3y]], [[2ddg|2ddg]]</div></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2HP:DIHYDROGENPHOSPHATE+ION'>2HP</scene>, <scene name='pdbligand=EOH:ETHANOL'>EOH</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ORP:2-DEOXY-5-PHOSPHONO-RIBOSE'>ORP</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ttUDGB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</td></tr>
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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=2dem FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dem OCA], [https://pdbe.org/2dem PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dem RCSB], [https://www.ebi.ac.uk/pdbsum/2dem PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dem ProSAT], [https://www.topsan.org/Proteins/RSGI/2dem 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=2dem FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dem OCA], [https://pdbe.org/2dem PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dem RCSB], [https://www.ebi.ac.uk/pdbsum/2dem PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dem ProSAT], [https://www.topsan.org/Proteins/RSGI/2dem TOPSAN]</span></td></tr>
</table>
</table>
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== Function ==
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[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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</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Thet8]]
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[[Category: Synthetic construct]]
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[[Category: Hoseki, J]]
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[[Category: Thermus thermophilus HB8]]
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[[Category: Kosaka, H]]
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[[Category: Hoseki J]]
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[[Category: Kuramitsu, S]]
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[[Category: Kosaka H]]
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[[Category: Masui, R]]
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[[Category: Kuramitsu S]]
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[[Category: Nakagawa, N]]
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[[Category: Masui R]]
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[[Category: Structural genomic]]
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[[Category: Nakagawa N]]
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[[Category: Base excision repair]]
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[[Category: Hydrolase-dna complex]]
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[[Category: Iron/sulfur cluster]]
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[[Category: National project on protein structural and functional analyse]]
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[[Category: Nppsfa]]
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[[Category: Rsgi]]
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[[Category: Thermophile]]
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[[Category: Uracil-dna glycosylase]]
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Current revision

Crystal structure of Uracil-DNA glycosylase in complex with AP:A containing DNA

PDB ID 2dem

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Proteopedia Page Contributors and Editors (what is this?)

OCA

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