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6dxt

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Current revision (06:15, 11 October 2023) (edit) (undo)
 
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<StructureSection load='6dxt' size='340' side='right'caption='[[6dxt]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
<StructureSection load='6dxt' size='340' side='right'caption='[[6dxt]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[6dxt]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DXT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DXT FirstGlance]. <br>
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<table><tr><td colspan='2'>[[6dxt]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DXT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DXT 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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HHY:3-(5-phenyl-1,3,4-oxadiazol-2-yl)propanoic+acid'>HHY</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">USP5, ISOT ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HHY:3-(5-phenyl-1,3,4-oxadiazol-2-yl)propanoic+acid'>HHY</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Ubiquitinyl_hydrolase_1 Ubiquitinyl hydrolase 1], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.19.12 3.4.19.12] </span></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=6dxt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dxt OCA], [https://pdbe.org/6dxt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dxt RCSB], [https://www.ebi.ac.uk/pdbsum/6dxt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dxt ProSAT]</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=6dxt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dxt OCA], [https://pdbe.org/6dxt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dxt RCSB], [https://www.ebi.ac.uk/pdbsum/6dxt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dxt ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[https://www.uniprot.org/uniprot/UBP5_HUMAN UBP5_HUMAN]] Cleaves linear and branched multiubiquitin polymers with a marked preference for branched polymers. Involved in unanchored 'Lys-48'-linked polyubiquitin disassembly. Binds linear and 'Lys-63'-linked polyubiquitin with a lower affinity. Knock-down of USP5 causes the accumulation of p53/TP53 and an increase in p53/TP53 transcriptional activity because the unanchored polyubiquitin that accumulates is able to compete with ubiquitinated p53/TP53 but not with MDM2 for proteasomal recognition.<ref>PMID:19098288</ref>
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[https://www.uniprot.org/uniprot/UBP5_HUMAN UBP5_HUMAN] Cleaves linear and branched multiubiquitin polymers with a marked preference for branched polymers. Involved in unanchored 'Lys-48'-linked polyubiquitin disassembly. Binds linear and 'Lys-63'-linked polyubiquitin with a lower affinity. Knock-down of USP5 causes the accumulation of p53/TP53 and an increase in p53/TP53 transcriptional activity because the unanchored polyubiquitin that accumulates is able to compete with ubiquitinated p53/TP53 but not with MDM2 for proteasomal recognition.<ref>PMID:19098288</ref>
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Human]]
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[[Category: Homo sapiens]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Ubiquitinyl hydrolase 1]]
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[[Category: Arrowsmith CM]]
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[[Category: Arrowsmith, C M]]
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[[Category: Bountra C]]
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[[Category: Bountra, C]]
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[[Category: Edwards AM]]
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[[Category: Edwards, A M]]
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[[Category: Ferreira de Freitas R]]
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[[Category: Franzoni, I]]
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[[Category: Franzoni I]]
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[[Category: Freitas, R Ferreira de]]
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[[Category: Harding RJ]]
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[[Category: Harding, R J]]
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[[Category: Mann MK]]
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[[Category: Mann, M K]]
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[[Category: Ravichandran M]]
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[[Category: Ravichandran, M]]
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[[Category: Schapira M]]
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[[Category: Structural genomic]]
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[[Category: Schapira, M]]
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[[Category: Deubiquitinase]]
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[[Category: Hydrolase]]
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[[Category: Sgc]]
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[[Category: Ubiquitin]]
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[[Category: Usp5]]
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Current revision

Structure of USP5 zinc-finger ubiquitin binding domain co-crystallized with 3-(5-phenyl-1,3,4-oxadiazol-2-yl)propanoate

PDB ID 6dxt

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