6upu

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Current revision (14:57, 13 March 2024) (edit) (undo)
 
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<StructureSection load='6upu' size='340' side='right'caption='[[6upu]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
<StructureSection load='6upu' size='340' side='right'caption='[[6upu]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[6upu]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human] and [https://en.wikipedia.org/wiki/Oriti Oriti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UPU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6UPU FirstGlance]. <br>
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<table><tr><td colspan='2'>[[6upu]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Orientia_tsutsugamushi_str._Ikeda Orientia tsutsugamushi str. Ikeda]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UPU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6UPU FirstGlance]. <br>
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</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[6ups|6ups]]</div></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]] 2.2&#8491;</td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">OTT_1962 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=334380 ORITI]), UBC ([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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6upu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6upu OCA], [https://pdbe.org/6upu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6upu RCSB], [https://www.ebi.ac.uk/pdbsum/6upu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6upu 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=6upu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6upu OCA], [https://pdbe.org/6upu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6upu RCSB], [https://www.ebi.ac.uk/pdbsum/6upu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6upu ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/B3CVM3_ORITI B3CVM3_ORITI]
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Ubiquitin mediated signaling contributes critically to host cell defenses during pathogen infection. Many pathogens manipulate the ubiquitin system to evade these defenses. Here we characterize a likely effector protein bearing a deubiquitylase (DUB) domain from the obligate intracellular bacterium Orientia tsutsugamushi, the causative agent of scrub typhus. The Ulp1-like DUB prefers ubiquitin substrates over ubiquitin-like proteins and efficiently cleaves polyubiquitin chains of three or more ubiquitins. The co-crystal structure of the DUB (OtDUB) domain with ubiquitin revealed three bound ubiquitins: one engages the S1 site, the second binds an S2 site contributing to chain specificity and the third binds a unique ubiquitin-binding domain (UBD). The UBD modulates OtDUB activity, undergoes a pronounced structural transition upon binding ubiquitin, and binds monoubiquitin with an unprecedented ~5 nM dissociation constant. The characterization and high-resolution structure determination of this enzyme should aid in its development as a drug target to counter Orientia infections.
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A deubiquitylase with an unusually high-affinity ubiquitin-binding domain from the scrub typhus pathogen Orientia tsutsugamushi.,Berk JM, Lim C, Ronau JA, Chaudhuri A, Chen H, Beckmann JF, Loria JP, Xiong Y, Hochstrasser M Nat Commun. 2020 May 11;11(1):2343. doi: 10.1038/s41467-020-15985-4. PMID:32393759<ref>PMID:32393759</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 6upu" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
*[[3D structures of ubiquitin|3D structures of ubiquitin]]
*[[3D structures of ubiquitin|3D structures of ubiquitin]]
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== References ==
 
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<references/>
 
__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: Oriti]]
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[[Category: Orientia tsutsugamushi str. Ikeda]]
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[[Category: Lim, C S]]
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[[Category: Lim CS]]
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[[Category: Ronau, J A]]
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[[Category: Ronau JA]]
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[[Category: Xiong, Y]]
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[[Category: Xiong Y]]
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[[Category: Ce clan]]
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[[Category: Deubiquitylase]]
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[[Category: Hydrolase]]
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[[Category: Orientia]]
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[[Category: Ubiquitin]]
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Current revision

Crystal structure of the Orientia tsutsugamushi OtDUB in complex with three molecules of ubiquitin

PDB ID 6upu

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