4bos

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(New page: '''Unreleased structure''' The entry 4bos is ON HOLD until Paper Publication Authors: Mevissen, T.E.T., Hospenthal, M.K., Geurink, P.P., Elliott, P.R., Akutsu, M., Arnaudo, N., Ekkebus,...)
Current revision (11:56, 20 December 2023) (edit) (undo)
 
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'''Unreleased structure'''
 
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The entry 4bos is ON HOLD until Paper Publication
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==Structure of OTUD2 OTU domain in complex with Ubiquitin K11-linked peptide==
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<StructureSection load='4bos' size='340' side='right'caption='[[4bos]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[4bos]] is a 5 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=4BOS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4BOS FirstGlance]. <br>
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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]] 2.35&#8491;</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene></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=4bos FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bos OCA], [https://pdbe.org/4bos PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4bos RCSB], [https://www.ebi.ac.uk/pdbsum/4bos PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4bos ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/OTU1_HUMAN OTU1_HUMAN] Hydrolase that can remove conjugated ubiquitin from proteins and participates in endoplasmic reticulum-associated degradation (ERAD) for misfolded lumenal proteins. May act by triming the ubiquitin chain on the associated substrate to facilitate their threading through the VCP/p97 pore. Ubiquitin moieties on substrates may present a steric impediment to the threading process when the substrate is transferred to the VCP pore and threaded through VCP's axial channel. Mediates deubiquitination of both 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains. Able to cleave both polyubiquitin and di-ubiquitin.
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Sixteen ovarian tumor (OTU) family deubiquitinases (DUBs) exist in humans, and most members regulate cell-signaling cascades. Several OTU DUBs were reported to be ubiquitin (Ub) chain linkage specific, but comprehensive analyses are missing, and the underlying mechanisms of linkage specificity are unclear. Using Ub chains of all eight linkage types, we reveal that most human OTU enzymes are linkage specific, preferring one, two, or a defined subset of linkage types, including unstudied atypical Ub chains. Biochemical analysis and five crystal structures of OTU DUBs with or without Ub substrates reveal four mechanisms of linkage specificity. Additional Ub-binding domains, the ubiquitinated sequence in the substrate, and defined S1' and S2 Ub-binding sites on the OTU domain enable OTU DUBs to distinguish linkage types. We introduce Ub chain restriction analysis, in which OTU DUBs are used as restriction enzymes to reveal linkage type and the relative abundance of Ub chains on substrates.
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Authors: Mevissen, T.E.T., Hospenthal, M.K., Geurink, P.P., Elliott, P.R., Akutsu, M., Arnaudo, N., Ekkebus, R., Kulathu, Y., Wauer, T., El Oualid, F., Freund, S.M.V., Ovaa, H., Komander, D.
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OTU Deubiquitinases Reveal Mechanisms of Linkage Specificity and Enable Ubiquitin Chain Restriction Analysis.,Mevissen TE, Hospenthal MK, Geurink PP, Elliott PR, Akutsu M, Arnaudo N, Ekkebus R, Kulathu Y, Wauer T, El Oualid F, Freund SM, Ovaa H, Komander D Cell. 2013 Jul 3;154(1):169-84. doi: 10.1016/j.cell.2013.05.046. PMID:23827681<ref>PMID:23827681</ref>
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Description: Structure of OTUD2 OTU domain in complex with Ubiquitin K11-linked peptide
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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 4bos" style="background-color:#fffaf0;"></div>
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==See Also==
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*[[Thioesterase 3D structures|Thioesterase 3D structures]]
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*[[3D structures of ubiquitin|3D structures of ubiquitin]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Homo sapiens]]
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[[Category: Large Structures]]
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[[Category: Akutsu M]]
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[[Category: Arnaudo N]]
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[[Category: Ekkebus R]]
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[[Category: El Oualid F]]
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[[Category: Elliott PR]]
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[[Category: Freund SMV]]
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[[Category: Geurink PP]]
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[[Category: Hospenthal MK]]
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[[Category: Komander D]]
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[[Category: Kulathu Y]]
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[[Category: Mevissen TET]]
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[[Category: Ovaa H]]
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[[Category: Wauer T]]

Current revision

Structure of OTUD2 OTU domain in complex with Ubiquitin K11-linked peptide

PDB ID 4bos

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