4bos

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{{STRUCTURE_4bos| PDB=4bos | SCENE= }}
 
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===Structure of OTUD2 OTU domain in complex with Ubiquitin K11-linked peptide===
 
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{{ABSTRACT_PUBMED_23827681}}
 
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==Function==
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==Structure of OTUD2 OTU domain in complex with Ubiquitin K11-linked peptide==
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[[http://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. [[http://www.uniprot.org/uniprot/UBC_HUMAN UBC_HUMAN]] Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.<ref>PMID:16543144</ref> <ref>PMID:19754430</ref>
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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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==About this Structure==
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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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[[4bos]] is a 5 chain structure with sequence from [http://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].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<ref group="xtra">PMID:023827681</ref><references group="xtra"/><references/>
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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>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Ubiquitinyl hydrolase 1]]
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[[Category: Large Structures]]
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[[Category: Akutsu, M.]]
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[[Category: Akutsu M]]
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[[Category: Arnaudo, N.]]
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[[Category: Arnaudo N]]
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[[Category: Ekkebus, R.]]
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[[Category: Ekkebus R]]
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[[Category: Elliott, P R.]]
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[[Category: El Oualid F]]
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[[Category: Freund, S M.V.]]
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[[Category: Elliott PR]]
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[[Category: Geurink, P P.]]
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[[Category: Freund SMV]]
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[[Category: Hospenthal, M K.]]
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[[Category: Geurink PP]]
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[[Category: Komander, D.]]
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[[Category: Hospenthal MK]]
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[[Category: Kulathu, Y.]]
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[[Category: Komander D]]
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[[Category: Mevissen, T E.T.]]
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[[Category: Kulathu Y]]
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[[Category: Oualid, F El.]]
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[[Category: Mevissen TET]]
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[[Category: Ovaa, H.]]
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[[Category: Ovaa H]]
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[[Category: Wauer, T.]]
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[[Category: Wauer T]]
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[[Category: Hydrolase]]
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Current revision

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

PDB ID 4bos

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