8ivb

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'''Unreleased structure'''
 
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The entry 8ivb is ON HOLD until Paper Publication
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==K113-Ubiquitinated BAK==
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<StructureSection load='8ivb' size='340' side='right'caption='[[8ivb]]' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[8ivb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8IVB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8IVB 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">Solution NMR</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=8ivb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8ivb OCA], [https://pdbe.org/8ivb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8ivb RCSB], [https://www.ebi.ac.uk/pdbsum/8ivb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8ivb ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/RS27A_HUMAN RS27A_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> Ribosomal protein S27a is a component of the 40S subunit of the ribosome.<ref>PMID:16543144</ref> <ref>PMID:19754430</ref>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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BAK permeabilizes the mitochondrial outer membrane, causing apoptosis. This apoptotic activity of BAK is stimulated by binding prodeath activators within its canonical hydrophobic groove. Parkin, an E3 ubiquitin (Ub) ligase, can ubiquitinate BAK, which inhibits BAK apoptotic activity. However, the molecular mechanism underlying the inhibition of ubiquitination remains structurally uncharacterized. Here, we utilize truncated and soluble BAK to construct a mimetic of K113-ubiquitinated BAK (disulfide-linked Ub(G76C) ~ BAK(K113C)) and further present its NMR-derived structure model. The classical L8-I44-H68-V70 hydrophobic patch of the conjugated Ub subunit binds within the canonical hydrophobic groove of BAK. This Ub occludes the binding of prodeath BID activators in the groove and impairs BID-triggered BAK activation and membrane permeabilization. Reduced interaction between Ub and BAK subunits allows BID to activate K113-ubiquitinated BAK. These mechanistic insights suggest a nonsignaling function of Ub in that it directly antagonizes stimuli targeting Ub-modified proteins rather than by recruiting downstream partners for cellular messaging.
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Authors: Dong, X., Cheng, P., Hou, Y.Z., Chen, Y.K., Liu, Z.
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Parkin-mediated ubiquitination inhibits BAK apoptotic activity by blocking its canonical hydrophobic groove.,Cheng P, Hou Y, Bian M, Fang X, Liu Y, Rao Y, Cao S, Liu Y, Zhang S, Chen Y, Dong X, Liu Z Commun Biol. 2023 Dec 12;6(1):1260. doi: 10.1038/s42003-023-05650-z. PMID:38087033<ref>PMID:38087033</ref>
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Description: K113-Ubiquitinated BAK
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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[[Category: Unreleased Structures]]
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</div>
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[[Category: Hou, Y.Z]]
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<div class="pdbe-citations 8ivb" style="background-color:#fffaf0;"></div>
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[[Category: Liu, Z]]
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== References ==
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[[Category: Cheng, P]]
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<references/>
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[[Category: Chen, Y.K]]
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__TOC__
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[[Category: Dong, X]]
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</StructureSection>
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[[Category: Homo sapiens]]
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[[Category: Large Structures]]
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[[Category: Chen YK]]
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[[Category: Cheng P]]
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[[Category: Dong X]]
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[[Category: Hou YZ]]
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[[Category: Liu Z]]

Revision as of 11:42, 1 February 2024

K113-Ubiquitinated BAK

PDB ID 8ivb

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