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2kde

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{{Seed}}
 
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[[Image:2kde.jpg|left|200px]]
 
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==NMR structure of major S5a (196-306):K48 linked diubiquitin species==
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The line below this paragraph, containing "STRUCTURE_2kde", creates the "Structure Box" on the page.
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<StructureSection load='2kde' size='340' side='right'caption='[[2kde]], [[NMR_Ensembles_of_Models | 7 NMR models]]' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2kde]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/African_clawed_frog African clawed frog] and [https://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KDE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KDE FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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;'>[[1yx4|1yx4]], [[1yx5|1yx5]], [[1yx6|1yx6]], [[1d3z|1d3z]], [[2kdf|2kdf]]</div></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PSMD4, MCB1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
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{{STRUCTURE_2kde| PDB=2kde | SCENE= }}
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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=2kde FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kde OCA], [https://pdbe.org/2kde PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2kde RCSB], [https://www.ebi.ac.uk/pdbsum/2kde PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2kde ProSAT]</span></td></tr>
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</table>
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== Function ==
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[[https://www.uniprot.org/uniprot/PSMD4_HUMAN PSMD4_HUMAN]] Binds and presumably selects ubiquitin-conjugates for destruction. Displays selectivity for longer polyubiquitin chains. Modulates intestinal fluid secretion. [[https://www.uniprot.org/uniprot/UBIQP_XENLA UBIQP_XENLA]] 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 (By similarity).
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kd/2kde_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2kde ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Degradation by the proteasome typically requires substrate ubiquitination. Two ubiquitin receptors exist in the proteasome, S5a/Rpn10 and Rpn13. Whereas Rpn13 has only one ubiquitin-binding surface, S5a binds ubiquitin with two independent ubiquitin-interacting motifs (UIMs). Here, we use nuclear magnetic resonance (NMR) and analytical ultracentrifugation to define at atomic level resolution how S5a binds K48-linked diubiquitin, in which K48 of one ubiquitin subunit (the "proximal" one) is covalently bonded to G76 of the other (the "distal" subunit). We demonstrate that S5a's UIMs bind the two subunits simultaneously with a preference for UIM2 binding to the proximal subunit while UIM1 binds to the distal one. In addition, NMR experiments reveal that Rpn13 and S5a bind K48-linked diubiquitin simultaneously with subunit specificity, and a model structure of S5a and Rpn13 bound to K48-linked polyubiquitin is provided. Altogether, our data demonstrate that S5a is highly adaptive and cooperative toward binding ubiquitin chains.
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===NMR structure of major S5a (196-306):K48 linked diubiquitin species===
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Structure of the s5a:k48-linked diubiquitin complex and its interactions with rpn13.,Zhang N, Wang Q, Ehlinger A, Randles L, Lary JW, Kang Y, Haririnia A, Storaska AJ, Cole JL, Fushman D, Walters KJ Mol Cell. 2009 Aug 14;35(3):280-90. PMID:19683493<ref>PMID:19683493</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 2kde" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_19683493}}, adds the Publication Abstract to the page
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*[[Proteasome 3D structures|Proteasome 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 19683493 is the PubMed ID number.
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*[[3D structures of ubiquitin|3D structures of ubiquitin]]
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-->
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== References ==
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{{ABSTRACT_PUBMED_19683493}}
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<references/>
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__TOC__
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==About this Structure==
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</StructureSection>
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2KDE is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Xenopus_laevis Xenopus laevis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KDE OCA].
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[[Category: African clawed frog]]
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[[Category: Human]]
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==Reference==
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[[Category: Large Structures]]
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<ref group="xtra">PMID:19683493</ref><references group="xtra"/>
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[[Category: Cole, J L]]
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[[Category: Homo sapiens]]
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[[Category: Ehlinger, A]]
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[[Category: Xenopus laevis]]
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[[Category: Fushman, D]]
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[[Category: Cole, J L.]]
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[[Category: Haririnia, A]]
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[[Category: Ehlinger, A.]]
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[[Category: Kang, Y]]
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[[Category: Fushman, D.]]
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[[Category: Lary, J W]]
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[[Category: Haririnia, A.]]
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[[Category: Randles, L]]
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[[Category: Kang, Y.]]
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[[Category: Walters, K J]]
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[[Category: Lary, J W.]]
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[[Category: Wang, Q]]
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[[Category: Randles, L.]]
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[[Category: Zhang, N]]
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[[Category: Walters, K J.]]
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[[Category: Wang, Q.]]
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[[Category: Zhang, N.]]
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[[Category: Alternative splicing]]
[[Category: Alternative splicing]]
[[Category: Cytoplasm]]
[[Category: Cytoplasm]]
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[[Category: Ubiquitin interacting motif]]
[[Category: Ubiquitin interacting motif]]
[[Category: Ubl conjugation]]
[[Category: Ubl conjugation]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Sep 3 15:54:30 2009''
 

Current revision

NMR structure of major S5a (196-306):K48 linked diubiquitin species

PDB ID 2kde

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