4o8x: Difference between revisions

Revision as of 09:00, 18 January 2023

Zinc-bound Rpn11 in complex with Rpn8

Structural highlights

4o8x is a 2 chain structure with sequence from Saccharomyces cerevisiae S288C. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	EDO, ZN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RPN8_YEAST Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins.^[1]

Publication Abstract from PubMed

Polyubiquitin chains target protein substrates to the 26S proteasome, where they are removed by the deubiquitinase Rpn11 to allow efficient substrate degradation. Despite Rpn11's essential function during substrate processing, its detailed structural and biochemical characterization has been hindered by difficulties in purifying the isolated enzyme. Here we report the 2.0-A crystal structures of Zn2+-free and Zn2+-bound Saccharomyces cerevisiae Rpn11 in an MPN-domain heterodimer with Rpn8. The Rpn11-Rpn8 interaction occurs via two distinct interfaces that may be conserved in related MPN-domain complexes. Our structural and mutational studies reveal that Rpn11 lacks a conserved surface to bind the ubiquitin Ile44 patch, does not interact with the moiety on the proximal side of the scissile isopeptide bond and exhibits no linkage specificity for ubiquitin cleavage. These findings explain how Rpn11 functions as a promiscuous deubiquitinase for cotranslocational substrate deubiquitination during proteasomal degradation.

Structure of the Rpn11-Rpn8 dimer reveals mechanisms of substrate deubiquitination during proteasomal degradation.,Worden EJ, Padovani C, Martin A Nat Struct Mol Biol. 2014 Jan 23. doi: 10.1038/nsmb.2771. PMID:24463465^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Glickman MH, Rubin DM, Fried VA, Finley D. The regulatory particle of the Saccharomyces cerevisiae proteasome. Mol Cell Biol. 1998 Jun;18(6):3149-62. PMID:9584156
↑ Worden EJ, Padovani C, Martin A. Structure of the Rpn11-Rpn8 dimer reveals mechanisms of substrate deubiquitination during proteasomal degradation. Nat Struct Mol Biol. 2014 Jan 23. doi: 10.1038/nsmb.2771. PMID:24463465 doi:https://dx.doi.org/10.1038/nsmb.2771

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OCA

[1] Glickman MH, Rubin DM, Fried VA, Finley D. The regulatory particle of the Saccharomyces cerevisiae proteasome. Mol Cell Biol. 1998 Jun;18(6):3149-62. PMID:9584156

[2] Worden EJ, Padovani C, Martin A. Structure of the Rpn11-Rpn8 dimer reveals mechanisms of substrate deubiquitination during proteasomal degradation. Nat Struct Mol Biol. 2014 Jan 23. doi: 10.1038/nsmb.2771. PMID:24463465 doi:https://dx.doi.org/10.1038/nsmb.2771

[1]

[2]

@@ Line 1: / Line 1: @@
 ==Zinc-bound Rpn11 in complex with Rpn8==
-<StructureSection load='4o8x' size='340' side='right' caption='[[4o8x]], [[Resolution|resolution]] 1.99&Aring;' scene=''>
+<StructureSection load='4o8x' size='340' side='right'caption='[[4o8x]], [[Resolution|resolution]] 1.99&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4o8x]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O8X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4O8X FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4o8x]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O8X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4O8X FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4o8y|4o8y]]</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=4o8x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o8x OCA], [https://pdbe.org/4o8x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4o8x RCSB], [https://www.ebi.ac.uk/pdbsum/4o8x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4o8x ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">RPN8, YOR261C, O5360 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPN11, MPR1, YFR004W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4o8x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o8x OCA], [http://pdbe.org/4o8x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4o8x RCSB], [http://www.ebi.ac.uk/pdbsum/4o8x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4o8x ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/RPN8_YEAST RPN8_YEAST]] Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins.<ref>PMID:9584156</ref>  [[http://www.uniprot.org/uniprot/RPN11_YEAST RPN11_YEAST]] Acts as a regulatory subunit of the 26 proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins.<ref>PMID:21075847</ref>
+[https://www.uniprot.org/uniprot/RPN8_YEAST RPN8_YEAST] Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins.<ref>PMID:9584156</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 20: / Line 18: @@
 </div>
 <div class="pdbe-citations 4o8x" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Proteasome 3D structures|Proteasome 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Baker's yeast]]
+[[Category: Large Structures]]
-[[Category: Martin, A]]
+[[Category: Saccharomyces cerevisiae S288C]]
-[[Category: Padovani, C]]
+[[Category: Martin A]]
-[[Category: Worden, E J]]
+[[Category: Padovani C]]
-[[Category: Deubiquitinase]]
+[[Category: Worden EJ]]
-[[Category: Hydrolase]]
-[[Category: Jamm]]
-[[Category: Mpn]]

4o8x: Difference between revisions

Revision as of 09:00, 18 January 2023

Zinc-bound Rpn11 in complex with Rpn8

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

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