3jck

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Revision as of 13:32, 4 May 2022

Structure of the yeast 26S proteasome lid sub-complex

3jck, resolution 3.50Å

Structural highlights

3jck is a 9 chain structure with sequence from Baker's yeast. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Gene:	RPN3, SUN2, YER021W (Baker's yeast), RPN5, NAS5, YDL147W, D1572 (Baker's yeast), RPN6, NAS4, YDL097C, D2381 (Baker's yeast), RPN7, YPR108W, P8283.8 (Baker's yeast), RPN8, YOR261C, O5360 (Baker's yeast), RPN9, NAS7, YDR427W, D9461.14 (Baker's yeast), RPN11, MPR1, YFR004W (Baker's yeast), RPN12, NIN1, YFR052W (Baker's yeast), SEM1, DSH1, YDR363W-A (Baker's yeast)
Activity:	Ubiquitinyl hydrolase 1, with EC number 3.4.19.12
Experimental data:	Check to display Experimental Data
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[RPN9_YEAST] Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins. [RPN6_YEAST] Component of the lid subcomplex of the 26S proteasome, a multiprotein complex involved in the ATP-dependent degradation of ubiquitinated proteins. In the complex, RPN6 is required for proteasome assembly.^[1] ^[2] ^[3] [RPN11_YEAST] Acts as a regulatory subunit of the 26 proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins.^[4] [SEM1_YEAST] Versatile protein that might stabilize multiple protein complexes involved in diverse pathways. Subunit of the 26S proteasome which plays a role in ubiquitin-dependent proteolysis. Associates also with the TREX-2 complex that is required for transcription-coupled mRNA export, and the COP9 signalosome, which is involved in deneddylation.^[5] ^[6] [RPN5_YEAST] Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins.^[7] [RPN12_YEAST] Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins. Necessary for activation of the CDC28 kinase. [RPN3_YEAST] Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins. [RPN7_YEAST] Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins (By similarity). [RPN8_YEAST] Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins.^[8]

Publication Abstract from PubMed

The 26S proteasome is responsible for the selective, ATP-dependent degradation of polyubiquitinated cellular proteins. Removal of ubiquitin chains from targeted substrates at the proteasome is a prerequisite for substrate processing and is accomplished by Rpn11, a deubiquitinase within the 'lid' sub-complex. Prior to the lid's incorporation into the proteasome, Rpn11 deubiquitinase activity is inhibited to prevent unwarranted deubiquitination of polyubiquitinated proteins. Here we present the atomic model of the isolated lid sub-complex, as determined by cryo-electron microscopy at 3.5 A resolution, revealing how Rpn11 is inhibited through its interaction with a neighboring lid subunit, Rpn5. Through mutagenesis of specific residues, we describe the network of interactions that are required to stabilize this inhibited state. These results provide significant insight into the intricate mechanisms of proteasome assembly, outlining the substantial conformational rearrangements that occur during incorporation of the lid into the 26S holoenzyme, which ultimately activates the deubiquitinase for substrate degradation.

Atomic structure of the 26S proteasome lid reveals the mechanism of deubiquitinase inhibition.,Dambacher CM, Worden EJ, Herzik MA, Martin A, Lander GC Elife. 2016 Jan 8;5. pii: e13027. doi: 10.7554/eLife.13027. PMID:26744777^[9]

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

References

↑ Saito A, Watanabe TK, Shimada Y, Fujiwara T, Slaughter CA, DeMartino GN, Tanahashi N, Tanaka K. cDNA cloning and functional analysis of p44.5 and p55, two regulatory subunits of the 26S proteasome. Gene. 1997 Dec 12;203(2):241-50. PMID:9426256
↑ Santamaria PG, Finley D, Ballesta JP, Remacha M. Rpn6p, a proteasome subunit from Saccharomyces cerevisiae, is essential for the assembly and activity of the 26 S proteasome. J Biol Chem. 2003 Feb 28;278(9):6687-95. Epub 2002 Dec 16. PMID:12486135 doi:10.1074/jbc.M209420200
↑ Isono E, Saito N, Kamata N, Saeki Y, Toh-E A. Functional analysis of Rpn6p, a lid component of the 26 S proteasome, using temperature-sensitive rpn6 mutants of the yeast Saccharomyces cerevisiae. J Biol Chem. 2005 Feb 25;280(8):6537-47. Epub 2004 Dec 15. PMID:15611133 doi:10.1074/jbc.M409364200
↑ Chen L, Romero L, Chuang SM, Tournier V, Joshi KK, Lee JA, Kovvali G, Madura K. Sts1 plays a key role in targeting proteasomes to the nucleus. J Biol Chem. 2011 Jan 28;286(4):3104-18. doi: 10.1074/jbc.M110.135863. Epub 2010 , Nov 12. PMID:21075847 doi:10.1074/jbc.M110.135863
↑ Faza MB, Kemmler S, Jimeno S, Gonzalez-Aguilera C, Aguilera A, Hurt E, Panse VG. Sem1 is a functional component of the nuclear pore complex-associated messenger RNA export machinery. J Cell Biol. 2009 Mar 23;184(6):833-46. doi: 10.1083/jcb.200810059. Epub 2009 Mar, 16. PMID:19289793 doi:http://dx.doi.org/10.1083/jcb.200810059
↑ Sone T, Saeki Y, Toh-e A, Yokosawa H. Sem1p is a novel subunit of the 26 S proteasome from Saccharomyces cerevisiae. J Biol Chem. 2004 Jul 2;279(27):28807-16. Epub 2004 Apr 26. PMID:15117943 doi:http://dx.doi.org/10.1074/jbc.M403165200
↑ Saito A, Watanabe TK, Shimada Y, Fujiwara T, Slaughter CA, DeMartino GN, Tanahashi N, Tanaka K. cDNA cloning and functional analysis of p44.5 and p55, two regulatory subunits of the 26S proteasome. Gene. 1997 Dec 12;203(2):241-50. PMID:9426256
↑ 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
↑ Dambacher CM, Worden EJ, Herzik MA, Martin A, Lander GC. Atomic structure of the 26S proteasome lid reveals the mechanism of deubiquitinase inhibition. Elife. 2016 Jan 8;5. pii: e13027. doi: 10.7554/eLife.13027. PMID:26744777 doi:http://dx.doi.org/10.7554/eLife.13027

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3jck"

@@ Line 3: / Line 3: @@
 <SX load='3jck' size='340' side='right' viewer='molstar' caption='[[3jck]], [[Resolution|resolution]] 3.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3jck]] is a 9 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=3JCK OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3JCK FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3jck]] is a 9 chain structure with sequence from [https://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=3JCK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3JCK FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">RPN3, SUN2, YER021W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPN5, NAS5, YDL147W, D1572 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPN6, NAS4, YDL097C, D2381 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPN7, YPR108W, P8283.8 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPN8, YOR261C, O5360 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPN9, NAS7, YDR427W, D9461.14 ([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]), RPN12, NIN1, YFR052W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), SEM1, DSH1, YDR363W-A ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">RPN3, SUN2, YER021W ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPN5, NAS5, YDL147W, D1572 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPN6, NAS4, YDL097C, D2381 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPN7, YPR108W, P8283.8 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPN8, YOR261C, O5360 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPN9, NAS7, YDR427W, D9461.14 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPN11, MPR1, YFR004W ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPN12, NIN1, YFR052W ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), SEM1, DSH1, YDR363W-A ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ubiquitinyl_hydrolase_1 Ubiquitinyl hydrolase 1], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.19.12 3.4.19.12] </span></td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Ubiquitinyl_hydrolase_1 Ubiquitinyl hydrolase 1], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.19.12 3.4.19.12] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=3jck FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jck OCA], [http://pdbe.org/3jck PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3jck RCSB], [http://www.ebi.ac.uk/pdbsum/3jck PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3jck ProSAT]</span></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=3jck FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jck OCA], [https://pdbe.org/3jck PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3jck RCSB], [https://www.ebi.ac.uk/pdbsum/3jck PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3jck ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/RPN9_YEAST RPN9_YEAST]] Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins. [[http://www.uniprot.org/uniprot/RPN6_YEAST RPN6_YEAST]] Component of the lid subcomplex of the 26S proteasome, a multiprotein complex involved in the ATP-dependent degradation of ubiquitinated proteins. In the complex, RPN6 is required for proteasome assembly.<ref>PMID:9426256</ref> <ref>PMID:12486135</ref> <ref>PMID:15611133</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>  [[http://www.uniprot.org/uniprot/SEM1_YEAST SEM1_YEAST]] Versatile protein that might stabilize multiple protein complexes involved in diverse pathways. Subunit of the 26S proteasome which plays a role in ubiquitin-dependent proteolysis. Associates also with the TREX-2 complex that is required for transcription-coupled mRNA export, and the COP9 signalosome, which is involved in deneddylation.<ref>PMID:19289793</ref> <ref>PMID:15117943</ref>  [[http://www.uniprot.org/uniprot/RPN5_YEAST RPN5_YEAST]] Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins.<ref>PMID:9426256</ref>  [[http://www.uniprot.org/uniprot/RPN12_YEAST RPN12_YEAST]] Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins. Necessary for activation of the CDC28 kinase. [[http://www.uniprot.org/uniprot/RPN3_YEAST RPN3_YEAST]] Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins. [[http://www.uniprot.org/uniprot/RPN7_YEAST RPN7_YEAST]] Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins (By similarity). [[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>
+[[https://www.uniprot.org/uniprot/RPN9_YEAST RPN9_YEAST]] Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins. [[https://www.uniprot.org/uniprot/RPN6_YEAST RPN6_YEAST]] Component of the lid subcomplex of the 26S proteasome, a multiprotein complex involved in the ATP-dependent degradation of ubiquitinated proteins. In the complex, RPN6 is required for proteasome assembly.<ref>PMID:9426256</ref> <ref>PMID:12486135</ref> <ref>PMID:15611133</ref>  [[https://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/SEM1_YEAST SEM1_YEAST]] Versatile protein that might stabilize multiple protein complexes involved in diverse pathways. Subunit of the 26S proteasome which plays a role in ubiquitin-dependent proteolysis. Associates also with the TREX-2 complex that is required for transcription-coupled mRNA export, and the COP9 signalosome, which is involved in deneddylation.<ref>PMID:19289793</ref> <ref>PMID:15117943</ref>  [[https://www.uniprot.org/uniprot/RPN5_YEAST RPN5_YEAST]] Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins.<ref>PMID:9426256</ref>  [[https://www.uniprot.org/uniprot/RPN12_YEAST RPN12_YEAST]] Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins. Necessary for activation of the CDC28 kinase. [[https://www.uniprot.org/uniprot/RPN3_YEAST RPN3_YEAST]] Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins. [[https://www.uniprot.org/uniprot/RPN7_YEAST RPN7_YEAST]] Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins (By similarity). [[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 ==

3jck

From Proteopedia

Revision as of 13:32, 4 May 2022

Structure of the yeast 26S proteasome lid sub-complex

Structural highlights

Function

Publication Abstract from PubMed

References

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