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| | ==yCP in complex with BOC-ALA-ALA-ALA-CHO== | | ==yCP in complex with BOC-ALA-ALA-ALA-CHO== |
| - | <StructureSection load='4qby' size='340' side='right' caption='[[4qby]], [[Resolution|resolution]] 3.00Å' scene=''> | + | <StructureSection load='4qby' size='340' side='right'caption='[[4qby]], [[Resolution|resolution]] 3.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4qby]] is a 32 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QBY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QBY FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4qby]] is a 20 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=4QBY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4QBY FirstGlance]. <br> |
| - | </td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3Å</td></tr> |
| - | <tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2A1:(2S)-2-AMINOPROPAN-1-OL'>2A1</scene>, <scene name='pdbligand=BOC:TERT-BUTYL+HYDROGEN+CARBONATE'>BOC</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2A1:(2S)-2-AMINOPROPAN-1-OL'>2A1</scene>, <scene name='pdbligand=BOC:TERT-BUTYL+HYDROGEN+CARBONATE'>BOC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> |
| - | <tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1ryp|1ryp]]</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=4qby FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qby OCA], [https://pdbe.org/4qby PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4qby RCSB], [https://www.ebi.ac.uk/pdbsum/4qby PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4qby ProSAT]</span></td></tr> |
| - | <tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Proteasome_endopeptidase_complex Proteasome endopeptidase complex], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.25.1 3.4.25.1] </span></td></tr> | + | </table> |
| - | <tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4qby FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qby OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qby RCSB], [http://www.ebi.ac.uk/pdbsum/4qby PDBsum]</span></td></tr>
| + | == Function == |
| - | <table> | + | [https://www.uniprot.org/uniprot/PSA2_YEAST PSA2_YEAST] The proteasome degrades poly-ubiquitinated proteins in the cytoplasm and in the nucleus. It is essential for the regulated turnover of proteins and for the removal of misfolded proteins. The proteasome is a multicatalytic proteinase complex that is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. It has an ATP-dependent proteolytic activity. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 4qby" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Proteasome 3D structures|Proteasome 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Proteasome endopeptidase complex]] | + | [[Category: Large Structures]] |
| - | [[Category: Saccharomyces cerevisiae]] | + | [[Category: Saccharomyces cerevisiae S288C]] |
| - | [[Category: Arciniega, M.]] | + | [[Category: Arciniega M]] |
| - | [[Category: Beck, P.]] | + | [[Category: Beck P]] |
| - | [[Category: Groll, M.]] | + | [[Category: Groll M]] |
| - | [[Category: Huber, R.]] | + | [[Category: Huber R]] |
| - | [[Category: Lange, O.]] | + | [[Category: Lange O]] |
| - | [[Category: 20s proteasome]]
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| - | [[Category: Allosteric regulation]]
| + | |
| - | [[Category: Hydrolase-hydrolase inhibitor complex]]
| + | |
| - | [[Category: Immunoproteasome]]
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| - | [[Category: Pca analysis]]
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| - | [[Category: Peptide aldehyde]]
| + | |
| Structural highlights
Function
PSA2_YEAST The proteasome degrades poly-ubiquitinated proteins in the cytoplasm and in the nucleus. It is essential for the regulated turnover of proteins and for the removal of misfolded proteins. The proteasome is a multicatalytic proteinase complex that is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. It has an ATP-dependent proteolytic activity.
Publication Abstract from PubMed
Two clusters of configurations of the main proteolytic subunit beta5 were identified by principal component analysis of crystal structures of the yeast proteasome core particle (yCP). The apo-cluster encompasses unliganded species and complexes with nonpeptidic ligands, and the pep-cluster comprises complexes with peptidic ligands. The murine constitutive CP structures conform to the yeast system, with the apo-form settled in the apo-cluster and the PR-957 (a peptidic ligand) complex in the pep-cluster. In striking contrast, the murine immune CP classifies into the pep-cluster in both the apo and the PR-957-liganded species. The two clusters differ essentially by multiple small structural changes and a domain motion enabling enclosure of the peptidic ligand and formation of specific hydrogen bonds in the pep-cluster. The immune CP species is in optimal peptide binding configuration also in its apo form. This favors productive ligand binding and may help to explain the generally increased functional activity of the immunoproteasome. Molecular dynamics simulations of the representative murine species are consistent with the experimentally observed configurations. A comparison of all 28 subunits of the unliganded species with the peptidic liganded forms demonstrates a greatly enhanced plasticity of beta5 and suggests specific signaling pathways to other subunits.
Differential global structural changes in the core particle of yeast and mouse proteasome induced by ligand binding.,Arciniega M, Beck P, Lange OF, Groll M, Huber R Proc Natl Acad Sci U S A. 2014 Jul 1;111(26):9479-84. doi:, 10.1073/pnas.1408018111. Epub 2014 Jun 16. PMID:24979800[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Arciniega M, Beck P, Lange OF, Groll M, Huber R. Differential global structural changes in the core particle of yeast and mouse proteasome induced by ligand binding. Proc Natl Acad Sci U S A. 2014 Jul 1;111(26):9479-84. doi:, 10.1073/pnas.1408018111. Epub 2014 Jun 16. PMID:24979800 doi:http://dx.doi.org/10.1073/pnas.1408018111
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