3dy4: Difference between revisions

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-{{Seed}}
-[[Image:3dy4.png|left|200px]]
-<!--
+==Crystal structure of yeast 20S proteasome in complex with spirolactacystin==
-The line below this paragraph, containing "STRUCTURE_3dy4", creates the "Structure Box" on the page.
+<StructureSection load='3dy4' size='340' side='right'caption='[[3dy4]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3dy4]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DY4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DY4 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SLA:OMURALIDE,+OPEN+FORM'>SLA</scene></td></tr>
-{{STRUCTURE_3dy4|  PDB=3dy4  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3dy4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dy4 OCA], [https://pdbe.org/3dy4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dy4 RCSB], [https://www.ebi.ac.uk/pdbsum/3dy4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dy4 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[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.
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dy/3dy4_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=3dy4 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Spiro beta-lactone-based proteasome inhibitors were discovered in the context of an asymmetric catalytic total synthesis of the natural product (+)-lactacystin (1). Lactone 4 was found to be a potent inhibitor of the 26S proteasome, while its C-6 epimer (5) displayed weak activity. Crystallographic studies of the two analogues covalently bound to the 20S proteasome permitted characterization of the important stabilizing interactions between each inhibitor and the proteasome's key catalytic N-terminal threonine residue. This structural data support the hypothesis that the discrepancy in potency between 4 and 5 may be due to differences in the hydrolytic stabilities of the resulting acyl enzyme complexes.
-===Crystal structure of yeast 20S proteasome in complex with spirolactacystin===
+Structural analysis of spiro beta-lactone proteasome inhibitors.,Groll M, Balskus EP, Jacobsen EN J Am Chem Soc. 2008 Nov 12;130(45):14981-3. Epub 2008 Oct 17. PMID:18928262<ref>PMID:18928262</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3dy4" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18928262}}, adds the Publication Abstract to the page
+*[[Proteasome 3D structures|Proteasome 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18928262 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18928262}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-DY4 is a 28 chains structure of sequences 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=3DY4 OCA].
-==Reference==
-<ref group="xtra">PMID:18928262</ref><references group="xtra"/>
-[[Category: Proteasome endopeptidase complex]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Balskus, E.]]
+[[Category: Balskus E]]
-[[Category: Groll, M.]]
+[[Category: Groll M]]
-[[Category: Jacobsen, E.]]
+[[Category: Jacobsen E]]
-[[Category: Cytoplasm]]
-[[Category: Hydrolase]]
-[[Category: Inhibitor]]
-[[Category: Nucleus]]
-[[Category: Phosphoprotein]]
-[[Category: Protease]]
-[[Category: Proteasome]]
-[[Category: Protein degradation]]
-[[Category: Threonine protease]]
-[[Category: Ubiquitin-proteasome-pathway]]
-[[Category: Ubl conjugation]]
-[[Category: Zymogen]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 17:03:05 2009''