3gpt: Difference between revisions

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-{{Seed}}
-[[Image:3gpt.jpg|left|200px]]
-<!--
+==Crystal structure of the yeast 20S proteasome in complex with Salinosporamide derivatives: slow substrate ligand==
-The line below this paragraph, containing "STRUCTURE_3gpt", creates the "Structure Box" on the page.
+<StructureSection load='3gpt' size='340' side='right'caption='[[3gpt]], [[Resolution|resolution]] 2.41&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'>[[3gpt]] 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=3GPT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GPT 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]] 2.41&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GPT:(2R,3S,4R)-2-[(S)-(1S)-CYCLOHEX-2-EN-1-YL(HYDROXY)METHYL]-4-(2-FLUOROETHYL)-3-HYDROXY-3-METHYL-5-OXOPYRROLIDINE-2-CARBALDEHYDE'>GPT</scene></td></tr>
-{{STRUCTURE_3gpt|  PDB=3gpt  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3gpt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gpt OCA], [https://pdbe.org/3gpt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gpt RCSB], [https://www.ebi.ac.uk/pdbsum/3gpt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gpt 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/gp/3gpt_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=3gpt ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Many marketed drugs contain fluorine, reflecting its ability to modulate a variety of biological responses. The unique 20S proteasome inhibition profile of fluorosalinosporamide compared to chlorinated anticancer agent salinosporamide A (NPI-0052) is exemplary and relates to each halogen's leaving group potential. Crystal structures of fluoro-, hydroxy-, and bromosalinosporamide in complex with the yeast 20S proteasome core particle (CP) provide mechanistic insights into ligand binding and leaving group elimination and the ability to fine-tune the duration of proteasome inhibition. Fluorosalinosporamide/CP crystal structures determined over time offer striking snapshots of the ligand trapped with an intact fluoroethyl group in anticipation of fluoride elimination, followed by complete nucleophilic displacement of fluoride to give the highly stabilized cyclic ether found for salinosporamide A and bromosalinosporamide. This two-step reaction pathway is consistent with a mechanism for partially reversible proteasome inhibition by fluorosalinosporamide. Proteasome catalyzed fluoride displacement provides preliminary insights into the active site Thr1N pK(a).
-===Crystal structure of the yeast 20S proteasome in complex with Salinosporamide derivatives: slow substrate ligand===
+Snapshots of the fluorosalinosporamide/20S complex offer mechanistic insights for fine tuning proteasome inhibition.,Groll M, McArthur KA, Macherla VR, Manam RR, Potts BC J Med Chem. 2009 Sep 10;52(17):5420-8. PMID:19678642<ref>PMID:19678642</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3gpt" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_19678642}}, adds the Publication Abstract to the page
+*[[Proteasome|Proteasome]]
-(as it appears on PubMed at http://www.pubmed.gov), where 19678642 is the PubMed ID number.
+*[[Proteasome 3D structures|Proteasome 3D structures]]
--->
+== References ==
-{{ABSTRACT_PUBMED_19678642}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-GPT 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=3GPT OCA].
+[[Category: Large Structures]]
-==Reference==
-<ref group="xtra">PMID:19678642</ref><references group="xtra"/>
-[[Category: Proteasome endopeptidase complex]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Arthur, K A.M.]]
+[[Category: Arthur KAM]]
-[[Category: Groll, M.]]
+[[Category: Groll M]]
-[[Category: Macherla, V R.]]
+[[Category: Macherla VR]]
-[[Category: Manam, R R.]]
+[[Category: Manam RR]]
-[[Category: Potts, C B.]]
+[[Category: Potts CB]]
-[[Category: Cancer therapy]]
-[[Category: Cytoplasm]]
-[[Category: Hydrolase]]
-[[Category: Immunology]]
-[[Category: Inhibitor]]
-[[Category: Isopeptide bond]]
-[[Category: Nucleus]]
-[[Category: Phosphoprotein]]
-[[Category: Protease]]
-[[Category: Proteasome]]
-[[Category: Threonine protease]]
-[[Category: Time dependent leaving group elimination]]
-[[Category: Ubiquitin]]
-[[Category: Ubl conjugation]]
-[[Category: Zymogen]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 16 09:01:45 2009''