3gpj

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{{Seed}}
 
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[[Image:3gpj.jpg|left|200px]]
 
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==Crystal structure of the yeast 20S proteasome in complex with syringolin B==
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The line below this paragraph, containing "STRUCTURE_3gpj", creates the "Structure Box" on the page.
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<StructureSection load='3gpj' size='340' side='right'caption='[[3gpj]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[3gpj]] 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=3GPJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GPJ FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.7&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SY2:N-{[(1S)-2-METHYL-1-{[(5S,8S)-5-(1-METHYLETHYL)-2,7-DIOXO-1,6-DIAZACYCLODODEC-3-EN-8-YL]CARBAMOYL}PROPYL]CARBAMOYL}-L-VALINE'>SY2</scene></td></tr>
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{{STRUCTURE_3gpj| PDB=3gpj | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3gpj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gpj OCA], [https://pdbe.org/3gpj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gpj RCSB], [https://www.ebi.ac.uk/pdbsum/3gpj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gpj ProSAT]</span></td></tr>
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</table>
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== Function ==
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[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.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gp/3gpj_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=3gpj ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Syrbactins, a family of natural products belonging either to the syringolin or glidobactin class, are highly potent proteasome inhibitors. Although sharing similar structural features, they differ in their macrocyclic lactam core structure and exocyclic side chain. These structural variations critically influence inhibitory potency and proteasome subsite selectivity. Here, we describe the total synthesis of syringolin A and B, which together with enzyme kinetic and structural studies, allowed us to elucidate the structural determinants underlying the proteasomal subsite selectivity and binding affinity of syrbactins. These findings were used successfully in the rational design and synthesis of a syringolin A-based lipophilic derivative, which proved to be the most potent syrbactin-based proteasome inhibitor described so far. With a K(i)' of 8.65 +/- 1.13 nM for the chymotryptic activity, this syringolin A derivative displays a 100-fold higher potency than the parent compound syringolin A. In light of the medicinal relevance of proteasome inhibitors as anticancer compounds, the present findings may assist in the rational design and development of syrbactin-based chemotherapeutics.
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===Crystal structure of the yeast 20S proteasome in complex with syringolin B===
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Synthetic and structural studies on syringolin A and B reveal critical determinants of selectivity and potency of proteasome inhibition.,Clerc J, Groll M, Illich DJ, Bachmann AS, Huber R, Schellenberg B, Dudler R, Kaiser M Proc Natl Acad Sci U S A. 2009 Apr 21;106(16):6507-12. Epub 2009 Apr 9. PMID:19359491<ref>PMID:19359491</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3gpj" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_19359491}}, adds the Publication Abstract to the page
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*[[Proteasome 3D structures|Proteasome 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 19359491 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_19359491}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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3GPJ 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=3GPJ OCA].
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==Reference==
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<ref group="xtra">PMID:19359491</ref><references group="xtra"/>
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[[Category: Proteasome endopeptidase complex]]
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[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
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[[Category: Groll, M.]]
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[[Category: Groll M]]
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[[Category: Huber, R.]]
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[[Category: Huber R]]
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[[Category: Kaiser, M.]]
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[[Category: Kaiser M]]
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[[Category: Cancer therapy]]
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[[Category: Cytoplasm]]
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[[Category: Hydrolase]]
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[[Category: Immunology]]
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[[Category: Isopeptide bond]]
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[[Category: Nucleus]]
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[[Category: Phosphoprotein]]
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[[Category: Protease]]
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[[Category: Proteasome]]
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[[Category: Threonine protease]]
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[[Category: Ubiquitin]]
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[[Category: Ubl conjugation]]
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[[Category: Virulence]]
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[[Category: Zymogen]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jun 4 07:27:21 2009''
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Current revision

Crystal structure of the yeast 20S proteasome in complex with syringolin B

PDB ID 3gpj

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