1k0c: Difference between revisions

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-[[Image:1k0c.jpg|left|200px]]<br /><applet load="1k0c" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1k0c, resolution 2.5&Aring;" />
-'''Ure2p in complex with S-p-nitrobenzylglutathione'''<br />
-==Overview==
+==Ure2p in complex with S-p-nitrobenzylglutathione==
-The [URE3] phenotype in yeast Saccharomyces cerevisiae is due to an, altered prion form of Ure2p, a protein involved in nitrogen catabolism. To, understand possible conformational changes at the origin of prion, propagation, we previously solved the crystal structure of the Ure2p, functional region [Bousset et al. (2001) Structure 9, 39-46]. We showed, the protein to have a fold similar to that of the beta class of, glutathione S-transferases (GSTs). Here we report crystal structures of, the Ure2p functional region (extending from residues 95-354) in complex, with glutathione (GSH), the substrate of all GSTs, and two widely used GST, inhibitors, namely, S-hexylglutathione and S-p-nitrobenzylglutathione. In, a manner similar to what is observed in many GSTs, ligand binding is not, accompanied by a significant change in the conformation of the protein. We, identify one GSH and one hydrophobic electrophile binding site per monomer, as observed in all other GSTs. The sulfur group of GSH, that conjugates, electrophiles, is located near the amide group of Asn124, allowing a, hydrogen bond to be formed. Biochemical data indicate that GSH binds to, Ure2p with high affinity. Its binding affects Ure2p oligomerization but, has no effect on the assembly of the protein into amyloid fibrils. Despite, results indicating that Ure2p lacks GST activity, we propose that Ure2p is, a member of the GST superfamily that may describe a novel GST class. Our, data bring new insights into the function of the Ure2p active region.
+<StructureSection load='1k0c' size='340' side='right'caption='[[1k0c]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1k0c]] is a 4 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=1K0C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K0C FirstGlance]. <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]] 2.5&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GSH:GLUTATHIONE'>GSH</scene>, <scene name='pdbligand=GTB:S-(P-NITROBENZYL)GLUTATHIONE'>GTB</scene></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=1k0c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k0c OCA], [https://pdbe.org/1k0c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k0c RCSB], [https://www.ebi.ac.uk/pdbsum/1k0c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k0c ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/URE2_YEAST URE2_YEAST] Plays an important role in nitrogen catabolite repression. Down-regulates the expression of many genes involved in nitrogen utilization by inhibiting the GATA transcriptional activators GLN3 and GAT1. Under good nitrogen conditions, binds to the phosphorylated forms of GLN3 and GAT1 and sequesters them in the cytoplasm, preventing transcription of genes expressed upon nitrogen limitation. Is also an atypical glutaredoxin without a catalytical cysteine residue. Has glutathione peroxidase and thiol:disulfide oxidoreductase activities in both native and fibrillar form. Also shows insulin disulfide reductase and dehydroascorbic acid reductase (DHAR) actvites.<ref>PMID:1990286</ref> <ref>PMID:8755910</ref> <ref>PMID:10604478</ref> <ref>PMID:10799523</ref> <ref>PMID:15371425</ref> <ref>PMID:19321443</ref>
+== 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/k0/1k0c_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1k0c ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-K0C is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] with GTB and GTT as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1K0C OCA].
+*[[Prion 3D structures|Prion 3D structures]]
+== References ==
-==Reference==
+<references/>
-Crystal structures of the yeast prion Ure2p functional region in complex with glutathione and related compounds., Bousset L, Belrhali H, Melki R, Morera S, Biochemistry. 2001 Nov 13;40(45):13564-73. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11695904 11695904]
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Single protein]]
+[[Category: Belrhali H]]
-[[Category: Belrhali, H.]]
+[[Category: Bousset L]]
-[[Category: Bousset, L.]]
+[[Category: Melki R]]
-[[Category: Melki, R.]]
+[[Category: Morera S]]
-[[Category: Morera, S.]]
-[[Category: GTB]]
-[[Category: GTT]]
-[[Category: nitrate assimilation]]
-[[Category: structural genomics]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 18:44:50 2007''