1nli: Difference between revisions

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OCA

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-[[Image:1nli.jpg|left|200px]]<br /><applet load="1nli" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1nli, resolution 1.93&Aring;" />
-'''Complex of [E160A-E189A] trichosanthin and adenine'''<br />
-==Overview==
+==Complex of [E160A-E189A] trichosanthin and adenine==
-Trichosanthin is a ribosome-inactivating protein that cleaves specifically, the N-glycosidic bond of A-4324 of 28S rRNA. Trichosanthin and its variant, [E160A-E189A]-trichosanthin were found to bind an adenine base with a K(d), value of approximately 0.2mM. To determine how this doubly mutated variant, of trichosanthin interacts with adenine, the co-crystal structure of, [E160A-E189A]-trichosanthin and adenine was resolved to 0.193nm which, revealed that the active site conformation of the doubly mutated variant, is isomorphous to wild-type trichosanthin. Water molecules were found at, locations corresponding to the eliminated side chain of Glu-160 and, Glu-189. On the other hand, the adenine base interacted with, [E160A-E189A]-trichosanthin in a manner similar to that in wild-type, trichosanthin. Our structural analysis illustrates that Glu-160 and, Glu-189 in trichosanthin do not play an important role in maintaining the, active site conformation and binding adenine, an essential step for, substrate-enzyme interaction. On the other hand, removal of two glutamate, residues changed a large patch of negatively charged surface to a positive, charge, which may account for the destabilization of the oxocarbenium-like, transition-state and the significant decrease in ribosome-inactivating, activity in [E160A-E189A]-trichosanthin.
+<StructureSection load='1nli' size='340' side='right'caption='[[1nli]], [[Resolution|resolution]] 1.93&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1nli]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Trichosanthes_kirilowii Trichosanthes kirilowii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NLI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NLI 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]] 1.93&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADE:ADENINE'>ADE</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=1nli FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nli OCA], [https://pdbe.org/1nli PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nli RCSB], [https://www.ebi.ac.uk/pdbsum/1nli PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nli ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RIPT_TRIKI RIPT_TRIKI] Inactivates eukaryotic 60S ribosomal subunits.
+== 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/nl/1nli_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=1nli ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Trichosanthin is a ribosome-inactivating protein that cleaves specifically the N-glycosidic bond of A-4324 of 28S rRNA. Trichosanthin and its variant [E160A-E189A]-trichosanthin were found to bind an adenine base with a K(d) value of approximately 0.2mM. To determine how this doubly mutated variant of trichosanthin interacts with adenine, the co-crystal structure of [E160A-E189A]-trichosanthin and adenine was resolved to 0.193nm which revealed that the active site conformation of the doubly mutated variant is isomorphous to wild-type trichosanthin. Water molecules were found at locations corresponding to the eliminated side chain of Glu-160 and Glu-189. On the other hand, the adenine base interacted with [E160A-E189A]-trichosanthin in a manner similar to that in wild-type trichosanthin. Our structural analysis illustrates that Glu-160 and Glu-189 in trichosanthin do not play an important role in maintaining the active site conformation and binding adenine, an essential step for substrate-enzyme interaction. On the other hand, removal of two glutamate residues changed a large patch of negatively charged surface to a positive charge, which may account for the destabilization of the oxocarbenium-like transition-state and the significant decrease in ribosome-inactivating activity in [E160A-E189A]-trichosanthin.
-==About this Structure==
+Structural basis for the interaction of [E160A-E189A]-trichosanthin with adenine.,Shaw PC, Wong KB, Chan DS, Williams RL Toxicon. 2003 Apr;41(5):575-81. PMID:12676436<ref>PMID:12676436</ref>
-NLI is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Trichosanthes_kirilowii Trichosanthes kirilowii] with ADE as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/rRNA_N-glycosylase rRNA N-glycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.22 3.2.2.22] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1NLI OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Structural basis for the interaction of [E160A-E189A]-trichosanthin with adenine., Shaw PC, Wong KB, Chan DS, Williams RL, Toxicon. 2003 Apr;41(5):575-81. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12676436 12676436]
+</div>
-[[Category: Single protein]]
+<div class="pdbe-citations 1nli" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Trichosanthes kirilowii]]
-[[Category: rRNA N-glycosylase]]
+[[Category: Chan DSB]]
-[[Category: Chan, D.S.B.]]
+[[Category: Shaw PC]]
-[[Category: Shaw, P.C.]]
+[[Category: Williams RL]]
-[[Category: Williams, R.L.]]
+[[Category: Wong KB]]
-[[Category: Wong, K.B.]]
-[[Category: ADE]]
-[[Category: protein-dna complex]]
-[[Category: ribosome-inactivating protein]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 22:21:55 2007''