1nli: Difference between revisions

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-[[Image:1nli.png|left|200px]]
-{{STRUCTURE_1nli|  PDB=1nli  |  SCENE=  }}
+==Complex of [E160A-E189A] trichosanthin and adenine==
+<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.
-===Complex of [E160A-E189A] trichosanthin and adenine===
+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>
-{{ABSTRACT_PUBMED_12676436}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 1nli" style="background-color:#fffaf0;"></div>
-[[1nli]] is a 1 chain structure with sequence from [http://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].
+== References ==
+<references/>
-==Reference==
+__TOC__
-<ref group="xtra">PMID:012676436</ref><references group="xtra"/>
+</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: Hydrolase]]
-[[Category: Protein-dna complex]]
-[[Category: Ribosome-inactivating protein]]