1nli

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[[Image:1nli.jpg|left|200px]]
 
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{{Structure
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==Complex of [E160A-E189A] trichosanthin and adenine==
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|PDB= 1nli |SIZE=350|CAPTION= <scene name='initialview01'>1nli</scene>, resolution 1.93&Aring;
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<StructureSection load='1nli' size='340' side='right'caption='[[1nli]], [[Resolution|resolution]] 1.93&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=ADE:ADENINE'>ADE</scene>
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<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>
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|ACTIVITY= <span class='plainlinks'>[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] </span>
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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]] 1.93&#8491;</td></tr>
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|GENE= Trichosanthin ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3677 Trichosanthes kirilowii])
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<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>
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|DOMAIN=
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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=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>
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|RELATEDENTRY=
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1nli FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nli OCA], [http://www.ebi.ac.uk/pdbsum/1nli PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1nli RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/RIPT_TRIKI RIPT_TRIKI] Inactivates eukaryotic 60S ribosomal subunits.
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== Evolutionary Conservation ==
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'''Complex of [E160A-E189A] trichosanthin and adenine'''
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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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==Overview==
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nl/1nli_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1nli 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 ==
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.
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.
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==About this Structure==
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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>
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1NLI is a [[Single protein]] structure of 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].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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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://www.ncbi.nlm.nih.gov/pubmed/12676436 12676436]
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</div>
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[[Category: Single protein]]
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<div class="pdbe-citations 1nli" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Trichosanthes kirilowii]]
[[Category: Trichosanthes kirilowii]]
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[[Category: rRNA N-glycosylase]]
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[[Category: Chan DSB]]
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[[Category: Chan, D S.B.]]
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[[Category: Shaw PC]]
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[[Category: Shaw, P C.]]
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[[Category: Williams RL]]
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[[Category: Williams, R L.]]
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[[Category: Wong KB]]
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[[Category: Wong, K B.]]
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[[Category: protein-dna complex]]
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[[Category: ribosome-inactivating protein]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:31:59 2008''
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Current revision

Complex of [E160A-E189A] trichosanthin and adenine

PDB ID 1nli

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