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| | <StructureSection load='1nli' size='340' side='right'caption='[[1nli]], [[Resolution|resolution]] 1.93Å' scene=''> | | <StructureSection load='1nli' size='340' side='right'caption='[[1nli]], [[Resolution|resolution]] 1.93Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1nli]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Chinese_cucumber Chinese cucumber]. 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> | + | <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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADE:ADENINE'>ADE</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.93Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Trichosanthin ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3677 Chinese cucumber])</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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/rRNA_N-glycosylase rRNA N-glycosylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.22 3.2.2.22] </span></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> | | <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> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/RIPT_TRIKI RIPT_TRIKI]] Inactivates eukaryotic 60S ribosomal subunits.
| + | [https://www.uniprot.org/uniprot/RIPT_TRIKI RIPT_TRIKI] Inactivates eukaryotic 60S ribosomal subunits. |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Chinese cucumber]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: RRNA N-glycosylase]] | + | [[Category: Trichosanthes kirilowii]] |
| - | [[Category: Chan, D S.B]] | + | [[Category: Chan DSB]] |
| - | [[Category: Shaw, P C]] | + | [[Category: Shaw PC]] |
| - | [[Category: Williams, R L]] | + | [[Category: Williams RL]] |
| - | [[Category: Wong, K B]] | + | [[Category: Wong KB]] |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Protein-dna complex]]
| + | |
| - | [[Category: Ribosome-inactivating protein]]
| + | |
| Structural highlights
Function
RIPT_TRIKI Inactivates eukaryotic 60S ribosomal subunits.
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
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.
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Shaw PC, Wong KB, Chan DS, Williams RL. Structural basis for the interaction of [E160A-E189A]-trichosanthin with adenine. Toxicon. 2003 Apr;41(5):575-81. PMID:12676436
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