This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
3zgz
From Proteopedia
(Difference between revisions)
m (Protected "3zgz" [edit=sysop:move=sysop]) |
|||
| (7 intermediate revisions not shown.) | |||
| Line 1: | Line 1: | ||
| - | '''Unreleased structure''' | ||
| - | + | ==Ternary complex of E. coli leucyl-tRNA synthetase, tRNA(leu) and toxic moiety from agrocin 84 (TM84) in aminoacylation-like conformation== | |
| + | <StructureSection load='3zgz' size='340' side='right'caption='[[3zgz]], [[Resolution|resolution]] 2.40Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[3zgz]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZGZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ZGZ 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]] 2.4Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=84T:[(2S,4S,5R)-5-(6-AMINOPURIN-9-YL)-4-OXIDANYL-OXOLAN-2-YL]METHOXY-N-[(2S,3R)-4-METHYL-2,3-BIS(OXIDANYL)PENTANOYL]PHOSPHONAMIDIC+ACID'>84T</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=3zgz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zgz OCA], [https://pdbe.org/3zgz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3zgz RCSB], [https://www.ebi.ac.uk/pdbsum/3zgz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3zgz ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/SYL_ECOLI SYL_ECOLI] | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Leucyl-tRNA synthetases (LeuRSs) have an essential role in translation and are promising targets for antibiotic development. Agrocin 84 is a LeuRS inhibitor produced by the biocontrol agent Agrobacterium radiobacter K84 that targets pathogenic strains of A. tumefaciens, the causative agent of plant tumours. Agrocin 84 acts as a molecular Trojan horse and is processed inside the pathogen into a toxic moiety (TM84). Here we show using crystal structure, thermodynamic and kinetic analyses, that this natural antibiotic employs a unique and previously undescribed mechanism to inhibit LeuRS. TM84 requires tRNA(Leu) for tight binding to the LeuRS synthetic active site, unlike any previously reported inhibitors. TM84 traps the enzyme-tRNA complex in a novel 'aminoacylation-like' conformation, forming novel interactions with the KMSKS loop and the tRNA 3'-end. Our findings reveal an intriguing tRNA-dependent inhibition mechanism that may confer a distinct evolutionary advantage in vivo and inform future rational antibiotic design. | ||
| - | + | Plant tumour biocontrol agent employs a tRNA-dependent mechanism to inhibit leucyl-tRNA synthetase.,Chopra S, Palencia A, Virus C, Tripathy A, Temple BR, Velazquez-Campoy A, Cusack S, Reader JS Nat Commun. 2013 Jan 29;4:1417. doi: 10.1038/ncomms2421. PMID:23361008<ref>PMID:23361008</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| + | </div> | ||
| + | <div class="pdbe-citations 3zgz" style="background-color:#fffaf0;"></div> | ||
| + | |||
| + | ==See Also== | ||
| + | *[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]] | ||
| + | *[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]] | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Escherichia coli]] | ||
| + | [[Category: Escherichia coli K-12]] | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Chopra S]] | ||
| + | [[Category: Cusack S]] | ||
| + | [[Category: Palencia A]] | ||
| + | [[Category: Reader JS]] | ||
| + | [[Category: Temple BR]] | ||
| + | [[Category: Tripathy A]] | ||
| + | [[Category: Velazquez-Campoy A]] | ||
| + | [[Category: Virus C]] | ||
Current revision
Ternary complex of E. coli leucyl-tRNA synthetase, tRNA(leu) and toxic moiety from agrocin 84 (TM84) in aminoacylation-like conformation
| |||||||||||
