3zgz

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[[Image:3zgz.png|left|200px]]
 
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{{STRUCTURE_3zgz| PDB=3zgz | SCENE= }}
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==Ternary complex of E. coli leucyl-tRNA synthetase, tRNA(leu) and toxic moiety from agrocin 84 (TM84) in aminoacylation-like conformation==
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<StructureSection load='3zgz' size='340' side='right'caption='[[3zgz]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
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== Structural highlights ==
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<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>
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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]] 2.4&#8491;</td></tr>
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<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>
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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=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>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/SYL_ECOLI SYL_ECOLI]
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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===Ternary complex of E. coli leucyl-tRNA synthetase, tRNA(leu) and toxic moiety from agrocin 84 (TM84) in aminoacylation-like conformation===
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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>
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{{ABSTRACT_PUBMED_23361008}}
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3zgz" style="background-color:#fffaf0;"></div>
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==About this Structure==
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==See Also==
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[[3zgz]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZGZ OCA].
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*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
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*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Leucine--tRNA ligase]]
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[[Category: Escherichia coli K-12]]
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[[Category: Chopra, S.]]
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[[Category: Large Structures]]
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[[Category: Cusack, S.]]
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[[Category: Chopra S]]
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[[Category: Palencia, A.]]
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[[Category: Cusack S]]
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[[Category: Reader, J S.]]
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[[Category: Palencia A]]
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[[Category: Temple, B R.]]
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[[Category: Reader JS]]
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[[Category: Tripathy, A.]]
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[[Category: Temple BR]]
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[[Category: Velazquez-Campoy, A.]]
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[[Category: Tripathy A]]
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[[Category: Virus, C.]]
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[[Category: Velazquez-Campoy A]]
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[[Category: Class i aminoacyl-trna synthetase]]
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[[Category: Virus C]]
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[[Category: Ligase]]
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[[Category: Ligase-rna complex]]
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[[Category: Protein biosynthesis]]
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Current revision

Ternary complex of E. coli leucyl-tRNA synthetase, tRNA(leu) and toxic moiety from agrocin 84 (TM84) in aminoacylation-like conformation

PDB ID 3zgz

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