7d5c
From Proteopedia
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==IleRS in complex with a tRNA site inhibitor== | ==IleRS in complex with a tRNA site inhibitor== | ||
| - | <StructureSection load='7d5c' size='340' side='right'caption='[[7d5c]]' scene=''> | + | <StructureSection load='7d5c' size='340' side='right'caption='[[7d5c]], [[Resolution|resolution]] 1.90Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7D5C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7D5C FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[7d5c]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7D5C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7D5C FirstGlance]. <br> |
| - | </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=7d5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7d5c OCA], [https://pdbe.org/7d5c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7d5c RCSB], [https://www.ebi.ac.uk/pdbsum/7d5c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7d5c ProSAT]</span></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GV6:[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]+(2S,3S)-2-azanyl-3-methyl-pentanoate'>GV6</scene>, <scene name='pdbligand=GVU:(2E,4S,5S,6E,8E)-10-[(2S,3R,6S,8R,9S)-3-butyl-9-methyl-2-[(1E,3E)-3-methyl-5-oxidanyl-5-oxidanylidene-penta-1,3-dienyl]-3-(4-oxidanyl-4-oxidanylidene-butanoyl)oxy-1,7-dioxaspiro[5.5]undecan-8-yl]-4,8-dimethyl-5-oxidanyl-deca-2,6,8-trienoic+acid'>GVU</scene></td></tr> |
| + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ILS1, YBL076C, YBL0734 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</td></tr> | ||
| + | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Isoleucine--tRNA_ligase Isoleucine--tRNA ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.5 6.1.1.5] </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=7d5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7d5c OCA], [https://pdbe.org/7d5c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7d5c RCSB], [https://www.ebi.ac.uk/pdbsum/7d5c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7d5c ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | The polyketide natural product reveromycin A (RM-A) exhibits antifungal, anticancer, anti-bone metastasis, anti-periodontitis and anti-osteoporosis activities by selectively inhibiting eukaryotic cytoplasmic isoleucyl-tRNA synthetase (IleRS). Herein, a co-crystal structure suggests that the RM-A molecule occupies the substrate tRNA(Ile) binding site of Saccharomyces cerevisiae IleRS (ScIleRS), by partially mimicking the binding of tRNA(Ile). RM-A binding is facilitated by the copurified intermediate product isoleucyl-adenylate (Ile-AMP). The binding assays confirm that RM-A competes with tRNA(Ile) while binding synergistically with L-isoleucine or intermediate analogue Ile-AMS to the aminoacylation pocket of ScIleRS. This study highlights that the vast tRNA binding site of the Rossmann-fold catalytic domain of class I aminoacyl-tRNA synthetases could be targeted by a small molecule. This finding will inform future rational drug design. | ||
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| + | Inhibitory mechanism of reveromycin A at the tRNA binding site of a class I synthetase.,Chen B, Luo S, Zhang S, Ju Y, Gu Q, Xu J, Yang XL, Zhou H Nat Commun. 2021 Mar 12;12(1):1616. doi: 10.1038/s41467-021-21902-0. PMID:33712620<ref>PMID:33712620</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 7d5c" style="background-color:#fffaf0;"></div> | ||
| + | |||
| + | ==See Also== | ||
| + | *[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]] | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| + | [[Category: Baker's yeast]] | ||
| + | [[Category: Isoleucine--tRNA ligase]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| - | [[Category: Chen B]] | + | [[Category: Chen, B]] |
| - | [[Category: Luo S]] | + | [[Category: Luo, S]] |
| - | [[Category: Zhou H]] | + | [[Category: Zhou, H]] |
| + | [[Category: Ligase-inhibitor complex]] | ||
| + | [[Category: Trna synthetase]] | ||
Revision as of 06:53, 24 March 2021
IleRS in complex with a tRNA site inhibitor
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