5y0n
From Proteopedia
(Difference between revisions)
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<StructureSection load='5y0n' size='340' side='right' caption='[[5y0n]], [[Resolution|resolution]] 2.30Å' scene=''> | <StructureSection load='5y0n' size='340' side='right' caption='[[5y0n]], [[Resolution|resolution]] 2.30Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[5y0n]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y0N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y0N FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5y0n]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y0N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y0N FirstGlance]. <br> |
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene></td></tr> | ||
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | ||
| + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">B4417_3650 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5y0n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y0n OCA], [http://pdbe.org/5y0n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y0n RCSB], [http://www.ebi.ac.uk/pdbsum/5y0n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y0n ProSAT]</span></td></tr> | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5y0n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y0n OCA], [http://pdbe.org/5y0n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y0n RCSB], [http://www.ebi.ac.uk/pdbsum/5y0n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y0n ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Modification of tRNA anticodons plays a critical role in ensuring accurate translation. N(4)-acetylcytidine (ac(4)C) is present at the anticodon first position (position 34) of bacterial elongator tRNA(Met). Herein, we identified Bacillus subtilis ylbM (renamed tmcAL) as a novel gene responsible for ac(4)C34 formation. Unlike general acetyltransferases that use acetyl-CoA, TmcAL activates an acetate ion to form acetyladenylate and then catalyzes ac(4)C34 formation through a mechanism similar to tRNA aminoacylation. The crystal structure of TmcAL with an ATP analog reveals the molecular basis of ac(4)C34 formation. The DeltatmcAL strain displayed a cold-sensitive phenotype and a strong genetic interaction with tilS that encodes the enzyme responsible for synthesizing lysidine (L) at position 34 of tRNA(Ile) to facilitate AUA decoding. Mistranslation of the AUA codon as Met in the DeltatmcAL strain upon tilS repression suggests that ac(4)C34 modification of tRNA(Met) and L34 modification of tRNA(Ile) act cooperatively to prevent misdecoding of the AUA codon. | ||
| + | |||
| + | Acetate-dependent tRNA acetylation required for decoding fidelity in protein synthesis.,Taniguchi T, Miyauchi K, Sakaguchi Y, Yamashita S, Soma A, Tomita K, Suzuki T Nat Chem Biol. 2018 Nov;14(11):1010-1020. doi: 10.1038/s41589-018-0119-z. Epub, 2018 Aug 27. PMID:30150682<ref>PMID:30150682</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 5y0n" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| + | [[Category: Vibrio subtilis ehrenberg 1835]] | ||
[[Category: Tomita, K]] | [[Category: Tomita, K]] | ||
[[Category: Yamashita, S]] | [[Category: Yamashita, S]] | ||
[[Category: Acetate ligase]] | [[Category: Acetate ligase]] | ||
| - | [[Category: | + | [[Category: Ligase]] |
Revision as of 08:30, 26 December 2018
Crystal structure of Bacillus subtilis TmcAL bound with ATP (SeMet derivative)
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