4eo4: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4eo4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EO4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4EO4 FirstGlance]. <br>
<table><tr><td colspan='2'>[[4eo4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EO4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4EO4 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SSA:5-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE'>SSA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.87&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SSA:5-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE'>SSA</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=4eo4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4eo4 OCA], [https://pdbe.org/4eo4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4eo4 RCSB], [https://www.ebi.ac.uk/pdbsum/4eo4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4eo4 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=4eo4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4eo4 OCA], [https://pdbe.org/4eo4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4eo4 RCSB], [https://www.ebi.ac.uk/pdbsum/4eo4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4eo4 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/SYTM_YEAST SYTM_YEAST]]
[https://www.uniprot.org/uniprot/SYTM_YEAST SYTM_YEAST]  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Accurate translation of mRNA into protein is a fundamental biological process critical for maintaining normal cellular functions. To ensure translational fidelity, aminoacyl-tRNA synthetases (aaRSs) employ pre-transfer and post-transfer editing activities to hydrolyze misactivated and mischarged amino acids, respectively. Whereas post-transfer editing, which requires either a specialized domain in aaRS or a trans-protein factor, is well described, the mechanism of pre-transfer editing is less understood. Here, we show that yeast mitochondrial threonyl-tRNA synthetase (MST1), which lacks an editing domain, utilizes pre-transfer editing to discriminate against serine. MST1 misactivates serine and edits seryl adenylate (Ser-AMP) in a tRNA-independent manner. MST1 hydrolyzes 80% of misactivated Ser-AMP at a rate 4-fold higher than that for the cognate threonyl adenylate (Thr-AMP) while releasing 20% of Ser-AMP into the solution. To understand the mechanism of pre-transfer editing, we solved the crystal structure of MST1 complexed with an analog of Ser-AMP. The binding of the Ser-AMP analog to MST1 induces conformational changes in the aminoacylation active site, and it positions a potential hydrolytic water molecule more favorably for nucleophilic attack. In addition, inhibition results reveal that the Ser-AMP analog binds the active site 100-fold less tightly than the Thr-AMP analog. In conclusion, we propose that the plasticity of the aminoacylation site in MST1 allows binding of Ser-AMP and the appropriate positioning of the hydrolytic water molecule.
 
The mechanism of pre-transfer editing in yeast mitochondrial threonyl-tRNA synthetase.,Ling J, Peterson KM, Simonovic I, Soll D, Simonovic M J Biol Chem. 2012 Aug 17;287(34):28518-25. doi: 10.1074/jbc.M112.372920. Epub, 2012 Jul 6. PMID:22773845<ref>PMID:22773845</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4eo4" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>

Latest revision as of 11:04, 1 March 2024

Crystal structure of the yeast mitochondrial threonyl-tRNA synthetase (MST1) in complex with seryl sulfamoyl adenylate

4eo4, resolution 2.87Å

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