3ugq: Difference between revisions

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 ==Crystal structure of the apo form of the yeast mitochondrial threonyl-tRNA synthetase determined at 2.1 Angstrom resolution==
-<StructureSection load='3ugq' size='340' side='right' caption='[[3ugq]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+<StructureSection load='3ugq' size='340' side='right'caption='[[3ugq]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3ugq]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UGQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3UGQ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3ugq]] is a 1 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=3UGQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UGQ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.1&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3ugt|3ugt]], [[3uh0|3uh0]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Threonine--tRNA_ligase Threonine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.3 6.1.1.3] </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=3ugq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ugq OCA], [https://pdbe.org/3ugq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ugq RCSB], [https://www.ebi.ac.uk/pdbsum/3ugq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ugq 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=3ugq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ugq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ugq RCSB], [http://www.ebi.ac.uk/pdbsum/3ugq PDBsum]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
+== Function ==
-== Publication Abstract from PubMed ==
+[https://www.uniprot.org/uniprot/SYTM_YEAST SYTM_YEAST]
-Aminoacyl-tRNA synthetases (aaRSs) ensure faithful translation of mRNA into protein by coupling an amino acid to a set of tRNAs with conserved anticodon sequences. Here, we show that in mitochondria of Saccharomyces cerevisiae, a single aaRS (MST1) recognizes and aminoacylates two natural tRNAs that contain anticodon loops of different size and sequence. Besides a regular with a threonine (Thr) anticodon, MST1 also recognizes an unusual , which contains an enlarged anticodon loop and an anticodon triplet that reassigns the CUN codons from leucine to threonine. Our data show that MST1 recognizes the anticodon loop in both tRNAs, but employs distinct recognition mechanisms. The size but not the sequence of the anticodon loop is critical for recognition, whereas the anticodon sequence is essential for aminoacylation of . The crystal structure of MST1 reveals that, while lacking the N-terminal editing domain, the enzyme closely resembles the bacterial threonyl-tRNA synthetase (ThrRS). A detailed structural comparison with Escherichia coli ThrRS, which is unable to aminoacylate , reveals differences in the anticodon-binding domain that probably allow recognition of the distinct anticodon loops. Finally, our mutational and modeling analyses identify the structural elements in MST1 (e.g., helix alpha11) that define tRNA selectivity. Thus, MTS1 exemplifies that a single aaRS can recognize completely divergent anticodon loops of natural isoacceptor tRNAs and that in doing so it facilitates the reassignment of the genetic code in yeast mitochondria.
-Yeast mitochondrial threonyl-tRNA synthetase recognizes tRNA isoacceptors by distinct mechanisms and promotes CUN codon reassignment.,Ling J, Peterson KM, Simonovic I, Cho C, Soll D, Simonovic M Proc Natl Acad Sci U S A. 2012 Feb 17. PMID:22343532<ref>PMID:22343532</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+==See Also==
-</div>
+*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Threonine--tRNA ligase]]
+[[Category: Large Structures]]
-[[Category: Cho, C]]
+[[Category: Saccharomyces cerevisiae S288C]]
-[[Category: Ling, J]]
+[[Category: Cho C]]
-[[Category: Peterson, K M]]
+[[Category: Ling J]]
-[[Category: Simonovic, I]]
+[[Category: Peterson KM]]
-[[Category: Simonovic, M]]
+[[Category: Simonovic I]]
-[[Category: Soll, D]]
+[[Category: Simonovic M]]
-[[Category: Aminoacyl-trna synthetase class ii]]
+[[Category: Soll D]]
-[[Category: Ligase]]
-[[Category: Threonine trna]]
-[[Category: Threonyl-trna synthetase]]
-[[Category: Trna]]