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4jxz

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==Structure of E. coli glutaminyl-tRNA synthetase bound to ATP and a tRNA(Gln) acceptor containing a UUG anticodon==
==Structure of E. coli glutaminyl-tRNA synthetase bound to ATP and a tRNA(Gln) acceptor containing a UUG anticodon==
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<StructureSection load='4jxz' size='340' side='right' caption='[[4jxz]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
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<StructureSection load='4jxz' size='340' side='right'caption='[[4jxz]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4jxz]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JXZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JXZ FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4jxz]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JXZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JXZ FirstGlance]. <br>
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</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>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4jxx|4jxx]], [[4jyz|4jyz]]</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=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">glnS, b0680, JW0666 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=4jxz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jxz OCA], [https://pdbe.org/4jxz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jxz RCSB], [https://www.ebi.ac.uk/pdbsum/4jxz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jxz ProSAT]</span></td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glutamine--tRNA_ligase Glutamine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.18 6.1.1.18] </span></td></tr>
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<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=4jxz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jxz OCA], [http://pdbe.org/4jxz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4jxz RCSB], [http://www.ebi.ac.uk/pdbsum/4jxz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4jxz ProSAT]</span></td></tr>
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</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/SYQ_ECOLI SYQ_ECOLI]
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The 2-thiouridine (s2U) at the wobble position of certain bacterial and eukaryotic tRNAs enhances aminoacylation kinetics, assists proper codon-anticodon base pairing at the ribosome A-site, and prevents frameshifting during translation. By mass spectrometry of affinity-purified native Escherichia coli tRNA1GlnUUG, we show that the complete modification at the wobble position 34 is 5-carboxyaminomethyl-2-thiouridine (cmnm5s2U). The crystal structure of E. coli glutaminyl-tRNA synthetase (GlnRS) bound to native tRNA1Gln and ATP demonstrates that cmnm5s2U34 improves the order of a previously unobserved 11-amino-acid surface loop in the distal beta-barrel domain of the enzyme and imparts other local rearrangements of nearby amino acids that create a binding pocket for the 2-thio moiety. Together with previously solved structures, these observations explain the degenerate recognition of C34 and modified U34 by GlnRS. Comparative pre-steady-state aminoacylation kinetics of native tRNA1Gln, synthetic tRNA1Gln containing s2U34 as sole modification, and unmodified wild-type and mutant tRNA1Gln and tRNA2Gln transcripts demonstrates that the exocyclic sulfur moiety improves tRNA binding affinity to GlnRS 10-fold compared with the unmodified transcript and that an additional fourfold improvement arises from the presence of the cmnm5 moiety. Measurements of Gln-tRNAGln interactions at the ribosome A-site show that the s2U modification enhances binding affinity to the glutamine codons CAA and CAG and increases the rate of GTP hydrolysis by E. coli EF-Tu by fivefold.
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Structural and Mechanistic Basis for Enhanced Translational Efficiency by 2-Thiouridine at the tRNA Anticodon Wobble Position.,Rodriguez-Hernandez A, Spears JL, Gaston KW, Limbach PA, Gamper H, Hou YM, Kaiser R, Agris PF, Perona JJ J Mol Biol. 2013 May 28. pii: S0022-2836(13)00332-X. doi:, 10.1016/j.jmb.2013.05.018. PMID:23727144<ref>PMID:23727144</ref>
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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 4jxz" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
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*[[TRNA|TRNA]]
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*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
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== References ==
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*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Ecoli]]
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[[Category: Escherichia coli K-12]]
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[[Category: Glutamine--tRNA ligase]]
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[[Category: Large Structures]]
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[[Category: Perona, J J]]
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[[Category: Synthetic construct]]
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[[Category: Rodriguez-Hernandez, A]]
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[[Category: Perona JJ]]
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[[Category: Ligase-rna complex]]
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[[Category: Rodriguez-Hernandez A]]
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[[Category: Protein translation]]
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[[Category: Protein-rna complex]]
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[[Category: Rossmann fold]]
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[[Category: Trna aminoacylation]]
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Current revision

Structure of E. coli glutaminyl-tRNA synthetase bound to ATP and a tRNA(Gln) acceptor containing a UUG anticodon

PDB ID 4jxz

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