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{{STRUCTURE_4jyz|  PDB=4jyz  |  SCENE=  }}
===Crystal structure of E. coli glutaminyl-tRNA synthetase bound to ATP and native tRNA(Gln) containing the cmnm5s2U34 anticodon wobble base===


==About this Structure==
==Crystal structure of E. coli glutaminyl-tRNA synthetase bound to ATP and native tRNA(Gln) containing the cmnm5s2U34 anticodon wobble base==
[[4jyz]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JYZ OCA].  
<StructureSection load='4jyz' size='340' side='right'caption='[[4jyz]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[4jyz]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JYZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JYZ FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1RN:(E)-N-{[4-OXO-1-(5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-2-THIOXO-1,2,3,4-TETRAHYDROPYRIMIDIN-5-YL]METHYLIDENE}GLYCINE'>1RN</scene>, <scene name='pdbligand=2MA:2-METHYLADENOSINE-5-MONOPHOSPHATE'>2MA</scene>, <scene name='pdbligand=4SU:4-THIOURIDINE-5-MONOPHOSPHATE'>4SU</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=4jyz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jyz OCA], [https://pdbe.org/4jyz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jyz RCSB], [https://www.ebi.ac.uk/pdbsum/4jyz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jyz ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/SYQ_ECOLI SYQ_ECOLI]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.
 
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>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4jyz" style="background-color:#fffaf0;"></div>
 
==See Also==
*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Escherichia coli k-12]]
[[Category: Escherichia coli K-12]]
[[Category: Glutamine--tRNA ligase]]
[[Category: Large Structures]]
[[Category: Perona, J J.]]
[[Category: Perona JJ]]
[[Category: Rodriguez-Hernandez, A.]]
[[Category: Rodriguez-Hernandez A]]
[[Category: Aminoacyl-trna synthetase]]
[[Category: Ligase]]
[[Category: Ligase-rna complex]]
[[Category: Protein-rna complex]]
[[Category: Rossmann fold]]
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