4jxz: Difference between revisions
No edit summary |
No edit summary |
||
| Line 1: | Line 1: | ||
==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== | ||
<StructureSection load='4jxz' size='340' side='right' caption='[[4jxz]], [[Resolution|resolution]] 2.40Å' scene=''> | <StructureSection load='4jxz' size='340' side='right'caption='[[4jxz]], [[Resolution|resolution]] 2.40Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4jxz]] is a 2 chain structure with sequence from [ | <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> | ||
</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><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> | ||
<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> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/SYQ_ECOLI SYQ_ECOLI] | |||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
| Line 21: | Line 20: | ||
==See Also== | ==See Also== | ||
*[[ | *[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]] | ||
*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Escherichia coli K-12]] | ||
[[Category: Large Structures]] | |||
[[Category: | [[Category: Synthetic construct]] | ||
[[Category: | [[Category: Perona JJ]] | ||
[[Category: | [[Category: Rodriguez-Hernandez A]] | ||
[[Category: | |||
Revision as of 14:30, 30 November 2022
Structure of E. coli glutaminyl-tRNA synthetase bound to ATP and a tRNA(Gln) acceptor containing a UUG anticodonStructure of E. coli glutaminyl-tRNA synthetase bound to ATP and a tRNA(Gln) acceptor containing a UUG anticodon
Structural highlights
FunctionPublication Abstract from PubMedThe 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
|
| ||||||||||||||||