4JXX

Crystal structure of E coli E. coli glutaminyl-tRNA synthetase bound to tRNA(Gln)(CUG) and ATP from novel cryostabilization conditions

Summary for 4JXX

• Entry DOI: 10.2210/pdb4jxx/pdb
• Related: 1GTR 4JXZ 4JYZ
• Descriptor: Glutamine--tRNA ligase, RNA (71-MER), ADENOSINE-5'-TRIPHOSPHATE, ... (5 entities in total)
• Functional Keywords: rossmann fold, protein-rna complex, transfer rna, trna aminoacylation, trna(gln), ligase-rna complex, ligase/rna
• Biological source: Escherichia coli
• Cellular location: Cytoplasm: P00962
• Total number of polymer chains: 2
• Total formula weight: 88098.17

Authors

Perona, J.J.,Rodriguez-Hernandez, A. (deposition date: 2013-03-28, release date: 2013-05-01, Last modification date: 2023-09-20)

Primary citation

Rodriguez-Hernandez, A.,Spears, J.L.,Gaston, K.W.,Limbach, P.A.,Gamper, H.,Hou, Y.M.,Kaiser, R.,Agris, P.F.,Perona, J.J.
Structural and Mechanistic Basis for Enhanced Translational Efficiency by 2-Thiouridine at the tRNA Anticodon Wobble Position.
J.Mol.Biol., 425:3888-3906, 2013

PubMed Abstract: The 2-thiouridine (s(2)U) 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 tRNA1(Gln)UUG, we show that the complete modification at the wobble position 34 is 5-carboxyaminomethyl-2-thiouridine (cmnm(5)s(2)U). The crystal structure of E. coli glutaminyl-tRNA synthetase (GlnRS) bound to native tRNA1(Gln) and ATP demonstrates that cmnm(5)s(2)U34 improves the order of a previously unobserved 11-amino-acid surface loop in the distal β-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 tRNA1(Gln), synthetic tRNA1(Gln) containing s(2)U34 as sole modification, and unmodified wild-type and mutant tRNA1(Gln) and tRNA2(Gln) 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 cmnm(5) moiety. Measurements of Gln-tRNA(Gln) interactions at the ribosome A-site show that the s(2)U 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.

PubMed: 23727144
DOI: 10.1016/j.jmb.2013.05.018

Experimental method

X-RAY DIFFRACTION (2.3 Å)