4JYZ

Crystal structure of E. coli glutaminyl-tRNA synthetase bound to ATP and native tRNA(Gln) containing the cmnm5s2U34 anticodon wobble base


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and Mechanistic Basis for Enhanced Translational Efficiency by 2-Thiouridine at the tRNA Anticodon Wobble Position.

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.

(2013) J.Mol.Biol. 425: 3888-3906

  • DOI: 10.1016/j.jmb.2013.05.018
  • Primary Citation of Related Structures:  

  • 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 sp ...

    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.


    Organizational Affiliation

    Department of Chemistry, Portland State University, PO Box 751, Portland, OR 97207, USA; Department of Biochemistry and Molecular Biology, Oregon Health and Sciences University, 3181 Southwest Sam Jackson Park Road, Portland, OR 97239, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamine--tRNA ligase
A
553Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: glnS
EC: 6.1.1.18
Find proteins for P00962 (Escherichia coli (strain K12))
Go to UniProtKB:  P00962
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (72-MER)B75Escherichia coli
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  8 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
B
RNA LINKINGC9 H13 N2 O9 PU
OMU
Query on OMU
B
RNA LINKINGC10 H15 N2 O9 PU
1RN
Query on 1RN
B
RNA LINKINGC12 H16 N3 O10 P SU
4SU
Query on 4SU
B
RNA LINKINGC9 H13 N2 O8 P SU
OMG
Query on OMG
B
RNA LINKINGC11 H16 N5 O8 PG
5MU
Query on 5MU
B
RNA LINKINGC10 H15 N2 O9 PU
2MA
Query on 2MA
B
RNA LINKINGC11 H16 N5 O7 PA
H2U
Query on H2U
B
RNA LINKINGC9 H15 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.234 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 93.400α = 90.00
b = 234.620β = 90.00
c = 113.700γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
d*TREKdata reduction
CNSphasing
StructureStudiodata collection
d*TREKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-29
    Type: Initial release
  • Version 1.1: 2013-08-21
    Type: Database references
  • Version 1.2: 2013-10-23
    Type: Database references