1EXD

CRYSTAL STRUCTURE OF A TIGHT-BINDING GLUTAMINE TRNA BOUND TO GLUTAMINE AMINOACYL TRNA SYNTHETASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Tertiary core rearrangements in a tight binding transfer RNA aptamer.

Bullock, T.L.Sherlin, L.D.Perona, J.J.

(2000) Nat.Struct.Mol.Biol. 7: 497-504

  • DOI: 10.1038/75910

  • PubMed Abstract: 
  • Guided by an in vitro selection experiment designed to obtain tight binding aptamers of Escherichia coli glutamine specific tRNA (tRNAGln) for glutaminyl-tRNA synthetase (GlnRS), we have engineered a tRNA mutant in which the five-nucleotide variable ...

    Guided by an in vitro selection experiment designed to obtain tight binding aptamers of Escherichia coli glutamine specific tRNA (tRNAGln) for glutaminyl-tRNA synthetase (GlnRS), we have engineered a tRNA mutant in which the five-nucleotide variable loop sequence 5'-44CAUUC48-3' is replaced by 5'-44AGGU48-3'. This mutant tRNA binds to GlnRS with 30-fold improved affinity compared to the wild type. The 2.7 A cocrystal structure of the RNA aptamer-GlnRS complex reveals major rearrangements in the central tertiary core of the tRNA, while maintaining an RNA-protein interface identical to the wild type. The repacked RNA core features a novel hydrogen bonding arrangement of the trans Levitt pair G15-U48, a new sulfate binding pocket in the major groove, and increased hydrophobic stacking interactions among the bases. These data suggest that enhanced protein binding to a mutant globular RNA can arise from stabilization of RNA tertiary interactions rather than optimization of RNA-protein contacts.


    Organizational Affiliation

    Department of Chemistry and Biochemistry and Interdepartmental Program in Biochemistry and Molecular Biology, University of California at Santa Barbara, 93106-9510, USA.




Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
GLUTAMINYL-TRNA SYNTHETASE
A
548Escherichia coli (strain K12)Gene Names: glnS
EC: 6.1.1.18
Find proteins for P00962 (Escherichia coli (strain K12))
Go to UniProtKB:  P00962
Entity ID: 1
MoleculeChainsLengthOrganism
GLUTAMINE TRNA APTAMERB73N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
A
Query on A

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Download CCD File 
A
ADENOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.216 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 236.940α = 90.00
b = 93.980β = 90.00
c = 113.910γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
CCP4data scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-05-15
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance