Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 87057.48 
• Atom Count: 5872 
• Residue Count: 621 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

1EXD

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

• DOI: 10.2210/pdb1EXD/pdb
• NDB: PR0027

• Classification: ligase/RNA
• Organism(s): Escherichia coli (strain K12)
• Expression System: Escherichia coli


• Deposited: 2000-05-02 Released: 2000-05-15 
• Deposition Author(s): Bullock, T.L., Sherlin, L.D., Perona, J.J.

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Experimental Data Snapshot

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

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

• PubMed: 10881199 
• 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 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.

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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

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
GLUTAMINYL-TRNA SYNTHETASE	A	548	Escherichia 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: 1
Molecule	Chains	Length	Organism
GLUTAMINE TRNA APTAMER	B	73	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A, B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
A	A	ADENOSINE-5'-MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N

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 = 236.940	α = 90.00
b = 93.980	β = 90.00
c = 113.910	γ = 90.00

Software Package:

Software Name	Purpose
X-PLOR	refinement
CCP4	data scaling
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-05-02 
• Released Date: 2000-05-15 
• Deposition Author(s): Bullock, T.L., Sherlin, L.D., Perona, J.J.

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