1GTR | pdb_00001gtr

STRUCTURAL BASIS OF ANTICODON LOOP RECOGNITION BY GLUTAMINYL-TRNA SYNTHETASE

• PDB DOI: https://doi.org/10.2210/pdb1GTR/pdb
• NAKB: 1GTR

• Classification: COMPLEX (LIGASE/TRNA)
• Organism(s): Escherichia coli
• Mutation(s): No 


• Deposited: 1993-09-15 Released: 1995-02-07 
• Deposition Author(s): Rould, M.A., Perona, J.J., Steitz, T.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work: 
  0.210 (Depositor) 
• R-Value Observed: 
  0.210 (Depositor) 

Literature

Structural basis of anticodon loop recognition by glutaminyl-tRNA synthetase.

Rould, M.A., Perona, J.J., Steitz, T.A.

(1991) Nature 352: 213-218

• PubMed: 1857417 
• DOI: https://doi.org/10.1038/352213a0
• Primary Citation Related Structures: 
  1GTR


• PubMed Abstract: 
  

  The refined crystal structure of Escherichia coli glutaminyl transfer RNA synthetase complexed with transfer RNA(Gln) and ATP reveals that the structure of the anticodon loop of the enzyme-bound tRNA(Gln) differs extensively from that of the known crystal structures of uncomplexed tRNA molecules. The anticodon stem is extended by two non-Watson-Crick base pairs, leaving the three anti-codon bases unpaired and splayed out to bind snugly into three separate complementary pockets in the protein. These interactions suggest that the entire anticodon loop provides essential sites for glutaminyl tRNA synthetase discrimination among tRNA molecules.

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Organizational Affiliation: 
• Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 87.7 kDa 
• Atom Count: 6,114 
• Modeled Residue Count: 603 
• Deposited Residue Count: 627 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GLUTAMINYL-tRNA SYNTHETASE	B [auth A]	553	Escherichia coli	Mutation(s): 0  EC: 6.1.1.18
UniProt
Find proteins for P00962 (Escherichia coli (strain K12)) Explore P00962  Go to UniProtKB:  P00962

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (74-MER)	A [auth B]	74	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	C [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work:  0.210 (Depositor) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 242.8	α = 90
b = 94.3	β = 90
c = 115.8	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1995-02-07 
Deposition Author(s): Rould, M.A., Perona, J.J., Steitz, T.A.

Revision History  

• Version 1.0: 1995-02-07
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-11-16
  Changes: Atomic model
• Version 1.4: 2024-02-07
  Changes: Data collection, Database references, Derived calculations, Other