1NYL | pdb_00001nyl

Unliganded glutaminyl-tRNA synthetase

• PDB DOI: https://doi.org/10.2210/pdb1NYL/pdb

• Classification: LIGASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-02-12 Released: 2003-02-25 
• Deposition Author(s): Sherlin, L.D., Perona, J.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.327 (Depositor) 
• R-Value Work: 
  0.251 (Depositor), 0.252 (DCC) 
• R-Value Observed: 
  0.251 (Depositor) 

Literature

tRNA-Dependent Active Site Assembly in a Class I Aminoacyl-tRNA Synthetase.

Sherlin, L.D., Perona, J.J.

(2003) Structure 11: 591-603

• PubMed: 12737824 
• DOI: https://doi.org/10.1016/s0969-2126(03)00074-1
• Primary Citation Related Structures: 
  1NYL


• PubMed Abstract: 
  

  The crystal structure of ligand-free E. coli glutaminyl-tRNA synthetase (GlnRS) at 2.4 A resolution shows that substrate binding is essential to construction of a catalytically proficient active site. tRNA binding generates structural changes throughout the enzyme, repositioning key active site peptides that bind glutamine and ATP. The structure gives insight into longstanding questions regarding the tRNA dependence of glutaminyl adenylate formation, the coupling of amino acid and tRNA selectivities, and the roles of specific pathways for transmission of tRNA binding signals to the active site. Comparative analysis of the unliganded and tRNA-bound structures shows, in detail, how flexibility is built into the enzyme architecture and suggests that the induced-fit transitions are a key underlying determinant of both amino acid and tRNA specificity.

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Organizational Affiliation: 
• Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 61.92 kDa 
• Atom Count: 4,240 
• Modeled Residue Count: 523 
• Deposited Residue Count: 539 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutaminyl-tRNA synthetase	A	539	Escherichia coli	Mutation(s): 0  Gene Names: glnS EC: 6.1.1.18
UniProt
Find proteins for P00962 (Escherichia coli (strain K12)) Explore P00962  Go to UniProtKB:  P00962

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.327 (Depositor) 
• R-Value Work:  0.251 (Depositor), 0.252 (DCC) 
• R-Value Observed: 0.251 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.4	α = 90
b = 64.12	β = 90
c = 208.88	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-02-25 
Deposition Author(s): Sherlin, L.D., Perona, J.P.

Revision History  

• Version 1.0: 2003-02-25
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Structure summary