1QF6 | pdb_00001qf6

STRUCTURE OF E. COLI THREONYL-TRNA SYNTHETASE COMPLEXED WITH ITS COGNATE TRNA

• PDB DOI: https://doi.org/10.2210/pdb1QF6/pdb
• NAKB: 1QF6

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


• Deposited: 1999-04-06 Released: 1999-05-06 
• Deposition Author(s): Sankaranarayanan, R., Dock-Bregeon, A.C., Rees, B., Moras, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.239 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.190 (DCC) 

Literature

The structure of threonyl-tRNA synthetase-tRNA(Thr) complex enlightens its repressor activity and reveals an essential zinc ion in the active site

Sankaranarayanan, R., Dock-Bregeon, A.C., Romby, P., Caillet, J., Springer, M., Rees, B., Ehresmann, C., Ehresmann, B., Moras, D.

(1999) Cell 97: 371-381

• PubMed: 10319817 
• DOI: https://doi.org/10.1016/s0092-8674(00)80746-1
• Primary Citation of Related Structures:  
  1QF6


• PubMed Abstract: 
  

  E. coli threonyl-tRNA synthetase (ThrRS) is a class II enzyme that represses the translation of its own mRNA. We report the crystal structure at 2.9 A resolution of the complex between tRNA(Thr) and ThrRS, whose structural features reveal novel strategies for providing specificity in tRNA selection. These include an amino-terminal domain containing a novel protein fold that makes minor groove contacts with the tRNA acceptor stem. The enzyme induces a large deformation of the anticodon loop, resulting in an interaction between two adjacent anticodon bases, which accounts for their prominent role in tRNA identity and translational regulation. A zinc ion found in the active site is implicated in amino acid recognition/discrimination.

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Organizational Affiliation: 

UPR 9004 Biologie Structurale, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, Illkirch, France.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 99.17 kDa 
• Atom Count: 7,093 
• Modeled Residue Count: 717 
• Deposited Residue Count: 718 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
THREONYL-TRNA SYNTHETASE	B [auth A]	642	Escherichia coli	Mutation(s): 0  EC: 6.1.1.3
UniProt
Find proteins for P0A8M3 (Escherichia coli (strain K12)) Explore P0A8M3  Go to UniProtKB:  P0A8M3

Entity ID: 1
Molecule	Chains	Length	Organism	Image
THREONINE TRNA	A [auth B]	76	Escherichia coli

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	D [auth A]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.239 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.190 (DCC) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 162.67	α = 90
b = 162.67	β = 90
c = 128.57	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CCP4	model building
CNS	refinement
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-05-06 
Deposition Author(s): Sankaranarayanan, R., Dock-Bregeon, A.C., Rees, B., Moras, D.

Revision History  

• Version 1.0: 1999-05-06
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations