Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 99167.72 
• Atom Count: 6849 
• Residue Count: 718 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

1QF6

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

• DOI: 10.2210/pdb1QF6/pdb
• NDB: PR0006

• Classification: LIGASE/RNA
• Organism(s): Escherichia coli, Escherichia coli (strain K12)


• 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: 2.9 Å
• R-Value Free: 0.239 
• R-Value Work: 0.195 

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 


• 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.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
THREONYL-TRNA SYNTHETASE	A	642	Escherichia coli (strain K12)	Gene Names: thrS EC: 6.1.1.3
Find proteins for P0A8M3 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A8M3

Entity ID: 1
Molecule	Chains	Length	Organism
THREONINE TRNA	B	76	Escherichia coli

Small Molecules

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

Modified Residues  5 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PSU	B	RNA LINKING	C9 H13 N2 O9 P		U
G7M	B	RNA LINKING	C11 H17 N5 O8 P		G
AET	B	RNA LINKING	C16 H23 N6 O11 P		A
5MU	B	RNA LINKING	C10 H15 N2 O9 P		U
H2U	B	RNA LINKING	C9 H15 N2 O9 P		U

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.9 Å
• R-Value Free: 0.239 
• R-Value Work: 0.195 
• Space Group: P 3₁ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 162.670	α = 90.00
b = 162.670	β = 90.00
c = 128.570	γ = 120.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-04-06 
• 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
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance