1C0A

CRYSTAL STRUCTURE OF THE E. COLI ASPARTYL-TRNA SYNTHETASE : TRNAASP : ASPARTYL-ADENYLATE COMPLEX

• PDB DOI:  https://doi.org/10.2210/pdb1C0A/pdb
• NAKB: 1C0A

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


• Deposited: 1999-07-15 Released: 1999-11-23 
• Deposition Author(s): Eiler, S., Dock-Bregeon, A.-C., Moulinier, L., Thierry, J.-C., Moras, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.249 
• R-Value Work: 0.208 
• R-Value Observed: 0.208 

Literature

Synthesis of aspartyl-tRNA(Asp) in Escherichia coli--a snapshot of the second step.

Eiler, S., Dock-Bregeon, A., Moulinier, L., Thierry, J.C., Moras, D.

(1999) EMBO J 18: 6532-6541

• PubMed: 10562565 
• DOI: https://doi.org/10.1093/emboj/18.22.6532
• Primary Citation of Related Structures:  
  1C0A


• PubMed Abstract: 
  

The 2.4 A crystal structure of the Escherichia coli aspartyl-tRNA synthetase (AspRS)-tRNA(Asp)-aspartyl-adenylate complex shows the two substrates poised for the transfer of the aspartic acid moiety from the adenylate to the 3'-hydroxyl of the terminal adenosine of the tRNA. A general molecular mechanism is proposed for the second step of the aspartylation reaction that accounts for the observed conformational changes, notably in the active site pocket. The stabilization of the transition state is mediated essentially by two amino acids: the class II invariant arginine of motif 2 and the eubacterial-specific Gln231, which in eukaryotes and archaea is replaced by a structurally non-homologous serine. Two archetypal RNA-protein modes of interactions are observed: the anticodon stem-loop, including the wobble base Q, binds to the N-terminal beta-barrel domain through direct protein-RNA interactions, while the binding of the acceptor stem involves both direct and water-mediated hydrogen bonds in an original recognition scheme.

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Organizational Affiliation: 

UPR 9004, Laboratoire de Biologie Structurale, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 1 rue Laurent Fries, BP 163, 67404 Illkirch Cedex, C.U. de Strasbourg, France.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 91.34 kDa 
• Atom Count: 6,820 
• Modelled Residue Count: 662 
• Deposited Residue Count: 662 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ASPARTYL TRNA SYNTHETASE	B [auth A]	585	Escherichia coli	Mutation(s): 0  EC: 6.1.1.12
UniProt
Find proteins for P21889 (Escherichia coli (strain K12)) Explore P21889  Go to UniProtKB:  P21889

Entity ID: 1
Molecule	Chains	Length	Organism	Image
ASPARTYL TRNA	A [auth B]	77	Escherichia coli

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMO	E [auth A]	ASPARTYL-ADENOSINE-5'-MONOPHOSPHATE C14 H19 N6 O10 P QPBSGQWTJLPZNF-VWJPMABRSA-N
AMP	D [auth A]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
SO4	C [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.249 
• R-Value Work: 0.208 
• R-Value Observed: 0.208 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.2	α = 90
b = 101.2	β = 90
c = 231.81	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-11-23 
Deposition Author(s): Eiler, S., Dock-Bregeon, A.-C., Moulinier, L., Thierry, J.-C., Moras, D.

Revision History  

• Version 1.0: 1999-11-23
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance