Biological Assembly 1  

 3D View: Structure | Electron Density

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 54.15 kDa 
• Atom Count: 3977 
• Modelled Residue Count: 448 
• Deposited Residue Count: 465 
• Unique protein chains: 1

1RIQ

The crystal structure of the catalytic fragment of the alanyl-tRNA synthetase

• DOI: 10.2210/pdb1RIQ/pdb

• Classification: LIGASE
• Organism(s): Aquifex aeolicus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-11-17 Released: 2004-04-06 
• Deposition Author(s): Swairjo, M.A., Otero, F.J., Yang, X.-L., Lovato, M.A., Skene, R.J., McRee, D.E., Ribas de Pouplana, L., Schimmel, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 0.251 
• R-Value Work: 0.207 
• R-Value Observed: 0.207 

Literature

Alanyl-tRNA Synthetase Crystal Structure and Design for Acceptor-Stem Recognition

Swairjo, M.A., Otero, F.J., Yang, X.-L., Lovato, M.A., Skene, R.J., McRee, D.E., Ribas De Pouplana, L., Schimmel, P.

(2004) Mol Cell 13: 829-841

• PubMed: 15053876 
• DOI: 10.1016/s1097-2765(04)00126-1
• Primary Citation of Related Structures:  
  1RIQ


• PubMed Abstract: 
  

Early work on aminoacylation of alanine-specific tRNA (tRNA(Ala)) by alanyl-tRNA synthetase (AlaRS) gave rise to the concept of an early "second genetic code" imbedded in the acceptor stems of tRNAs. A single conserved and position-specific G:U base pair in the tRNA acceptor stem is the key identity determinant. Further understanding has been limited due to lack of a crystal structure of the enzyme. We determined a 2.14 A crystal structure of the 453 amino acid catalytic fragment of Aquifex aeolicus AlaRS. It contains the catalytic domain characteristic of class II synthetases, a helical domain with a hairpin motif critical for acceptor-stem recognition, and a C-terminal domain of a mixed alpha/beta fold. Docking of tRNA(Ala) on AlaRS shows critical contacts with the three domains, consistent with previous mutagenesis and functional data. It also suggests conformational flexibility within the C domain, which might allow for the positional variation of the key G:U base pair seen in some tRNA(Ala)s.

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Organizational Affiliation: 

Skaags Institute for Chemical Biology, Departments of Molecular Biology and Chemistry, The Scripps Research Institute, BCC-379, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alanyl-tRNA synthetase	A	465	Aquifex aeolicus	Mutation(s): 8  Gene Names: alaS, aq_1293 EC: 6.1.1.7
UniProt
Find proteins for O67323 (Aquifex aeolicus (strain VF5)) Explore O67323  Go to UniProtKB:  O67323

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 0.251 
• R-Value Work: 0.207 
• R-Value Observed: 0.207 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.89	α = 90
b = 74.89	β = 90
c = 179.95	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
SHARP	phasing
CNS	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-11-17 
• Released Date: 2004-04-06 
Deposition Author(s): Swairjo, M.A., Otero, F.J., Yang, X.-L., Lovato, M.A., Skene, R.J., McRee, D.E., Ribas de Pouplana, L., Schimmel, P.

Revision History  

• Version 1.0: 2004-04-06
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance