3G98 | pdb_00003g98

Crystal Structure of the C-Ala domain from Aquifex aeolicus alanyl-tRNA synthetase

• PDB DOI: https://doi.org/10.2210/pdb3G98/pdb

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


• Deposited: 2009-02-13 Released: 2009-10-06 
• Deposition Author(s): Guo, M., Yang, X.L., Schimmel, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.219 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Literature

The C-Ala domain brings together editing and aminoacylation functions on one tRNA.

Guo, M., Chong, Y.E., Beebe, K., Shapiro, R., Yang, X.L., Schimmel, P.

(2009) Science 325: 744-747

• PubMed: 19661429 
• DOI: https://doi.org/10.1126/science.1174343
• Primary Citation Related Structures: 
  3G98


• PubMed Abstract: 
  

  Protein synthesis involves the accurate attachment of amino acids to their matching transfer RNA (tRNA) molecules. Mistranslating the amino acids serine or glycine for alanine is prevented by the function of independent but collaborative aminoacylation and editing domains of alanyl-tRNA synthetases (AlaRSs). We show that the C-Ala domain plays a key role in AlaRS function. The C-Ala domain is universally tethered to the editing domain both in AlaRS and in many homologous free-standing editing proteins. Crystal structure and functional analyses showed that C-Ala forms an ancient single-stranded nucleic acid binding motif that promotes cooperative binding of both aminoacylation and editing domains to tRNA(Ala). In addition, C-Ala may have played an essential role in the evolution of AlaRSs by coupling aminoacylation to editing to prevent mistranslation.

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Organizational Affiliation: 
• The Skaggs Institute for Chemical Biology and the Department of Molecular Biology, The Scripps Research Institute, BCC-379, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 24.32 kDa 
• Atom Count: 1,857 
• Modeled Residue Count: 222 
• Deposited Residue Count: 222 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alanyl-tRNA synthetase	A, B	111	Aquifex aeolicus	Mutation(s): 0  Gene Names: alaS EC: 6.1.1.7
UniProt
Find proteins for O67323 (Aquifex aeolicus (strain VF5)) Explore O67323  Go to UniProtKB:  O67323

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.219 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.74	α = 90
b = 54.506	β = 90
c = 66.256	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
SOLVE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-06 
Deposition Author(s): Guo, M., Yang, X.L., Schimmel, P.

Revision History  

• Version 1.0: 2009-10-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references