1RIQ

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • Also Cited By: 1YGB, 1YFT, 1YFS, 1YFR

  • 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 ...

    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.


    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alanyl-tRNA synthetase
A
465Aquifex aeolicus (strain VF5)Mutation(s): 0 
Gene Names: alaS
EC: 6.1.1.7
Find proteins for O67323 (Aquifex aeolicus (strain VF5))
Go to UniProtKB:  O67323
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.207 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 74.890α = 90.00
b = 74.890β = 90.00
c = 179.950γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
HKL-2000data collection
SHARPphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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