Alanyl-tRNA synthetase crystal structure and design for acceptor-stem recognition

Mol Cell. 2004 Mar 26;13(6):829-41. doi: 10.1016/s1097-2765(04)00126-1.


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.

Publication types

  • Comparative Study
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Alanine-tRNA Ligase / chemistry*
  • Alanine-tRNA Ligase / genetics
  • Amino Acid Motifs
  • Amino Acid Sequence
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / genetics
  • Base Pairing
  • Binding Sites
  • Cloning, Molecular
  • Crystallography, X-Ray
  • Escherichia coli / enzymology
  • Escherichia coli / genetics
  • Hydrophobic and Hydrophilic Interactions
  • Kinetics
  • Models, Molecular
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • RNA, Bacterial / metabolism
  • Sequence Homology, Amino Acid
  • Substrate Specificity


  • Bacterial Proteins
  • RNA, Bacterial
  • Alanine-tRNA Ligase

Associated data

  • PDB/1RIQ