Tryptophanyl-tRNA synthetase from Bacillus subtilis. Characterization and role of hydrophobicity in substrate recognition

J Biol Chem. 1989 Mar 15;264(8):4304-11.


The tryptophanyl-tRNA synthetase from Bacillus subtilis was purified to homogeneity and characterized. It has an alpha 2 subunit structure and a molecular weight of 77,000. Tryptophanyl-tRNA synthetase does not catalyze any significant proofreading. It activates tryptophan as well as the three fluorinated analogues, DL-4-fluoro-, DL-5-fluoro-, or DL-6-fluorotryptophan (4F-, 5F-, and 6F-Trp), in the ATP-pyrophosphate exchange reaction. In the aminoacylation reaction, the fluorotryptophans act as competitive inhibitors of Trp. Their relative activities follow the same order in both reactions: Trp greater than 4F-Trp greater than 6F-Trp greater than 5F-Trp. This order is the inverse of the order of relative hydrophobicities of these compounds, pointing to the importance of hydrophobic interactions in the selective recognition by tryptophanyl-tRNA synthetase among this group of substrates. To define the physical basis of the relative hydrophobicities, the crystallographic structure of 4F-Trp was determined and compared to that of trptophan. Charge distributions calculated for tryptophan and its different fluoroanalogues on the basis of molecular structures were supported by their carbon-13 NMR spectra. Correlations between charge distributions and relative hydrophobicities suggest that the polarity of the C-F bond represents an underlying factor determining the hydrophobicities of 4F-, 5F-, and 6F-Trp, thus relating tryptophanyl-tRNA synthetase selectivity toward tryptophan and its fluoroanalogues directly to their electronic configurations.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine Monophosphate / metabolism
  • Adenosine Triphosphate / metabolism
  • Amino Acid Sequence
  • Amino Acyl-tRNA Synthetases / metabolism*
  • Bacillus subtilis / enzymology*
  • Binding, Competitive
  • Chemical Phenomena
  • Chemistry, Physical
  • Hydrogen-Ion Concentration
  • Kinetics
  • Molecular Sequence Data
  • Molecular Weight
  • Phosphates / metabolism
  • RNA, Transfer, Trp / metabolism
  • Tryptophan / analogs & derivatives
  • Tryptophan / metabolism
  • Tryptophan-tRNA Ligase / antagonists & inhibitors
  • Tryptophan-tRNA Ligase / metabolism*
  • X-Ray Diffraction


  • Phosphates
  • RNA, Transfer, Trp
  • 4-fluorotryptophan
  • 5-fluorotryptophan
  • 6-fluorotryptophan
  • Adenosine Monophosphate
  • Tryptophan
  • Adenosine Triphosphate
  • Amino Acyl-tRNA Synthetases
  • Tryptophan-tRNA Ligase