Abstract: Three aminoacyl-tRNA synthetases from yeast, one from plants and one
from mammals possess unusual structures at their N termini, namely α
helices with basic residues distributed asymmetrically, on a single face of the
helix. It is unknown if these 'basic faced' α helices (BFAHs) are
unique to the aminoacyl-tRNA synthetases. Analysis of the amino acid sequences
of these five aminoacyl-tRNA synthetases using the hydrophobic moment algorithm
failed to accurately identify the BFAHs. A new algorithm was therefore
developed, called the 'basic moment'. This is a Fourier analysis procedure that
predicts the distribution of basic residues within protein secondary structure.
The basic moment identifies with a high degree of accuracy the five known BFAHs
and also identifies further potential BFAHs at evolutionarily conserved
positions in the peptide extensions of aspartyl-, lysyl- and valyl- tRNA
synthetases from a range of eukaryotic species. In addition, the algorithm
identifies the two-helix pair tRNA binding domain of alanyl-tRNA synthetase,
implying that the domain includes a BFAH. The functional and evolutionary
aspects of these structural features are discussed.
