Sequence determination and modeling of structural motifs for the smallest monomeric aminoacyl-tRNA synthetase

Polypeptide chains of 19 previously studied Escherichia coli aminoacyl-tRNA synthetases are as large as 951 amino acids and, depending on the enzyme, have quaternary structures of alpha, alpha 2, alpha 2 beta 2, and alpha 4. These enzymes have been organized into two classes which are defined by sequence motifs that are associated with specific three-dimensional structures. We isolated, cloned, and sequenced the previously uncharacterized gene for E. coli cysteine-tRNA synthetase (EC 6.1.1.16) and showed that it encodes a protein of 461 amino acids. Biochemical analysis established that the protein is a monomer, thus establishing this enzyme as the smallest known monomeric synthetase. The sequence shows that cysteine-tRNA synthetase is a class I enzyme that is most closely related to a subgroup that includes the much larger methionine-, isoleucine-, leucine-, and valine-tRNA synthetases, which range in size from 677 to 951 amino acids. The amino-terminal 293 amino acids of the cysteine enzyme can be modeled as a nucleotide-binding fold that is more compact than that of its closest relatives by virtue of truncations of two insertions that split the fold. This smaller nucleotide-binding fold accounts for much of the reduced size of the cysteine enzyme and establishes the limit to which the structure of this domain is contracted in the five members of this subgroup of class I enzymes.