The 2.9 Å Crystal Structure of T. thermophilus Seryl-tRNA Synthetase Complexed with tRNA ^Ser

Abstract

The crystal structure of Thermus thermophilus seryl-transfer RNA synthetase, a class 2 aminoacyl-tRNA synthetase, complexed with a single tRNA(Ser) molecule was solved at 2.9 A resolution. The structure revealed how insertion of conserved base G20b from the D loop into the core of the tRNA determines the orientation of the long variable arm, which is a characteristic feature of most serine specific tRNAs. On tRNA binding, the antiparallel coiled-coil domain of one subunit of the synthetase makes contacts with the variable arm and T psi C loop of the tRNA and directs the acceptor stem of the tRNA into the active site of the other subunit. Specificity depends principally on recognition of the shape of tRNA(Ser) through backbone contacts and secondarily on sequence specific interactions.

α-Helical Protein Assembly Motifs

“…Examples of interchain dimerization to form antiparallel coiled-coils are observed in the crystal structures of the replication terminator protein of B. subtilis (20) and pilin protein of N. gonorrhoeae (21). Examples of the more common intrachain antiparallel coiled-coils have been found in several enzymes, including bacterial seryl-tRNA synthetase (22), the GreA transcript cleavage factor of E. coli (23), and the T-cell protein tyrosine kinase ZAP-70 (24). The simplicity of the dimeric coiled-coil structure makes it an ideal system to use in understanding the fundamentals of protein folding and stability and in testing the principles of de novo design for a wide range of medical applications (4).…”

Yeast mitochondrial threonyl-tRNA synthetase recognizes tRNA isoacceptors by distinct mechanisms and promotes CUN codon reassignment

“…in a manner resembling AlaRS and SerRS (11,12). Surprisingly, mutational and biochemical results show that the anticodon loops of both tRNA Thr species are recognized by S. cerevisiae MST1.…”

“…The major identity elements reside in the anticodon loop and the amino acid acceptor stem of tRNA (9). Except for tRNA Ala (11) and tRNA Ser (12), mutations in the anticodon loop result in significant loss of aminoacylation efficiency (9), suggesting that the isoacceptor tRNAs must carry similar anticodon loops or else they would not be recognized by a given aaRS.…”

Unique protein architecture of alanyl-tRNA synthetase for aminoacylation, editing, and dimerization

“…Discussion tRNA Interactions. In the crystal structures of tRNA-bound class-II aaRSs, including ThrRS, seryl-tRNA synthetase, and aspartyl-tRNA synthetase, the amino acid acceptor arm of the tRNA binds to a common site on the class II aminoacylation domain (20,36,37). The binding site corresponds to the groove formed between Mid1 and Mid2 in the tRNA-recognition domain of A. fulgidus AlaRS.…”