Crystal structure of glycyl-tRNA synthetase from Thermus thermophilus.

Abstract

The sequence and crystal structure at 2.75 A resolution of the homodimeric glycyl‐tRNA synthetase from Thermus thermophilus, the first representative of the last unknown class II synthetase subgroup, have been determined. The three class II synthetase sequence motifs are present but the structure was essential for identification of motif 1, which does not possess the proline previously believed to be an essential class II invariant. Nevertheless, crucial contacts with the active site of the other monomer involving motif 1 are conserved and a more comprehensive description of class II now becomes possible. Each monomer consists of an active site strongly resembling that of the aspartyl and seryl enzymes, a C‐terminal anticodon recognition domain of 100 residues and a third domain unusually inserted between motifs 1 and 2 almost certainly interacting with the acceptor arm of tRNA(Gly). The C‐terminal domain has a novel five‐stranded parallel‐antiparallel beta‐sheet structure with three surrounding helices. The active site residues most probably responsible for substrate recognition, in particular in the Gly binding pocket, can be identified by inference from aspartyl‐tRNA synthetase due to the conserved nature of the class II active site.

The Accessory Subunit of Xenopus laevis Mitochondrial DNA Polymerase γ Increases Processivity of the Catalytic Subunit of Human DNA Polymerase γ and Is Related to Class II Aminoacyl-tRNA Synthetases

“…Class II enzymes contain a seven-stranded antiparallel ␤-sheet motif (18). Three sequence motifs have been identified in class II aminoacyl-tRNA synthetases.…”

“…The fact that the regions of aminoacyl-tRNA synthetases that are conserved as functional domains show the greatest similarity to pol ␥B is striking and may suggest a functional relationship between both types of proteins. It will be interesting to determine whether the structure of X. laevis DNA pol ␥B is similar to the known structure of T. thermophilus glycyl-tRNA synthetase (18).…”

Glycyl‐tRNA synthetase from Thermus thermophilus

“…The variability of this Pro in Gly-tRNA synthetases is puzzling. In yeast Asp-tRNA synthetase, this residue is implicated in subunit association and determines the active conformation of the mononucleotide-binding site through sion angles around Ser67 closely imitate those of Pro [49]. The stabilization of flexible residues in the loop between the two β preference for a small oxygen-containing side chains can be strands of motif 2 [65].…”

“…The GC content of 65.7% geneity of the enzyme was at least of 95% as judged by SDS/ is slightly lower than the overall content in Thermus DNA PAGE and high quality crystals were obtained with similar char-(69% ; [33]). Codons with G or C at the third position are clearly acteristics as those prepared from enzyme isolated from T. preferred, since out of the 507 codons only 39 contain A or T thermophilus [48,49]. at this position.…”

Crystallization of threonyl‐tRNA synthetase from Thermus thermophilus and preliminary crystallographic data

“…TRS constitutes with the aaRS specific for serine (SRS), proline (PRS), histidine (HRS) and glycine (GRS) a subgroup of closely related enzymes (subclass 2a) according to strong sequence homologies in the active site [5,6]. In addition, X-ray structures of three members of this subclass have been determined: SRS from Escherichia coli [7], GRS from T. thermophilus [8] and HRS from E. coli [9], confirming the existence of a modular organization of these enzymes already observed for other aaRS [5]. However, TRS differs from the other subclass members by its larger size due to a particularly substantial N-terminal module comprising 45% of the whole protein weight which is conserved through evolution [10].…”