No abstract

The 2.2 A Ê crystal structure of a ternary complex formed by yeast arginyl-tRNA synthetase and its cognate tRNA Arg in the presence of the L-arginine substrate highlights new atomic features used for speci®c substrate recognition. This ®rst example of an active complex formed by a class Ia aminoacyl-tRNA synthetase and its natural cognate tRNA illustrates additional strategies used for speci®c tRNA selection. The enzyme speci®cally recognizes the D-loop and the anticodon of the tRNA, and the mutually induced ®t produces a conformation of the anticodon loop never seen before. Moreover, the anticodon binding triggers conformational changes in the catalytic center of the protein. The comparison with the 2.9 A Ê structure of a binary complex formed by yeast arginyl-tRNA synthetase and tRNA Arg reveals that L-arginine binding controls the correct positioning of the CCA end of the tRNA Arg . Important structural changes induced by substrate binding are observed in the enzyme. Several key residues of the active site play multiple roles in the catalytic pathway and thus highlight the structural dynamics of the aminoacylation reaction.

The crystal structure of arginyl-tRNA synthetase (ArgRS) from Saccharomyces cerevisiae, a class I aminoacyl-tRNA synthetase (aaRS), with L-arginine bound to the active site has been solved at 2.75 Å resolution and refined to a crystallographic R-factor of 19.7%. ArgRS is composed predominantly of α-helices and can be divided into five domains, including the class I-specific active site. The N-terminal domain shows striking similarity to some completely unrelated proteins and defines a module which should participate in specific tRNA recognition. The C-terminal domain, which is the putative anticodon-binding module, displays an all-α-helix fold highly similar to that of Escherichia coli methionyl-tRNA synthetase. While ArgRS requires tRNA Arg for the first step of the aminoacylation reaction, the results show that its presence is not a prerequisite for L-arginine binding. All H-bond-forming capability of L-arginine is used by the protein for the specific recognition. The guanidinium group forms two salt bridge interactions with two acidic residues, and one H-bond with a tyrosine residue; these three residues are strictly conserved in all ArgRS sequences. This tyrosine is also conserved in other class I aaRS active sites but plays several functional roles. The ArgRS structure allows the definition of a new framework for sequence alignments and subclass definition in class I aaRSs.

Despite very low sequence homology between ETA and other trypsin-like serine proteases, the ETA crystal structure, together with biochemical data and site-directed mutagenesis studies, strongly confirms the classification of ETA in the Glu-endopeptidase family. Direct links can be made between the protease architecture of ETA and its biological activity.