L-arginine recognition by yeast arginyl-tRNA synthetase.
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 A resolution and refined to a crystallographic R-factor of 19.7%. ArgRS is composed predominantly of alpha-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-alpha-helix fold highly similar to that of Escherichia coli methionyl-tRNA synthetase. While ArgRS requires tRNAArg 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.
Cavarelli
J
J
UPR 9004 Biologie Structurale, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, BP 163, 67404 Illkirch Cedex, France.
Delagoutte
B
B
Eriani
G
G
Gangloff
J
J
Moras
D
D
D000595:Amino Acid Sequence; D000926:Anticodon; D001120:Arginine / Q000737:chemistry*; D001126:Arginine-tRNA Ligase / Q000737:chemistry*; D001665:Binding Sites; D018360:Crystallography, X-Ray; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D012347:RNA, Transfer, Arg / Q000737:chemistry; D012441:Saccharomyces cerevisiae / Q000201:enzymology*; D016415:Sequence Alignment
D000926:Anticodon; D012347:RNA, Transfer, Arg; D001120:Arginine; D001126:Arginine-tRNA Ligase