1BS2

YEAST ARGINYL-TRNA SYNTHETASE

Summary for 1BS2

• Entry DOI: 10.2210/pdb1bs2/pdb
• Descriptor: PROTEIN (ARGINYL-TRNA SYNTHETASE), ARGININE (3 entities in total)
• Functional Keywords: ligase, aminoacyl-trna synthetase, protein biosynthesis
• Biological source: Saccharomyces cerevisiae (baker's yeast)
• Cellular location: Cytoplasm : Q05506
• Total number of polymer chains: 1
• Total formula weight: 69793.08

Authors

Cavarelli, J.,Delagouute, B.,Eriani, G.,Gangloff, J.,Moras, D. (deposition date: 1998-08-31, release date: 1999-08-27, Last modification date: 2024-03-13)

Primary citation

Cavarelli, J.,Delagoutte, B.,Eriani, G.,Gangloff, J.,Moras, D.
L-arginine recognition by yeast arginyl-tRNA synthetase.
EMBO J., 17:5438-5448, 1998

PubMed Abstract: 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.

PubMed: 9736621
DOI: 10.1093/emboj/17.18.5438

Experimental method

X-RAY DIFFRACTION (2.75 Å)