Structural and mutational studies of the recognition of the arginine tRNA-specific major identity element, A20, by arginyl-tRNA synthetase

Abstract

Arginyl-tRNA synthetase (ArgRS) recognizes two major identity elements of tRNA Arg : A20, located at the outside corner of the L-shaped tRNA, and C35, the second letter of the anticodon. Only a few exceptional organisms, such as the yeast Saccharomyces cerevisiae, lack A20 in tRNA Arg . In the present study, we solved the crystal structure of a typical A20-recognizing ArgRS from Thermus thermophilus at 2.3 Å resolution. The structure of the T. thermophilus ArgRS was found to be similar to that of the previously reported

Mechanism of molecular interactions for tRNAVal recognition by valyl-tRNA synthetase

“…Adenosine at position 20 is the major identity element of most tRNA Arg species (McClain and Foss 1988;, and is recognized by the N-terminal domain of ArgRS (Delagoutte et al 2000;Shimada et al 2001), which has a completely different structure from that of the position 20-interacting ValRS coiled-coil domain. Actually, the specific A20 recognition by the N-terminal domain of ArgRS differs from the electrostatic interactions between the ValRS coiled-coil domain and position 20 of tRNA Val .…”

“…ValRS has an ␣-helix bundle domain to recognize A35 and C36 on the anticodon loop of tRNA Val (Fukai et al 2000). The ␣-helix bundle domain is also found in IleRS (Nureki et al 1998;Silvian et al 1999), arginyl-tRNA synthetase (ArgRS; Cavarelli et al 1998;Delagoutte et al 2000;Shimada et al 2001), methionyl-tRNA synthetase (MetRS; Mechulam et al 1999;Sugiura et al 2000), LeuRS (Cusack et al 2000), and cysteinyl-tRNA synthetase (CysRS; T. Nakama, O. Nureki, and S. Yokoyama, in prep. ; Newberry et al 2002).…”

Revisiting the operational RNA code for amino acids: Ensemble attributes and their implications

“…The most parsimonious way for maintaining the fidelity of the genetic code should have been through the direct recognition of tRNA anticodons by cognate synthetases. Yet, the anticodon is not always the principal determinant for aminoacylation (Shimada et al 2001;Weygand-Durasevic et al 2002;Jones et al 2008), and in some cases, no physical contact is made between the aaRS and the anticodon (Park and Schimmel 1988). A set of ''identity elements'' classified as ''determinants'' and ''antideterminants'' ), distributed over the stems and loops of the tRNA molecule, participate in its interaction with enzymes and the ribosome during maturation, modification, biological function, and degradation (Wolfson et al 2001).…”

“…In a series of groundbreaking experiments, Paul Schimmel and colleagues identified nucleotides and specific structural features within and outside the tRNA acceptor stem that affect the efficiency of aminoacylation Schimmel 1989, 1990;Martinis and Schimmel 1993;Schimmel et al 1993;Hamann and Hou 1995;Schimmel 1995;Saks and Sampson 1996;Di Giulio 1997;MusierForsyth and Schimmel 1999;Ribas de Pouplana and Schimmel 2001a;Shimada et al 2001;Weygand-Durasevic et al 2002). In particular, determinants at various positions along the acceptor stem that were found to be directly responsible for proper tRNA aminoacylation led to the concept of an ''operational RNA code for amino acids'' Schimmel 1995), indicating that the relationship between amino acids and tRNAs is encrypted not once but twice in the molecule.…”

“…It encompasses all nucleotides in the tRNA, exclusive of the anticodon, that affect the efficiency of specific aminoacylation. The two most prominent examples are the A20 nucleotide in the D-loop of tRNA Arg and the nucleotides in the long variable arm of tRNA Ser , which are recognized by unique domains in the N termini of ArgRS and SerRS, respectively (Cavarelli et al 1998;Giegé et al 1998;Hendrickson 2001;Shimada et al 2001;WeygandDurasevic et al 2002).…”