Tyrosyl-tRNA Synthetases (original) (raw)

2005, The Aminoacyl-tRNA Synthetases - Landes Bioscience

Tyrosyl-tRNA synthetase (TyrRS) comprises an N-terminal domain, which has the fold of the class I aminoacyl-tRNA synthetases, followed by idiosynchratic domains, which differ in eubacteria, archaebacteria and eukaryotes. The eubacterial TyrRSs have recruited an RNA binding domain which is found in a large family of proteins. The crystal structures of the TyrRSs from Bacillus stearothermophilus (Bst-TyrRS) and Thermus thermophilus (Tth-TyrRS) have been solved, free, or in complex with tyrosine, or with tyrosyl-adenylate (Tyr-AMP). A quaternary complex between Tth-TyrRS, tRNATyr , tyrosinol and ATP has been solved at 2.8 Å resolution. The dimer of Bst-TyrRS is symmetrical in the crystals but asymmetrical in solution. It unfolds through a folded compact monomeric intermediate, by dissociation of the subunits (KD = 84 pM). A C-terminal domain is loosely linked to an intermediate α -helical domain through a fully flexible peptide. The tRNA binding site straddles the two subunits of TyrRS, which interacts with tRNATyr according to a class II mode. The conserved sequences of class I, HIGH and KMSKS, are involved in the catalysis of tyrosine activation. The HIGH sequence is not involved in the transfer of tyrosine from Tyr-AMP to tRNATyr, and the KMSKS sequence is involved in this transfer only through the initial binding of tRNATyr. Other residues (Thr40, Lys82 and Arg86 in Bst-TyrRS), are involved in both steps of the catalytic reaction, by interacting first with ATP then with residue Ade76 of tRNATyr. The identity elements of tRNATyr comprise nucleotidic base Ade73, the anticodon, and either base-pair Gua1:Cyt72 in eubacteria or Cyt1:Gua72 in archaebacteria and eukaryotes. The residues of TyrRS which interact with tRNATyr or recognize its identity elements have been identified by extensive mutagenesis and kinetic studies of Bst-TyrRS and from the structure of the Tth-TyrRS·tRNATyr complex. The two approaches are in excellent agreement. TyrRS catalyses the activation of tyrosine and its transfer to tRNATyr by stabilizing the transition states for these two reaction steps, through interactions with ATP, Ade76, and the identity elements of tRNATyr. The role of base pair 1:72 in the recognition of tRNATyr results in a species specificity and makes TyrRS a potential target for antibiotics. This specificity relies on a short segment (<41 residues) of TyrRS and can be swapped between species. The specific recognition between TyrRS and tRNATyr depends on the correct balance between the cellular concentrations of synthetases and tRNAs. Moreover, a residue (Glu152) of Bst-TyrRS is involved in the rejection of noncognate tRNAs but not in the interaction with tRNATyr, and thus is a purely negative determinant of specificity. Inhibitors of TyrRS have been discovered and characterized: tyrosinol, tyrosinyl-adenylate and tyrosyl-aryl dipeptides (e.g., Tyr-Tyr); however, they cross the bacterial envelope very inefficiently. Tyr-Gly dipeptides, derivatized with a sugar, have been isolated from microorganisms or synthesized, and shown to inhibit bacterial growth. The specificity of TyrRS towards the amino acid has been modified by screening or selecting mutants from random libraries which were targeted to residues of the tyrosine binding pocket. The species specificity of TyrRS towards tRNATyr and the absence of an editing mechanism towards the amino acid, have made it possible to create a 21st triplet of synthetase, tRNA and amino acid, and thus to extend the genetic code. TyrRS has additional functions in some organisms: it charges plant viral RNAs; acts as a kinase or a cytokine; plays a role in the splicing of the group I introns (as an RNA chaperone), in the maintenance of the mitochondrial genome, in yeast sporulation and in the quality control of tRNAs in the cell nucleus. TyrRS has been used in the synthesis of analgesic neuro-dipeptides.