Structural analyses clarify the complex control of mistranslation by tRNA synthetases

Abstract

Proteins are precisely assembled with amino acids by matching the anticodons of charged transfer RNAs to nucleotide triplets in mRNA sequences. Accurate translation depends on the specific coupling of cognate amino acids and tRNAs - a step carried out by aminoacyl-tRNA synthetases (aaRSs) and that generates the genetic code. Owing to their intrinsic similarity, aaRSs developed highly differentiated structures to discriminate between amino acids at the active site for aminoacylation. Because this discrimination is not sufficient to prevent toxic mistranslation, aaRSs developed separate structures to further refine recognition by proofreading. From comprehensive structural studies on aaRSs, many of the molecular details have been elucidated for the recognition of cognate amino acids and for the misactivation and editing of noncognate amino acids, Here we review recent advances in the structural description of the binding, activation and editing of amino acids, which collectively reveal many aspects of the fine-tuned systems that resulted in a robust and universal genetic code.

Figure 1. Thr/Ser recognition by ThrRS

(a) Structure of E. coli ThrRS (in complex with the Ser-A76 analog, pdb1TKY) represents the editing site for bacterial and eukaryotic ThrRS to hydrolyze mischarged Ser-tRNA^Thr. A hydrophobic pocket that recognizes the -OH group of Ser also excludes Thr [21]. (b) Editing domain of P. abyssi ThrRS shows that the editing site of archaeal ThrRS is homologous to D-amino acid deacylases. A chemical differentiation mechanism that only hydrolyzes Ser-tRNA^Thr is evidenced by its structures in complex with Ser-A76 and Thr-A76 (pdb3PD2, 3PD3) [22].

Figure 2. Phe/Tyr recognition by PheRS

(a) Aminoacylation site of T. thermophilus PheRS in complex with Phe, p-Cl-phe, m-Tyr and Tyr (pdb1B70, 2AKW, 3HFZ and 2AMC). The pocket envelope and the protein residue conformations are plotted from the structure of the complex with Phe. Two water molecules are located in the spacious pocket for amino acid activation in the α subunit of PheRS. One of the two Phe residues (F258) that forms the edge-to-face interactions with the benzene ring of the substrate is shown here. The other (F260) is on top of the binding pocket. (b) Editing site of T. thermophilus PheRS in complex with Tyr (pdb2AMC).

Figure 3. Gly/Ala/Ser recognition by AlaRS

Interactions with alanine and serine as shown in their ligand-bound structures (Ala-AMS, alanyl-adenylate sulfamoyl analog versus native Ala-AMP, and Ser-AMS, pdb3HXU, 3HXW) [45]. The aromatic ring of Trp¹⁷⁰ stacks with the backbone of amino-acid substrates. Repulsion for Ser comes from a close contact between Gly237–Ser(OH). Asp²³⁵ forms a common hydrogen bond with the α-amino group of bound amino acids. One extra H-bond between Asp²³⁵ and the γ-OH of Ser retains Ser in the pocket for Ala.

Figure 4. AlaRS editing domain and AlaXps redundancy

(a) Structural model of AlaXp-II combined from the solved AlaXp-I and AlaRS structures [46,52]. C-Ala domain is linked to the editing active site by a long coiled-coil linker. The characteristic G3:U70 signature of tRNA^Ala (yellow) is recognized by the editing domain while the C-Ala domain anchors the elbow region of the L-shaped tRNA. (b) Continuous evolution of the editing activity for Ser-tRNA^Ala. Early addition of a Gly-rich motif to the editing core of AlaXp in primordial life is followed by the acquirement of the C-Ala domain and the subsequent fusion with the aminoacylation domain to form AlaRS. A regulated AlaXp editing activity is achieved with the addition of the p23^H domain in mammals. The p23^H polypeptide (gray-blue) is added as a covalent fusion or can bind in trans [58,60].