tRNA synthetase: tRNA aminoacylation and beyond

Abstract

The aminoacyl-tRNA synthetases are prominently known for their classic function in the first step of protein synthesis, where they bear the responsibility of setting the genetic code. Each enzyme is exquisitely adapted to covalently link a single standard amino acid to its cognate set of tRNA isoacceptors. These ancient enzymes have evolved idiosyncratically to host alternate activities that go far beyond their aminoacylation role and impact a wide range of other metabolic pathways and cell signaling processes. The family of aminoacyl-tRNA synthetases has also been suggested as a remarkable scaffold to incorporate new domains that would drive evolution and the emergence of new organisms with more complex function. Because they are essential, the tRNA synthetases have served as pharmaceutical targets for drug and antibiotic development. The recent unfolding of novel important functions for this family of proteins offers new and promising pathways for therapeutic development to treat diverse human diseases.

Figure 1

Conserved structure motifs and ATP binding in class I and II aaRSs. A. Class I LeuRS enzyme [Thermus thermophilus (T. thermophilus)] binds to an extended conformation of a sulphamoyl analogue of leucyl-adenylate (black) within the synthetic active site. The conserved signature sequences “HIGH” (HMGH) and “KMSKS” (MSKSK) are highlighted in blue and green respectively (PDB: 2V0C) [240]. While these signature sequences can vary as shown in this example, they are readily recognizable in a sequence alignment of all class I aaRSs. B. Class II glycyl-tRNA synthetase (GlyRS) binds ATP (black) in a bent conformation. The three conserved sequences, motifs 1, 2, and 3 of class II aaRSs are highlighted orange, purple, and blue respectively (PDB: 1B76) [247].

Figure 2

Structurally similar amino acids. A. IleRS discriminates isoleucine from valine. B. AlaRS discriminates alanine from glycine. The colored balls represent as follows: red, oxygen; blue, nitrogen; and gray, carbon. (Hydrogens are not shown.)

Figure 3

The double sieve of LeuRS. A. The double sieve for LeuRS contains a coarse sieve (red) for aminoacylation that excludes larger amino acids and a “fine sieve” (blue) that blocks cognate amino acid, but allows non-cognate amino acids to be hydrolyzed. B. The crystal structure of T. thermophilus LeuRS has an ancient canonical aminoacylation core (red) and CP1 hydrolytic editing domain (blue) that are linked by β-strands (green). Residues that impact editing within the hydrolytic active site are in orange. Cartoon on the left is adapted from [248] and structure on right (PDB: 2BTE) is adapted from [48].

Fig 4

Pathways for aaRS editing. Post-transfer editing occurs when the incorrectly charged tRNA is hydrolyzed, while pre-transfer editing cleaves activated aminoacyl-adenylate.

Figure 5

Secondary and tertiary structure of tRNA. The secondary cloverleaf structure (left) and tertiary structure of tRNA (right) show how the dihydrouridine (D; red) and TΨC (green) loops interact for folding. The colors represented on the tRNA are: orange, 3′ acceptor stem; purple, acceptor stem; green, TΨC stem-loop; red, D stem-loop; light green, variable loop; blue, anticodon stem-loop; and black, anticodon trinucleotide.

Figure 6

Non-canonical activities and paralogs of aaRSs. A. The aaRSs are adapted for dual roles that coexist with their aminoacylation activity. B. Paralogs of aaRSs and their domains can provide important non-aminoacylation functions within the cell [183].

Figure 7

Organization of the multi-aaRS complex. The aaRS complex consists of nine aaRSs (gray) and three auxiliary proteins (green). The varied sizes of the proteins are schematically indicated by different sized balls. Dashed lines indicate sub-complexes. Solid lines represent protein-protein interactions with the exception of Glu-ProRS, which is covalently fused by a repeating peptide motif.

Figure 8

Structure of boron-containing AN2690