Aminoacyl‐tRNA Synthetases


Aminoacyl‐tRNA synthetases catalyse a key reaction in protein biosynthesis. They match the 20 amino acids to the genetic code by specifically attaching them to their adaptors, transfer ribonucleic acid (tRNA) molecules. The reaction proceeds in two steps: the amino acid is first activated by adenosine triphosphate (ATP) to form aminoacyl adenylate and then the aminoacyl group is transferred to the terminal ribose of tRNA. This family of enzymes is divided into two classes, based on the similarities in primary structure and architecture of the active site domains; the two architectures are characterised by two modes of binding of ATP, the intermediate aminoacyl adenylate and the acceptor end of tRNA, which result in two regioselectivities of amino acid attachment to the terminal ribose of the tRNA. Aminoacyl‐tRNA synthetases are modular enzymes; to the central active site module are attached various domains with diverse functions such as tRNA‐binding and amino acid editing. The primary subject of this article are structural and functional aspects of these enzymes.

Key Concepts

  • Highly specific attachment of amino acids to their corresponding adaptor molecules, the transfer ribonucleic acids.
  • Synthetases are partitioned into two classes according to structural features of their catalytic site and their functional correlation.
  • Class II enzymes exhibit a unique fold and bind ATP in a unique bent conformation.
  • The two classes bind the acceptor arm of tRNA in two ways that constitute mirror images of each other.
  • Aminoacyl‐tRNA synthetases are modular enzymes, various domains of diverse functions being attached to the active site domain.
  • Continuous editing is part of the tRNA aminoacylation process in living organisms.

Keywords: aminoacyl‐tRNA synthetases; class I; class II; signature motifs; Rossmann fold; editing; ATP‐binding motifs

Figure 1. (a) Active site domains of aminoacyl‐tRNA synthetases in complex with the acceptor arms of their cognate tRNAs. Left: Class I glutaminyl‐tRNA synthetase:tRNAGln (PDB ID 2CV1), the protein approaches the acceptor stem from the minor grove side, the ATP conformation is extended. Right: Class II aspartyl‐tRNA synthetase:tRNAAsp (PDB ID 1ASZ), the protein contacts the tRNA acceptor stem at its major grove side, the ATP exhibits an unusual bent conformation. (b) Domain architectures: class I (left, PDB ID 2CV1), the nucleotide‐binding fold (Rossmann fold) is shown in orange, the two class I characteristic motifs HIGH and KMSKS are highlighted in yellow and pink, respectively. Class II (right, PDB ID 1ASZ), the three class II characteristic motifs are highlighted: motif 1 in yellow, motif 2 in blue and motif 3 in pink. The insertion modules, shown in light blue or red, provide additional binding elements for the tRNA; in some enzymes, they contain editing activities. (c) Close‐up views of ATP binding (left: PDB ID 1N75, right: PDB ID 2XTI). (d) Two views (top and bottom) of the canonical class II dimer showing the role of motif 1 helix for the dimer architecture and stability.
Figure 2. Modular organisation of aminoacyl‐tRNA synthetases and mirror‐symmetrical binding modes characteristic of the two classes. (a) Left: The glutaminyl‐tRNA synthetase:tRNAGln complex (class I, PDB ID 2CV1, Bacteria, the active site domain is orange and the codon‐binding site is blue). Right: Aspartyl‐tRNA synthetase:tRNAAsp complex (class II, PDB ID 1ASZ, Eukaryote, with its active site domain shown in red and the codon‐binding site in green). Two views of the superimposed tRNAs are shown in the centre with their CCA 3′‐end highlighted in red. (b) Two up and down views of the dimeric aspartyl‐tRNA synthetase:tRNAAsp complex (PDB ID 1ASZ). (c) Further illustration of the modular character of synthetases: two class I enzymes on the left side (the Arginyl‐tRNA synthetase:tRNAarg complex (PDB ID 2ZUE, Archaea) and the bacterial cysteinyl‐tRNA synthetase:tRNAcys complex (PDB ID 1U0B, Bacteria) and two class II structures on the right side (the prokaryotic aspartyl‐tRNA synthetase:tRNAAsp complex (PDB ID 1IL2, Prokaryote) and seryl‐tRNA synthetase:tRNAser complex (PDB ID 1SER, Prokaryote). For the class I enzymes, the active site domain is orange and the codon‐binding domain is blue. For the class II, the active site domain is red and the codon‐binding site is green. The others colours are for specific additional domains present in one or a subgroup of aminoacyl‐tRNA synthetases (see main text).
Figure 3. Post‐transfer editing mechanisms in class I and II enzymes illustrated by the crystal structures of IleRS (a, PDB ID 1QUZ) and ThrRS (b, PDB ID 1QF6), respectively. Editing occurs at the synthetic active site by hydrolysis of non‐cognate aminoacyl‐adenylates ( ) and/or at a dedicated editing site located in a separate domain by deacylation of mischarged aminoacyl‐tRNA ( ). IleRS, LeuRS and ValRS share a homologous CP‐I domain (yellow in the figure) harbouring the editing site for deacylation of mischarged aa‐tRNA. The CP‐I domain is a globular insertion domain separated by approximately 35 Å from the catalytic domain (orange colour). The mischarged terminal adenosine of tRNA (red circle) is translocated from the synthetic to the editing site, where the mischarged aa‐tRNA is deacylated. A similar translocation of the 3′‐end of charged tRNA from the active site to the editing site separated at a distance of 39 Å occurs in ThrRS.


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Further Reading

Arnez JG and Cavarelli J (1997) Structures of RNA‐binding proteins. Quarterly Reviews of Biophysics 30: 195–240.

Arnez JG and Moras D (1997) Structural and functional considerations of the aminoacylation reaction. Trends in Biochemical Sciences 22: 211–216.

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Giegé R, Sissler M and Florentz C (1998) Universal rules and idiosyncratic features in tRNA identity. Nucleic Acids Research 26 (22): 5017–5035.

Ibba M, Francklyn CS and Cusack S (eds) (2005) The aminoacyl‐tRNA synthetases. Georgetown, TX: Landes Bioscience.

Ibba M and Soll D (2000) Aminoacyl‐tRNA synthesis. Annual Review of Biochemistry 69: 617–650.

Jakubowski H (2012) Quality control in tRNA charging WIREs. RNA 2012 (3): 295–310.

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Arnez, John G, Beinsteiner, Brice, and Moras, Dino(Jan 2015) Aminoacyl‐tRNA Synthetases. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0000530.pub3]