Isoleucyl tRNA Synthetase

Isoleucyl-tRNA synthetase (IleRS) is an enzyme that plays a crucial role in protein synthesis by catalyzing the attachment of the amino acid isoleucine to its cognate tRNA: $ \text{Ile} + \text{tRNA}^\text{Ile} + \text{ATP} \xrightarrow{\text{IleRS}} \text{Ile-tRNA}^\text{Ile} + \text{AMP} + \text{PP}_i $ IleRS features a N-terminal catalytic domain, C-terminal tRNA binding domains, and a post-transfer editing domain inserted within the catalytic domain (Nordin and Schimmel 2005). IleRS is closely related to the [LeuRS-A](/class1/leu2), [LeuRS-B](/class1/leu1), [ValRS](/class1/val), and [MetRS](/class1/met) families, which comprise subclass Ia (Perona and Hadd 2012, Gomez and Ibba, 2020). Members of subclass Ia are characterized by their hydrophobic amino acid substrates, as well as the connecting peptide 2 (CP2) and zinc finger (ZF) insertions, depicted below. CP2 is a 30-40 amino acid two-helix bundle on the surface of the catalytic domain (Starzyk et al. 1987) and appears to be essential for amino acid activation (Zhou at al. 2008). Upstream from this resides a cysteine-rich zinc finger, 20-40 amino acids in length, also essential for effective aminoacylation (Nureki et al. 1993, Sugiura et al. 2000). IleRS, LeuRS, and ValRS share a a post-transfer [editing domain](/superfamily/class1/Editing_domain_1a), absent from MetRS. The editing domain typically resides within the zinc finger, providing further amino acid selectivity by expelling a wide range of mistargetted amino acids such alanine, cysteine, threonine, valine, isoleucine, methionine, homocysteine, and norvaline (Gomez and Ibba, 2020). IleRS, ValRS, and the bacterial-like LeuRS-B are further characterized by connecting peptide 3 (CP3), which contains a second zinc-finger motif in certain organisms (Fukunaga et al. 2005). Its functional role is unclear. There are two types of IleRS, which have distinct sequences and C-terminal domain architectures. Both forms possess a [helical domain](/superfamily/class1/Anticodon_binding_domain_CRIMVL), that recognises the anticodon loop, residing downstream from the catalytic domain. The domain is universal across the members of subclass Ia, as well as [CysRS](/class1/cys) and [ArgRS](/class1/arg). However, the remaining C-terminal regions vary between the two types. The first type, IleRS-1, is found in certain bacteria, organelles, and eukaryotic cytosols. It possesses a [C-terminal junction domain](/superfamily/class1/C-terminal_junction_domain) and a zinc finger downstream from the helical bundle. Together with an N-terminal extension, the three C-terminal domains recognise the anticodon loop (Silvian et al. 1999). The second type, IleRS-2, is found in many archaea, bacteria, and eukaryotic cytosols. It lacks the N-terminal extension and zinc finger motif (Brkic et al. 2023), and achieves anticodon loop recognition through a much larger variation of the C-terminal junction domain. Many bacteria express both types of IleRS. Certain bacteria, such as *Staphylococcus aureus*, have an abnormal GxHH sequence profile in place of the standard HxGH motif in IleRS-2, promoting antibiotic resistance (Brkic et al. 2023).

References

Douglas, J, Bouckaert, R., Carter, C., & Wills, P. R. Enzymic recognition of amino acids drove the evolution of primordial genetic codes. Research Square (2023). Gomez, Miguel Angel Rubio, and Michael Ibba. "Aminoacyl-tRNA synthetases." Rna 26.8 (2020): 910-936. Brian E. Nordin and Paul Schimmel. "The Aminoacyl-tRNA Synthetases" CRC Press (2005): Chapter 4: Isoleuyl-tRNA Synthetases. Zhou, Xiao-Long, Bin Zhu, and En-Duo Wang. "The CP2 domain of leucyl-tRNA synthetase is crucial for amino acid activation and post-transfer editing." Journal of Biological Chemistry 283.52 (2008): 36608-36616. Starzyk, Ruth M., Teresa A. Webster, and Paul Schimmel. "Evidence for dispensable sequences inserted into a nucleotide fold." Science 237.4822 (1987): 1614-1618. Perona, John J., and Andrew Hadd. "Structural diversity and protein engineering of the aminoacyl-tRNA synthetases." Biochemistry 51.44 (2012): 8705-8729. Nureki, O., et al. "Chemical modification and mutagenesis studies on zinc binding of aminoacyl-tRNA synthetases." Journal of Biological Chemistry 268.21 (1993): 15368-15373. Sugiura, Ikuko, et al. "The 2.0 Å crystal structure of Thermus thermophilus methionyl-tRNA synthetase reveals two RNA-binding modules." Structure 8.2 (2000): 197-208. Fukunaga, Ryuya, and Shigeyuki Yokoyama. "Crystal structure of leucyl-tRNA synthetase from the archaeon Pyrococcus horikoshii reveals a novel editing domain orientation." Journal of molecular biology 346.1 (2005): 57-71. Nureki, Osamu, et al. "Enzyme structure with two catalytic sites for double-sieve selection of substrate." Science 280.5363 (1998): 578-582. Silvian, Laura F., Jimin Wang, and Thomas A. Steitz. "Insights into editing from an ile-tRNA synthetase structure with tRNAile and mupirocin." Science 285.5430 (1999): 1074-1077. Chen, Bingyi, et al. "Inhibitory mechanism of reveromycin A at the tRNA binding site of a class I synthetase." Nature communications 12.1 (2021): 1616. Brkic, Alojzije, et al. "Antibiotic hyper-resistance in a class I aminoacyl-tRNA synthetase with altered active site signature motif." bioRxiv (2023): 2023-01.