Leucyl-tRNA Synthetase (Bacterial-like)

The bacterial-like leucyl-tRNA synthetase (LeuRS-B) is an enzyme that plays a crucial role in protein synthesis by catalyzing the attachment of the amino acid leucine to its cognate tRNA: $ \text{Leu} + \text{tRNA}^\text{Leu} + \text{ATP} \xrightarrow{\text{LeuRS-B}} \text{Leu-tRNA}^\text{Leu} + \text{AMP} + \text{PP}_i $ LeuRS-B is found in most bacteria and organelles, and differs from the archaeal-like form [LeuRS-A](/class1/leu2), which is found in most archaea. Either type may reside in a eukaryotic cytosol. The two forms are characterized by their abilities to charge tRNAs corresponding to six different codons. In the standard genetic code, [ArgRS](/class1/arg) and [SerRS](/class1/ser1) are the only other AARS which decode as many as six codons. The structures of LeuRS-A and -B are distinguished by i) the placement of the editing domain within their primary sequence (Fukunaga et al. 2005), ii) the C-terminal domain which recognises tRNA (Tukalo et al. 2005), and iii) the LeuRS-B insertion module below, also known as the leucyl-specific domain (Cusack et al. 2000). LeuRS-A and -B alike are closely related to the [IleRS](/class1/ile), [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 et 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). ValRS, IleRS, and LeuRS share a post-transfer [editing domain](/superfamily/class1/Editing_domain_1a), absent from MetRS. This 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). However, unlike LeuRS-A, ValRS, and IleRS, the editing domain of LeuRS-B resides downstream of the zinc finger and CP2 (Fukunaga et al. 2005). Thus, the domain appears to have hopped between the two positions, or may have originated as a trans-acting factor. IleRS, ValRS, and 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. The tRNA is recognised by two C-terminal domains (Tukalo et al. 2005, Rock et al. 2007). The first is a [helical domain](/superfamily/class1/Anticodon_binding_domain_CRIMVL) that recognises the anticodon binding domain, and is universal across the members of subclass Ia plus [CysRS](/class1/cys) and ArgRS. The second is a compact $\alpha$-$\beta$ domain unique to LeuRS-B. The domain is flexibly linked with the rest of the protein and mutational studies suggest it is essential for effective aminoacylation (Tukalo et al. 2005).

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). Tommie L. Lincecum, Jr. and Susan A. Martinis. "The Aminoacyl-tRNA Synthetases" CRC Press (2005): Chapter 5: Leucyl-tRNA Synthetases. Gomez, Miguel Angel Rubio, and Michael Ibba. "Aminoacyl-tRNA synthetases." Rna 26.8 (2020): 910-936. Cusack, Stephen, Anna Yaremchuk, and Michael Tukalo. "The 2 Å crystal structure of leucyl-tRNA synthetase and its complex with a leucyl-adenylate analogue." The EMBO Journal 19.10 (2000): 2351-2361. 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. Rock, Fernando L., et al. "An antifungal agent inhibits an aminoacyl-tRNA synthetase by trapping tRNA in the editing site." science 316.5832 (2007): 1759-1761. Tukalo, Michael, et al. "The crystal structure of leucyl-tRNA synthetase complexed with tRNALeu in the post-transfer–editing conformation." Nature structural & molecular biology 12.10 (2005): 923-930.