Pyrrolysyl-tRNA Synthetase

Pyrrolysyl-tRNA synthetase (PylRS) is an enzyme that plays a crucial role in protein synthesis by catalyzing the attachment of the 22nd amino acid pyrrolysine to its cognate tRNA: $ \text{Pyl} + \text{tRNA}^\text{Pyl} + \text{ATP} \xrightarrow{\text{PylRS}} \text{Pyl-tRNA}^\text{Pyl} + \text{AMP} + \text{PP}_i $ PylRS is among the rarest of AARS, found only in a small group of bacteria and archaea. For these organisms, pyrrolysine is encoded by the stop codon UAG (Srinivasan et al. 2002), which is achieved through a specialized molecule tRNA$^\text{Pyl}$. The domain architecture of PylRS differs between organisms (Srinivasan et al. 2002). The archaeal-like PylRS contains two domains: an N-terminal domain involved in tRNA recognition, and a C-terminal catalytic domain, which is also involved in tRNA binding. The full-length archaeal PylRS was found to be quite insoluble (Suzuki et al. 2017) and behaves as a homodimer (Lee et al. 2008). In contrast, the bacterial-like PylRS is produced by two genes, pylSn (encoding the N-terminal domain), and pylCn (encoding the C-terminal domain). The fusion or fission of AARS genes that results in switching between homodimeric and heterotetrameric enzymes has also been observed in [AlaRS](/class2/ala) and [GlyRS-B](/class2/gly2). The structure of PylRS's catalytic domain is similar to that of [HisRS](/class2/his), [SepRS](/class2/sep) and [PheRS](/class2/phe1), which are part of subclass IIc (Kavran et al. 2007, Perona et al. 2012, Valencia-Sánchez et al. 2016, Douglas et al. 2023). However, its sequence closely resembles subclass IIb - [AsnRS](/class2/asn/), [AspRS](/class2/asp1), and [LysRS-II](/class2/lys/) (Fournier et al. 2009). Accordingly, PylRS is assigned to subclass IIe (Douglas et al. 2023). The binding of ATP in the active site is coordinated by the arginine tweezers, located in motifs 2 and 3 (Kaiser et al. 2018). The N-terminal domain binds the T-loop and variable loop of tRNA$^\text{Pyl}$ (Suzuki et al. 2017) in contrast with many aminoacyl-tRNA synthetases which instead recognise the anticodon. PylRS lacks editing activity (Gomez and Ibba, 2020) and is one of the most promiscuous of all AARS, with respect to both amino acid substrate and tRNA recognition, making it a favorable target for engineering unnatural amino acids into the genetic code (Wan et al. 2014).

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). Kavran, Jennifer M., et al. "Structure of pyrrolysyl-tRNA synthetase, an archaeal enzyme for genetic code innovation." Proceedings of the National Academy of Sciences 104.27 (2007): 11268-11273. Suzuki, Tateki, et al. "Crystal structures reveal an elusive functional domain of pyrrolysyl-tRNA synthetase." Nature chemical biology 13.12 (2017): 1261-1266. Lee, Marianne M., et al. "Structure of Desulfitobacterium hafniense PylSc, a pyrrolysyl-tRNA synthetase." Biochemical and biophysical research communications 374.3 (2008): 470-474. Srinivasan, Gayathri, Carey M. James, and Joseph A. Krzycki. "Pyrrolysine encoded by UAG in Archaea: charging of a UAG-decoding specialized tRNA." Science 296.5572 (2002): 1459-1462. Valencia-Sánchez, Marco Igor, et al. "Structural Insights into the Polyphyletic Origins of Glycyl tRNA Synthetases." Journal of Biological Chemistry 291.28 (2016): 14430-14446. Gomez, Miguel Angel Rubio, and Michael Ibba. "Aminoacyl-tRNA synthetases." Rna 26.8 (2020): 910-936. Kaiser, Florian, et al. "Backbone brackets and arginine tweezers delineate class I and class II aminoacyl tRNA synthetases." PLoS computational biology 14.4 (2018): e1006101. Fournier, Gregory P., Jinling Huang, and J. Peter Gogarten. "Horizontal gene transfer from extinct and extant lineages: biological innovation and the coral of life." Philosophical Transactions of the Royal Society B: Biological Sciences 364.1527 (2009): 2229-2239. Perona, John J., and Andrew Hadd. "Structural diversity and protein engineering of the aminoacyl-tRNA synthetases." Biochemistry 51.44 (2012): 8705-8729. Wan, Wei, Jeffery M. Tharp, and Wenshe R. Liu. "Pyrrolysyl-tRNA synthetase: an ordinary enzyme but an outstanding genetic code expansion tool." Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics 1844.6 (2014): 1059-1070.