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You may include any references to papers as in: the use of JSmol in Proteopedia ^[1] or to the article describing Jmol ^[2] to the rescue.

Function of your protein

Pyrrolysyl-tRNA synthase (PylRS) is a protein found in anaerobic archaea and bacteria. PylRS facilitates the installation of pyrrolysine. It binds to the pyrrolysine substrate. This protein has two functional domains. It has a C-terminus, which is the catalytic domain (PylSc) and has a Rossmann fold, which is a tertiary fold that binds to nucleotides. The other functional domain is the N-terminus that does the tRNA binding (PylSn). These two functional domains can work together to install two noncanonical amino acids at the same time.

There are three types of ligands in this protein, , (Pyrophosphate 2-) and EDO (1,2-ethanediol).

Biological relevance and broader implications

This protein is able to install noncanonical amino acids (ncAAs), amino acids that are found in organisms naturally or are synthetically made in a laboratory. These amino acids are not located in the genetic code of naturally occurring organisms, though. The importance of this protein is that it could be used as a tool for the expansion of genetic code. Since it can install ncAAs into many proteins, it can be sued in many organisms. The protein minimizes the suppression of UAG codons, which code to end a polypeptide chain. This means it can stop the end of that chain and help the expansion of the genetic code.

Important amino acids

Pyrrolysine is the important amino acid in this protein. This 22nd proteinogenic amino acid is achieved by PylRS and tRNA. It works together at the N- and C- terminus to be able to achieve this amino acid. This could lead to more ncAAs being discovered and used for genetic code expansion. There is no catalytic diad/triad area on this protein. The ligand is connected to the enzyme by hydrogen bonds to the rest of the protein.

Structural highlights

These are the of this protein PylRS has two domains, an N-terminal and a C-terminal. The N-terminal is responsible for tRNA-binding, PylSn. The C-terminal is the catalytic domain, PylSc. This is the most important aspect of PylRS. This is the location that allows the protein to interact with tRNA as well as the rest of the protein. In between the terminals, there is a single polypeptide chain connected by a linker of about 40 to 155 amino acids. The protein has a Pyl-Sn and Pyl-Sc that fuse together at this location. The PylSn has been recently discovered though, so with the intereaction of the C-terminal part (Pyl-Sc), it has not been fully characterized to see if it will expand the genetic code.

References

1. ↑ Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:http://dx.doi.org/10.1002/ijch.201300024
2. ↑ Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644

Ancestral Archaea Expanded the Genetic Code with Pyrrolysine. https://www.jbc.org/article/S0021-9258(22)00964-4/fulltext.