6JP2

Crystal structure of pyrrolysyl-tRNA synthetase from Methanomethylophilus alvus

Summary for 6JP2

• Entry DOI: 10.2210/pdb6jp2/pdb
• Descriptor: Pyrrolysyl-tRNA synthetase (2 entities in total)
• Functional Keywords: aminoacyl-trna synthetase, trna, pyrrolysyl-trna synthetase, non-natural amino acids, translation, ligase
• Biological source: Candidatus Methanomethylophilus alvus
• Total number of polymer chains: 4
• Total formula weight: 124513.47

Authors

Yanagisawa, T.,Kuratani, M.,Yokoyama, S. (deposition date: 2019-03-25, release date: 2019-05-22, Last modification date: 2023-11-22)

Primary citation

Seki, E.,Yanagisawa, T.,Kuratani, M.,Sakamoto, K.,Yokoyama, S.
Fully Productive Cell-Free Genetic Code Expansion by Structure-Based Engineering ofMethanomethylophilus alvusPyrrolysyl-tRNA Synthetase.
Acs Synth Biol, 9:718-732, 2020

PubMed Abstract: Pyrrolysyl-tRNA synthetase (PylRS)/tRNA pairs from and are widely used for site-specific incorporations of non-canonical amino acids into proteins (genetic code expansion). In this study, we achieved the full productivity of cell-free protein synthesis for difficult, bulky non-canonical amino acids, such as -(((()-cyclooct-2-en-1-yl)oxy)carbonyl)-l-lysine (TCO*Lys), by using PylRS. First, based on the crystal structure of PylRS, the productivities for various non-canonical amino acids were greatly increased by rational engineering of the amino acid-binding pocket. The productivities were further enhanced by using a much higher concentration of PylRS over that of PylRS, or by mutating the outer layer of the amino acid-binding pocket. Thus, we achieved full productivity even for TCO*Lys. The quantity and quality of the cell-free-produced antibody fragment containing TCO*Lys were drastically improved. These results demonstrate the importance of full productivity for the expanded genetic code.

PubMed: 32182048
DOI: 10.1021/acssynbio.9b00288

Experimental method

X-RAY DIFFRACTION (2.272 Å)