Journal
CELL CHEMICAL BIOLOGY
Volume 26, Issue 7, Pages 936-+Publisher
CELL PRESS
DOI: 10.1016/j.chembiol.2019.03.008
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Funding
- Platform Project for Supporting Drug Discovery and Life Science Research (Basis for Supporting Innovative Drug Discovery and Life Science Research [BINDS]) from AMED, Japan [JP17am0101081]
- Uehara Memorial Foundation
- MEXT, Japan [24550203]
- Grants-in-Aid for Scientific Research [24550203] Funding Source: KAKEN
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Pyrrolysyl-tRNA synthetase (PylRS) and tRNA(Pyl) have been extensively used for genetic-code expansion. A Methanosarcina mazei PylRS mutant bearing the Y306A and Y384F mutations (PylRS(Y306A/Y384F)) encodes various bulky non-natural lysine derivatives by UAG. In this study, we examined how PylRS(Y306A/Y384F) recognizes many amino acids. Among 17 non-natural lysine derivatives, N-epsilon-(benzyl-oxycarbonyl)lysine (ZLys) and 10 ortho/meta/parasubstituted ZLys derivatives were efficiently ligated to tRNA(Pyl) and were incorporated into proteins by PylRS(Y306A/Y384F). We determined crystal structures of 14 non-natural lysine derivatives bound to the PylRS(Y306A/Y384F) catalytic fragment. The meta-and para-substituted ZLys derivatives are snugly accommodated in the productive mode. In contrast, ZLys and the unsubstituted or ortho-substituted ZLys derivatives exhibited an alternative binding mode in addition to the productive mode. PylRS(Y306A/Y384F) displayed a high aminoacylation rate for ZLys, indicating that the double-binding mode minimally affects aminoacylation. These precise substrate recognition mechanisms by PylRS (Y306A/Y384F) may facilitate the structure-based design of novel non-natural amino acids.
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