6AB8

Crystal structure of Methanosarcina mazei PylRS(Y306A/Y384F) complexed with ZLys

Summary for 6AB8

• Entry DOI: 10.2210/pdb6ab8/pdb
• Related: 6AAC 6AAD 6AAN 6AAO 6AAP 6AAQ 6AAZ 6AB0 6AB1 6AB2
• Descriptor: Pyrrolysine--tRNA ligase, MAGNESIUM ION, ADENOSINE-5'-TRIPHOSPHATE, ... (6 entities in total)
• Functional Keywords: aminoacyl-trna synthetase, pyrrolysyl-trna synthetase, trna, non-natural amino acids, translation
• Biological source: Methanosarcina mazei JCM 9314 (Methanosarcina frisia)
• Total number of polymer chains: 1
• Total formula weight: 32565.91

Authors

Yanagisawa, T.,Kuratani, M.,Yokoyama, S. (deposition date: 2018-07-20, release date: 2019-04-17, Last modification date: 2023-11-22)

Primary citation

Yanagisawa, T.,Kuratani, M.,Seki, E.,Hino, N.,Sakamoto, K.,Yokoyama, S.
Structural Basis for Genetic-Code Expansion with Bulky Lysine Derivatives by an Engineered Pyrrolysyl-tRNA Synthetase.
Cell Chem Biol, 26:936-, 2019

PubMed Abstract: Pyrrolysyl-tRNA synthetase (PylRS) and tRNA 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-(benzyloxycarbonyl)lysine (ZLys) and 10 ortho/meta/para-substituted ZLys derivatives were efficiently ligated to tRNA 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.

PubMed: 31031143
DOI: 10.1016/j.chembiol.2019.03.008

Experimental method

X-RAY DIFFRACTION (1.753 Å)