Glycyl-tRNA synthetase from Nanoarchaeum equitans: The first crystal structure of archaeal GlyRS and analysis of its tRNA glycylation

Alma Fujisawa; Risako Toki; Hideaki Miyake; Tomoko Shoji; Hiromi Doi; Hiromi Hayashi; Rina Hanabusa; Hiromi Mutsuro-Aoki; Takuya Umehara; Tadashi Ando; Hiroki Noguchi; Arnout Voet; Sam-Yong Park; Koji Tamura

doi:10.1016/j.bbrc.2019.01.142

Glycyl-tRNA synthetase from Nanoarchaeum equitans: The first crystal structure of archaeal GlyRS and analysis of its tRNA glycylation

Biochem Biophys Res Commun. 2019 Apr 2;511(2):228-233. doi: 10.1016/j.bbrc.2019.01.142. Epub 2019 Feb 13.

Authors

Affiliations

¹ Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan.
² Department of Applied Electronics, Tokyo University of Science, Katsushika-ku, Tokyo 125-8585, Japan; Research Institute for Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan.
³ Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Tsurumi-ku, Yokohama 230-0045, Japan; Laboratory of Biomolecular Modelling and Design, Department of Chemistry, KU Leuven, Celestijnenlaan 200G-bus2403, 3001 Leuven, Belgium.
⁴ Laboratory of Biomolecular Modelling and Design, Department of Chemistry, KU Leuven, Celestijnenlaan 200G-bus2403, 3001 Leuven, Belgium.
⁵ Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Tsurumi-ku, Yokohama 230-0045, Japan.
⁶ Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan; Research Institute for Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan. Electronic address: koji@rs.tus.ac.jp.

PMID: 30771900
DOI: 10.1016/j.bbrc.2019.01.142

Abstract

This study reports the X-ray crystallographic structure of the glycyl-tRNA synthetase (GlyRS) of Nanoarchaeum equitans - a hyperthermophilic archaeal species. This is the first archaeal GlyRS crystal structure elucidated. The GlyRS comprises an N-terminal catalytic domain and a C-terminal anticodon-binding domain with a long β-sheet inserted between these domains. An unmodified transcript of the wild-type N. equitans tRNA^Gly was successfully glycylated using GlyRS. Substitution of the discriminator base A73 of tRNA^Gly with any other nucleotide caused a significant decrease in glycylation activity. Mutational analysis of the second base-pair C2G71 of the acceptor stem of tRNA^Gly elucidated the importance of the base-pair, especially G71, as an identity element for recognition by GlyRS. Glycylation assays using tRNA^Gly G71 substitution mutants and a GlyRS mutant where Arg223 is mutated to alanine strengthen the possibility that the carbonyl oxygen at position 6 of G71 would hydrogen-bond with the guanidine nitrogen of Arg223 in N. equitans GlyRS.

Keywords: Acceptor-stem recognition; Aminoacylation; Crystal structure; Glycyl-tRNA synthetase; Nanoarchaeum equitans; tRNA.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Amino Acid Sequence
Archaeal Proteins / chemistry*
Archaeal Proteins / metabolism
Crystallography, X-Ray
Glycine-tRNA Ligase / chemistry*
Glycine-tRNA Ligase / metabolism
Models, Molecular
Nanoarchaeota / chemistry
Nanoarchaeota / enzymology*
Nanoarchaeota / metabolism
Protein Conformation
RNA, Transfer / chemistry
RNA, Transfer / metabolism
Sequence Alignment

Substances

Archaeal Proteins
RNA, Transfer
Glycine-tRNA Ligase