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J Biol Chem. 2016 Mar 11;291(11):5740-52. doi: 10.1074/jbc.M115.679126. Epub 2016 Jan 21.

Large Conformational Changes of Insertion 3 in Human Glycyl-tRNA Synthetase (hGlyRS) during Catalysis.

Author information

1
From the State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong 510275, China, the Center for Cellular and Structural Biology and.
2
the South China Sea Institute, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, China.
3
the Hefei National Laboratory for Physical Science at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China, and.
4
the Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720.
5
the Center for Cellular and Structural Biology and the School of Pharmaceutical Sciences, Sun Yat-Sen University, University City, Guangzhou, Guangdong 510006, China.
6
From the State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong 510275, China, the Center for Cellular and Structural Biology and xiewei6@mail.sysu.edu.cn.

Abstract

Glycyl-tRNA synthetase (GlyRS) is the enzyme that covalently links glycine to cognate tRNA for translation. It is of great research interest because of its nonconserved quaternary structures, unique species-specific aminoacylation properties, and noncanonical functions in neurological diseases, but none of these is fully understood. We report two crystal structures of human GlyRS variants, in the free form and in complex with tRNA(Gly) respectively, and reveal new aspects of the glycylation mechanism. We discover that insertion 3 differs considerably in conformation in catalysis and that it acts like a "switch" and fully opens to allow tRNA to bind in a cross-subunit fashion. The flexibility of the protein is supported by molecular dynamics simulation, as well as enzymatic activity assays. The biophysical and biochemical studies suggest that human GlyRS may utilize its flexibility for both the traditional function (regulate tRNA binding) and alternative functions (roles in diseases).

KEYWORDS:

Charcot-Marie-Tooth disease (CMT); aminoacyl tRNA synthetase; conformational change; crystal structure; enzyme mechanism

PMID:
26797133
PMCID:
PMC4786711
DOI:
10.1074/jbc.M115.679126
[Indexed for MEDLINE]
Free PMC Article

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