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

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

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Aminoacylation
  • Charcot-Marie-Tooth Disease / enzymology
  • Charcot-Marie-Tooth Disease / genetics
  • Crystallography, X-Ray
  • Glycine-tRNA Ligase / chemistry*
  • Glycine-tRNA Ligase / genetics
  • Glycine-tRNA Ligase / metabolism*
  • Humans
  • Molecular Dynamics Simulation
  • Molecular Sequence Data
  • Mutation
  • Protein Conformation
  • RNA, Transfer, Gly / metabolism*

Substances

  • RNA, Transfer, Gly
  • Glycine-tRNA Ligase

Associated data

  • PDB/2PME
  • PDB/2ZT8
  • PDB/4KQE
  • PDB/4KR2
  • PDB/4KR3
  • PDB/4QEI