Cocrystal structures of glycyl-tRNA synthetase in complex with tRNA suggest multiple conformational states in glycylation

J Biol Chem. 2014 Jul 18;289(29):20359-69. doi: 10.1074/jbc.M114.557249. Epub 2014 Jun 4.

Abstract

Aminoacyl-tRNA synthetases are an ancient enzyme family that specifically charges tRNA molecules with cognate amino acids for protein synthesis. Glycyl-tRNA synthetase (GlyRS) is one of the most intriguing aminoacyl-tRNA synthetases due to its divergent quaternary structure and abnormal charging properties. In the past decade, mutations of human GlyRS (hGlyRS) were also found to be associated with Charcot-Marie-Tooth disease. However, the mechanisms of traditional and alternative functions of hGlyRS are poorly understood due to a lack of studies at the molecular basis. In this study we report crystal structures of wild type and mutant hGlyRS in complex with tRNA and with small substrates and describe the molecular details of enzymatic recognition of the key tRNA identity elements in the acceptor stem and the anticodon loop. The cocrystal structures suggest that insertions 1 and 3 work together with the active site in a cooperative manner to facilitate efficient substrate binding. Both the enzyme and tRNA molecules undergo significant conformational changes during glycylation. A working model of multiple conformations for hGlyRS catalysis is proposed based on the crystallographic and biochemical studies. This study provides insights into the catalytic pathway of hGlyRS and may also contribute to our understanding of Charcot-Marie-Tooth disease.

Keywords: Aminoacyl tRNA Synthetase; Cocrystal; Crystal Structure; Neurological Disease; Protein Conformation; RNA-Protein Interaction; Transfer RNA (tRNA).

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / chemistry
  • Bacterial Proteins / genetics
  • Catalytic Domain / genetics
  • 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
  • Glycosylation
  • HeLa Cells
  • Humans
  • Macromolecular Substances / chemistry
  • Macromolecular Substances / metabolism
  • Models, Molecular
  • Mutagenesis, Insertional
  • Mutant Proteins / chemistry
  • Mutant Proteins / genetics
  • Mutant Proteins / metabolism
  • Nucleic Acid Conformation
  • Protein Conformation
  • RNA, Transfer, Gly / chemistry*
  • RNA, Transfer, Gly / metabolism
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / genetics
  • Recombinant Proteins / metabolism
  • Thermus thermophilus / enzymology
  • Thermus thermophilus / genetics

Substances

  • Bacterial Proteins
  • Macromolecular Substances
  • Mutant Proteins
  • RNA, Transfer, Gly
  • Recombinant Proteins
  • Glycine-tRNA Ligase

Associated data

  • PDB/4KR2
  • PDB/4KR3