Understanding the structure of eukaryotic glutaminyl-TRNA synthetase: Combining X-ray crystallography with statistical evaluations of small angle scattering data

Abstract

Proteins are the machinery of the cell, carrying out critical functions in living organisms. Amino acyl tRNA synthetases perform the vital cellular function of attaching amino acids to their cognate tRNA molecule for their use in protein synthesis. In essence, these enzymes function as the "codebook" of life by translating information inscribed in codons into amino acid sequence. While a dedicated tRNA synthetase is used to attach most amino acids to their cognate tRNA molecules, glutaminyl-tRNA synthetase (GlnRS) is absent in most prokaryotes. These organisms instead use an indirect method of attaching glutamine to tRNA by first misacylating tRNA^gln with glutamic acid. Glutamic acid is then converted to glutamine by an amidotransferase enzyme, GatCAB. Eukaryotes, however, do not employ this indirect route, but encode a dedicated GlnRS to directly attach glutamine to tRNA^gln. Additionally, eukaryotic GlnRS has an appended N-terminal domain that is absent from its prokaryotic homolog, whose function is currently unknown. To date, no eukaryotic GlnRS structure is known.

This work describes a complementary approach to understanding the structure and function of yeast GlnRS, Gln4. To determine the structure and function of Gln4, we used molecular biology, X-ray crystallography, small angle X-ray scattering (SAXS), and bioinformatics. To objectively evaluate SAXS data, we have developed statistical methods using data from high-throughput structural genomics initiatives. Using SAXS data and the crystal structures of both the N and C-terminal domains of Gln4, we present a model of the first full-length eukaryotic GlnRS in solution. Our results describe a previously unknown structural homology between the appended N-terminal domain of Gln4 and the B subunit of GatCAB. Using this structural homology, coupled with the known structure of E. coli GlnRS bound to tRNA and molecular dynamics simulations, we present the first model of a full-length eukaryotic GlnRS bound to tRNA and a mechanism of binding to tRNA.