Ligand co-crystallization of aminoacyl-tRNA synthetases from infectious disease organisms

Spencer O. Moen,Colin Manoil,Bart L. Staker,Wesley C. Van Voorhis,David M. Dranow,Amit Sharma,Thomas E. Edwards,Donald D. Lorimer,Matthew C. Clifton,Peter J. Myler,Banumathi Sankaran

doi:10.1038/s41598-017-00367-6

Abstract

Aminoacyl-tRNA synthetases (aaRSs) charge tRNAs with their cognate amino acid, an essential precursor step to loading of charged tRNAs onto the ribosome and addition of the amino acid to the growing polypeptide chain during protein synthesis. Because of this important biological function, aminoacyl-tRNA synthetases have been the focus of anti-infective drug development efforts and two aaRS inhibitors have been approved as drugs. Several researchers in the scientific community requested aminoacyl-tRNA synthetases to be targeted in the Seattle Structural Genomics Center for Infectious Disease (SSGCID) structure determination pipeline. Here we investigate thirty-one aminoacyl-tRNA synthetases from infectious disease organisms by co-crystallization in the presence of their cognate amino acid, ATP, and/or inhibitors. Crystal structures were determined for a CysRS from Borrelia burgdorferi bound to AMP, GluRS from Borrelia burgdorferi and Burkholderia thailandensis bound to glutamic acid, a TrpRS from the eukaryotic pathogen Encephalitozoon cuniculi bound to tryptophan, a HisRS from Burkholderia thailandensis bound to histidine, and a LysRS from Burkholderia thailandensis bound to lysine. Thus, the presence of ligands may promote aaRS crystallization and structure determination. Comparison with homologous structures shows conformational flexibility that appears to be a recurring theme with this enzyme class.

Highlights

During protein synthesis aminoacylated tRNAs bind to the ribosome with the anticodon loop pairing with the codon of the mRNA template while delivering the incoming amino acid to the elongating polypeptide
The methicillin-resistant Staphylococcus aureus (MRSA) IleRS inhibitor mupirocin has been approved for clinical use, and its binding site has been shown by X-ray crystallography to overlap with the Ile-AMP reactive
One hundred aaRSs have entered the Seattle Structural Genomics Center for Infectious Disease (SSGCID)[26,27,28] structure determination pipeline, both as internally selected targets and as targets nominated by the scientific community

Summary

Introduction

During protein synthesis aminoacylated tRNAs bind to the ribosome with the anticodon loop pairing with the codon of the mRNA template while delivering the incoming amino acid to the elongating polypeptide. The crystal structures of P. falciparum LysRS and ProRS with cladosporin or halofuginone represent valuable studies of aaRS complexes with nature product-like anti-malarial inhibitors[18, 19] Due to their biological importance and potential as therapeutic targets, aminoacyl-tRNA synthetases have been targeted by a number of structural genomics centers. We describe our efforts to obtain aminoacyl-tRNA synthetase structures from infectious disease organisms, which have resulted in six new aaRS co-crystal structures; the initial structure of a seventh target identified via this strategy was recently reported along with inhibitor complexes[31] All of these structures contain a ligand which may be important for stabilizing the enzyme and promoting crystallizability

Methods

Results

Conclusion