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

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.

Figure 1

Overview of co-crystal structures of aaRS enzymes from infectious disease organisms. In the current study, we have determined 6 co-crystal structures of aminoacyl tRNA synthetase (aaRS) enzymes from infectious disease organisms: CysRS from Borrelia burgdorferi (A), GluRS from B. burgdorferi (B) and Burkholderia thailandensis (C), TrpRS from Encephalitozoon cuniculi (D), HisRS from B. thailandensis (E), and LysRS from B. thailandensis (F). For sake of simplicity, only a single monomer is shown although some are biological oligomers such as HisRS which is a dimer.

Figure 2

Ligand recognition by class 1 aaRS enzymes from infectious disease organisms. (A) class 1a CysRS from Borrelia burgdorferi (B) class 1b GluRS from B. burgdorferi (C) class 1b GluRS from Burkholderia thailandensis and (D) class 1c TrpRS from Encephalitozoon cuniculi.

Figure 3

Ligand recognition by class 2 aaRS enzymes from infectious disease organisms. (A) Class 2a HisRS from B. thailandensis and (B) class 2b LysRS from B. thailandensis.

Figure 4

Comparison of the active sites and cognate ligand recognition between aaRSs from human and infectious disease organisms. (A) Overlay of E. cuniculi TrpRS (PDB ID 3TZE) showing the cognate amino acid binding pocket with human TrpRS (2QUH) also containing the cognate amino acid, (B) B. thailandensis HisRS (4E51) showing the cognate amino acid binding pocket with human HisRS (4 × 5O) which lacks the cognate amino acid, (C) B. thailandensis LysRS (4EX5) showing the cognate amino acid binding pocket with human LysRS (3BJU) also containing the cognate amino acid and an ATP molecule.