Crystal structures of glutamyl-tRNA synthetase from Elizabethkingia anopheles and E. meningosepticum

Abstract

Elizabethkingia bacteria are globally emerging pathogens that cause opportunistic and nosocomial infections, with up to 40% mortality among the immunocompromised. Elizabethkingia species are in the pipeline of organisms for high-throughput structural analysis at the Seattle Structural Genomics Center for Infectious Disease (SSGCID). These efforts include the structure-function analysis of potential therapeutic targets. Glutamyl-tRNA synthetase (GluRS) is essential for tRNA aminoacylation and is under investigation as a bacterial drug target. The SSGCID produced, crystallized and determined high-resolution structures of GluRS from E. meningosepticum (EmGluRS) and E. anopheles (EaGluRS). EmGluRS was co-crystallized with glutamate, while EaGluRS is an apo structure. EmGluRS shares ∼97% sequence identity with EaGluRS but less than 39% sequence identity with any other structure in the Protein Data Bank. EmGluRS and EaGluRS have the prototypical bacterial GluRS topology. EmGluRS and EaGluRS have similar binding sites and tertiary structures to other bacterial GluRSs that are promising drug targets. These structural similarities can be exploited for drug discovery.

Keywords: Elizabethkingia anopheles; Elizabethkingia meningosepticum; Seattle Structural Genomics Center for Infectious Disease; emerging infectious diseases; glutamyl-tRNA synthetases; infectious diseases; undergraduate education and training.

Figure 1

Structures of EmGluRS and EaGluRS. (a) The EmGluRS monomer has a Rossmann fold (orange), a zinc-binding domain (green) and an anticodon-binding domain (blue). The Rossmann fold and zinc-binding domain make up the N-terminal tRNA synthetase binding domain that binds the glutamate (spheres). (b) Superposed structures of EmGluRS (gray) and EaGluRS (cyan). The Mg²⁺ ion in EaGluRS is shown as a green sphere, the glutamate molecule is shown as spheres (C atoms in gray, O atoms in red and N atoms in blue) and formate and ethylene glycol from crystallization are shown as sticks. (c) Ribbon diagram calculated by ENDScript. The circumference of the ribbon (sausage) represents the relative structural conservation compared with other GluRS structures (these structures are indicated in Supplementary Fig. S2). Thinner ribbons represent more highly conserved regions, while thicker ribbons represent less conserved regions. (d) Solvent-accessible surface area of EmGluRS colored by sequence conservation, with red indicating identical residues. (e) Superposed structures of PaGluRS (PDB entry 5tgt, yellow), EmGluRS (gray) and EaGluRS (cyan). The sequence alignment of PaGluRS is shown in Fig. 3 ▸.

Figure 2

LigPlot representations of (a) glutamate binding and (b) Mg²⁺ ion binding in EmGluRS and EaGluRS, respectively.

Figure 3

Structural and primary-sequence alignment of EaGluRS, EmGluRS and PaGluRS. The secondary-structure elements are as follows: α-helices are shown as large coils, 3₁₀-helices are shown as small coils labeled η, β-strands are shown as arrows labeled β and β-turns are labeled TT. Identical residues are shown on a red background, with conserved residues in red and conserved regions in blue boxes. This figure was generated using ESPript (Gouet et al., 1999, 2003 ▸).