Zn-coordination in Eco-GluRS and its comparison to other GluRSs
One Zn2+ ion was bound in the acceptor-stem binding domain of Eco -GluRS [Figure 1B]. Previous studies onEco -GluRS had shown that depletion of this zinc induced conformation changes in the protein, reducing its catalytic activity (19). It was proposed by Liu et al [26] that the zinc coordinating ligands in Eco -GluRS are Cys98, Cys100, Cys125 and His127 and the domain belong to the SWIM domain family (21). Contrary to the above claim, the Zn2+ ion in the Eco -GluRS structure is ligated by Cys98, Cys100, Cys125 and Tyr121, in a tetrahedral coordination [Figure 1C]. Residue His127, which was proposed to be the fourth coordinating ligand of Zn2+ points away from it. This observation supports our previous report (20), where we had predicted the coordinating ligands of zinc in Eco -GluRS to be Cys98, Cys100, Cys125 and Tyr121, based on its sequence similarity to GluRS from Borrelia burgdorferri (Bbu -GluRS; PDB ID: 4gri), the only other bacterial GluRS structure that contains a Zn2+ (22). It is worth mentioning here that the coordination environment of Zn2+ in Eco -GluRS is similar to that of YadB gene product of E. coli (23,24),Eco -Glu-Q-RS (pdb ID: 1nzj), the N-terminal only paralogue of GluRS. The Zn-binding domains of Eco -GluRS, Bbu -GluRS andEco -Glu-Q-RS are shown superimposed in Figure 1C, along with a structure-guided sequence alignment in Figure S2. Despite large deletions, when compared to Eco-GluRS or Bbu-GluRS, the coordination residues and geometry of coordination in Eco -Glu-Q-RS were conserved. It is interesting to note that a conserved cation-π interaction between an arginine residue and the tyrosine coordinating the Zn2+ ion was also conserved in all.