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.