The H8-loop-H9 in Eco-GluRS as a
tRNAGln-discriminatory feature
Having determined the structure of Eco -GluRS, we compared the
sequence and structural features of its N-terminal catalytic domain with
that of tRNAGln-bound Eco -GlnRS (PDB Id: 1gts).
Being homologous, the overall folds of the two catalytic domains are
similar. However, the structural superimposition brought out some
important differences. Specifically, we looked at amino acid stretches
in the two proteins at the binding interface of the D-helix region of
tRNAGln, focussing on differences, since it must be
this region that differentially interacts with the uniquely different
D-helix regions of tRNAGlu and
tRNAGln, triggering
tRNAGlx-specificity. The analysis identified two
stretches (Figure 2), residues 303-335 in Eco -GlnRS and residues
257-311 in Eco -GluRS, both end-capped with helices (Helix 11 and
Helix 12 in GlnRS; Helix 8 and Helix 10 in GluRS). While the two
terminal helices are well superposed in both, the intervening stretches
are not. The ~10 residue inter-helical stretch in GlnRS
assumes an extended structure and is proximal to the
tRNAGln D-helix. In contrast, the inter-helical
stretch in GluRS is almost three times longer, of which the conformation
and tRNAGln proximity of 10 residue stretch at the
C-terminal are similar to the inter-helical stretch in GlnRS. However,
conformation adopted by the first 20 residues (towards the N-terminal)
in GluRS has no counterpart in GlnRS. This stretch contains a helix
(Helix 9) in GluRS with no counterpart in GlnRS. In addition, it
contains a loop between Helix 8 and Helix 9 that is at the interface of
the D-helix of tRNAGln. In other words, GluRS exhibits
a unique [Helix 8]-[loop]-[Helix 9] (H8-L -H9) motif
situated at the tRNAGln D-helix interface that is
absent in GlnRS.