3 CONCLUSION
From an analysis of available crystal structures of bacterial GluRSs,
including Eco -GluRS that
we report here, and bacterial whole genomes to identify the presence or
absence of GlnRS and gatCAB, we have identified a loop, spanning between
Helix 8 and Helix 9, to be responsible for
tRNAGln-discrimination by some but not all bacterial
GluRSs. Specifically we show that the loop, which interacts with the
D-helix of tRNAGlx, broadly adopts two conformations:
[>>t] (towards RNA) or
[t>>] (away from RNA). The
[t>>] conformation is compatible with the
two canonical conformations of the D-helix: augmented and non-augmented.
The [>>t] conformation, which appears in
various forms (Figure 7), displays a carboxylic side-chain towards
tRNAGlx, that participates in favorable interactions
with the augmented D-helix but either loses the favorable interactions
or generates steric clashes (or both) when interacting with the
non-augmented D Helix. The [>>t]
conformation is most prevalent in proteobacterial GluRSs which also
dominantly possess D-helix augmented tRNAGlu and
non-augmented tRNAGln. That
tRNAGln-discrimination by proteobacterial GluRSs are
mediated by the [>>t] conformation was
validated with known experimental data on
tRNAGln-discrimination by GluRS or from genomic
compulsions of a GluRS to be tRNAGln-discriminatory.
Until now, the structural features of
tRNAGln-discrimination by proteobacterial GluRSs were
known to be present in tRNAGln, manifested as
augmented versus non-augmented D-helix. This work, for the first time,
identifies structural features on GluRS that complements the D-helix
signatures on tRNAGln that gives rise to
tRNAGln-discrimination by proteobacterial GluRSs.