A dynamic
α-[>>t]-H8-L-H9 conformation
in proteobacterial GluRS
In proteobacterial Hpy (T1)-GluRS, the H8-L -H9 loop length
remains the same but the central four-residue sequence motif
–[HGD(Q/A)]– observed for the rigid
α-[>>t ] conformation is replaced by
-[YQDK]-. In the crystal structure (Figure 5D), this stretch forms a
distorted Type II β-turn (φQ: -129.1,
ψQ: 66.8; φD: 60.3, ψD:
21.4) with side-chains of Asp
protruding out of the turn almost overlapping with D273 ofEco -GluRS. However, B-factors for this stretch are quite high
(Figure S4), indicating dynamics (electron density for the side-chain
atoms of Q are also not seen). Therefore, we also used an AlphaFold
model of Hpy (T1)-GluRS (with >95% confidence for
the YQDK stretch), which is also shown superimposed in Figure 5D. Like
in the rigid α-[>>t ] conformation,
the YQDK stretch in the model forms a Type II’ β-turn
(φQ: 49.1, ψQ: -137.8;
φD: -92.8, ψD: 7.1) with side-chains of
D, protruding out of the turn (overlapping with D273 ofEco -GluRS); in addition, unlike in the crystal structure, the
backbone atoms of Gln overlaps
well with the corresponding residue (Gly) in Eco -GluRS. Clearly,
the H8-L -H9 motif in Hpy (T1)-GluRS is also an example of
[>>t] motif, similar to
α-[>>t ], but more dynamic where
YQDK can either adopt a Type II’ or a distorted Type II β-turn.