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.