A dynamic
β-[>>t]-H8-L-H9 conformation
in proteobacterial GluRS
In the proteobacterial Pae -GluRS, H8-L -H9 loop length
increases to 13 (from 12) and the central Type II’ motif -HGD(Q/A)- of
α-[>>t ] is replaced by a
five-residue stretch (MPDER). Since this stretch is disordered in the
crystal structure, we used AlphaFold to model this stretch (95%
confidence in the MPDER stretch). The H8-L -H9 conformations ofEco -GluRS and Pae -GluRS are shown superimposed in Figure
5E. –[MPDE]- forms a Type I β-turn (φP: -59.6,
ψP: -29.6; φD: -93.1,
ψD: 11.0) while E288 assumes a left-handed helical
conformation (φ: 60.4, ψ: 15.6) and forms a H-bond with S284 (S270 inEco -GluRS) and R305, along with several other H-bonds in the
loop. Interestingly, when the H-bonded (and side-chain locked) E288 was
allowed to assume other accessible side-chain rotameric states, its
orientation overlapped with D273 of Eco -GluRS. Therefore, despite
exhibiting a Type I β-turn motif arising from [MPDE], dissimilar to
the earlier observed Type II’ β-turn motif arising from [HGD(Q/A)],
and a 13-residue loop, both H8-L -H9 conformations displayed a
carboxylic side-chain protruding towards tRNA (D273 in Eco -GluRS
and E288 in Pae -GluRS) compatible with A - but notN -type tRNA interaction. We call the H8-L -H9 conformation
of Pae -GluRS asβ-[>>t] (type β “towards
tRNA” conformation). The β-[>>t ]
conformation seems to be more dynamic (no electron density in crystal
structure) than the rigid α-[>>t ]
conformation.