The rigid α-[>>t]
conformation of H8-L-H9 in proteobacterial GluRSs
Sequence alignment of H8-L -H9 motifs from the 13 bacterial GluRSs
with known crystal structures is shown Figure 4A. The top six sequences
(ECO, SML, XOP, BTE, PAE and HPY) belong to the proteobacterial class of
which the first four share a common loop sequence
(LGWS-[HGD(Q/A)]-E(I/L)FT). We first focus on these four GluRSs
whose H8-L -H9 conformations are shown superimposed in Figure 4B.
The central –[HGD(Q/A)]– segment in these form a Type II’ β-turn
(φG: 62.1 ± 4.3, ψG: -134.5 ± 15.3 ;
φD: -89.4 ± 12.6, ψD: -4.3 ± 9.4). As
shown Figures 4A-B, the H8-L -H9 loop is tightly packed, with a
number of participating hydrophobic/aromatic residues (W269, H271, F277,
M/L/F282, Y/L/W285, F286; residue numbering according to theEco -GluRS). Further, the side-chain of R266, appearing at the
C-terminal end of Helix 8, protrudes into the loop and forms H-bonds
with E275 side-chain and the backbone of W269, effectively stapling the
two sides of the Type II’ turn. The residue R266 was identified to be a
proteo-bacterial GluRS specific residue and its mutation resulted in a
significant decrease in the activity of Eco -GluRS (16). This
results in a highly packed and rigid loop that displays a conserved Asp
side-chain (D273) at its tip. We call the specific H8-L -H9
conformation, observed for the four proteobacterial GluRSs, astype α (more types are discussed later) “towards tRNA” orα-[>>t] conformation.
Stapled by R266, the tightly packed
α-[>>t ] conformation is rigid.