Interaction between α-[>>t]
conformation and augmented/non-augmented tRNAGlx
Next we looked at the interactions between the
α-[>>t ] H8-L -H9 conformation
and tRNAGlx with augmented D-helix
(A -tRNAGlx) and with non-augmented D-helix
(N -tRNAGlx). In the absence of a structure of
proteobacterial A -tRNAGlu, the interaction
between α-[>>t ] and the D-helix ofA -tRNAGlu was modelled using the structure ofTth -GluRS complexed withTth -A -tRNAGlu (pdb ID: 2cv0). TheEco -GluRS α-[>>t ] motif was
structurally superimposed on to the H8-L -H9 motif ofTth -GluRS inTth -GluRS::Tth -A -tRNAGlu complex
and interactions of α-[>>t ] with
the D-helix of Tth -A -tRNAGlu were
analyzed. As shown Figure 5A, the modelled structure exhibited two
protein-tRNA H-bonds (D273-G23 and S270-A14). In addition, the
negatively charged oxygen atoms of D273 side-chain were favorably placed
within interacting distance (4.4 Å) of G22 amino nitrogen atom. This
clearly indicated that the α-[>>t ]
conformational motif can favorably interact withA -tRNAGlu.
Interactions between α-[>>t ] andN -tRNAGln was also gauged by modeling studies.
The N-terminal domain of Eco -GluRS was superimposed on the
N-terminal domain of Eco -GlnRS in theEco -GlnRS::Eco -N -tRNAGln complex
(Figure 2A) and interactions between
α-[>>t ] (Eco -GluRS) andEco -N -tRNAGln were analyzed. As shown in
Figure 5B, this resulted in a severe steric clash between G22/G23 ofN -tRNA and D273/E275 of Eco -GluRS. Interactions betweenEco -GluRS α-[>>t ] motif andN -tRNAGln were also analyzed by a different
model. In the second model, the template was Tth -GluRS complexed
with A -tRNAGlu. Eco -GluRS
α-[>>t ] motif was superimposed onTth -GluRS and Eco -N -tRNAGln was
superimposed on the Tth -A -tRNAGln.
Subsequently, interactions between Eco -GluRS
α-[>>t ] andEco -N-tRNAGln were analyzed. Although there
were no steric clashes as in the previous case, favorable interactions
of D273 with G22 of A -tRNAGlu (seen in Figure
5A) were lost. The two models indicated that the rigid
α-[>>t ] conformation would either
give rise to steric clashes with N -tRNAGln or
lose favorable interactions (as seen withA -tRNAGlu) or both. In other words, the rigid
[>t ]-H8-L-H9 conformation seems geared towards
discriminating against N-tRNAGln. A key residue
involved behind the A -tRNA compatibility and N -tRNA
incompatibility of α-[>>t ] is D273,
protruding towards tRNA.