tRNAGln-discriminatory status of
proteobacterial GluRSs in outlier PCA cluster D
PCA performed on H8-L -H9 proteobacterial motifs resulted in three
clusters, of which cluster D was more towards the tRNA-nondiscriminatory
clusters along PC1. Two members of cluster D have been discussed: (i)
HPY(T1), which was designated asN -tRNAGln-discriminatory based on its dymanic
α-[>>t ] conformation and (ii)
PAE(D+), which was designated asN -tRNAGln-discriminatory based on its dynamic
β-[>>t ] conformation. Here we
closely examine sequence and structural patterns of all members of
cluster D. In addition to PAE, cluster D contains 13 more D(+)-GluRSs
from the γ-proteobacterial class (TTU, MMW, CSA, HEL, ABO, CJA, MAQ,
HCH, PAR, SDE, AVN, ACI and MCT) whose H8-L-H9 sequences are very
similar to that of Pae -GluRS (Figure S10), all associated withA -tRNAGlu andN -tRNAGln. Since Pae -GluRS displayed the
β-[>>t]-H8-L -H9 motif, compatible
with both A -tRNAGlu and incompatible withN -tRNAGln, we predict all 13 D(+)-GluRSs to be
tRNAGln-non-discriminatory.
Cluster D contained 5 D(+)-GluRSs from the δ-proteobacterial class (HOH,
DPS, DAK, DPR and BBA). Although the H8-L -H9 loop length in these
were one residue longer than Eco -GluRS, interestingly, all except
BBA displayed G-(D/T)-D sequence motif at its center (Figure S11A). In
absence of experimental structures we assessed the loop conformations of
all 5 GluRSs using AlphaFold models. As shown in Figure S11B, except BBA
(that lacked the central G-(D/T)-D sequence motif) all H8-L-H9 motifs
assumed the [>>t] conformation where the
side-chain of the second Asp residue in G-(D/T)-D protruded out of the
tip of the loop overlapping well with D273 of Eco -GluRS.
Interestingly, like other [>>t]
conformations encountered so far, the loop did not shown α- or β-turns;
to emphasize this point we name this conformation as
ε-[>>t] (13-residue loop with no
α-/β-turns in the loop). A summary of all types of
[>>t] conformations identified so far is
shown in Figure 7.
The presence of the N -tRNAGlx-discriminating
ε-[>>t] conformation implies thatHoh -GluRS (with A -tRNAGln1 andA -tRNAGln2) will be
tRNAGln-non-discriminatory, Dps -GluRS (withN -tRNAGln1) will be
tRNAGln-discriminatory, Dak -GluRS and andDpr -GluRS (both with N -tRNAGln1 andA -tRNAGln2), on the other hand, will be
tRNAGln2-non-discriminatory but
tRNAGln1-discriminatory. Bba -GluRS (with the
away from tRNA conformation [t>> ]
and N -tRNAGln1) will beN -tRNAGln-non-discriminatory.