ISSN 0006-2979, Biochemistry (Moscow), 2025, Vol. 90, No. 11, pp. 1553-1565 © Pleiades Publishing, Ltd., 2025.
Russian Text © The Author(s), 2025, published in Biokhimiya, 2025, Vol. 90, No. 11, pp. 1657-1669.
1553
REVIEW
The NeverEnding E-Story
Valeriy G. Metelev
1
and Alexey A. Bogdanov
1,2,3,a
*
1
Faculty of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
2
Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
3
Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
a
e-mail: bogdanov@belozersky.msu.ru
Received August 11, 2025
Revised September 16, 2025
Accepted September 17, 2025
Abstract— The review discusses the functional role of the ribosomal E-site in the context of recent structural
data. Traditionally, the E-site has been considered to serve only as a binding site for deacylated tRNA (E-tRNA)
prior to its dissociation from the protein synthesis complex. Here, we examine specific contacts formed be-
tween E-tRNA and rRNA of the large ribosomal subunit in different organisms, as well as the sequence of
their formation and disruption. The mechanism of translation suppression by inhibitors that bind to the ri-
bosomal E-site is discussed. Based on current evidence regarding the location of aminoacyl-tRNA synthetases
(ARSs) in the immediate vicinity of the ribosome, we propose a hypothesis that one of the primary functions
of the ribosomal E-site is to prepare tRNA (through its modulation) for the formation of a specific complex
with ARS, in the content of which it is released from the ribosome.
DOI: 10.1134/S0006297925602503
Keywords: E-site of the ribosome, E-tRNA, translation inhibitors, aminoacyl-tRNA synthetases
* To whom correspondence should be addressed.
INTRODUCTION
Ribosomes are macromolecular machines that
synthesize proteins by a fundamentally conserved
cellular mechanism across all three domains of life.
They contain three binding sites for one of the key
players in translation – transfer RNAs (tRNAs) – which
are designated the A, P, and E sites. These sites serve
to bind the substrates of the peptidyl transferase re-
action (PTR), aminoacyl-tRNA (A-tRNA) and peptidyl-
tRNA (P-tRNA), as well as deacylated tRNA released
from the ribosome (E-tRNA). Each site is formed by
the two parts located on the small (SSU) and large
(LSU) ribosomal subunits, respectively [1].
From the earliest days of molecular biology, it
has become clear that the A- and P-tRNAs, in their
aminoacyl- and peptidyl-forms, respectively, are in-
volved in decoding genetic information recorded in
the nucleotide sequence of mRNA during translation
and serve as the PTR substrates. In contrast, the func-
tion of the ribosomal E-site has been a subject of long
debates, since it binds E-tRNA produced in the PTR
(see reviews by Nierhaus [2] and Semenkov etal. [3]).
Despite decades of studies, the functional significance
of this site, which provides only a temporary refuge
for tRNA dissociating from the ribosome, remains un-
clear. About twenty years ago, D. Wilson and K. Nier-
haus published a comprehensive review entitled “The
E-site story: the importance of maintaining two tRNAs
on the ribosome during protein synthesis.” In it, the
authors not only summarized the efforts aimed to
elucidate the role of the ribosomal E-site, but also
insisted that these studies are far from being over.
The only conclusion they regarded as firmly estab-
lished was that E-tRNA is involved in the maintenance
of correct reading frame of mRNA [4]. To the best
of our knowledge, no reviews have been since then
that were focused specifically on this most crucial
functional center of the ribosome. It should be noted
that the review by Wilson and Nierhaus [4] appeared
only a few years after a new era in the ribosome
research had begun – the era of near-atomic resolu-
tion studies of the structure of a functional ribosome
[5-8]. Initially, this era was dominated by X-ray crys-
tallography of archaeal and bacterial ribosomes and
their functional complexes. In the following years,
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the leading method has become cryogenic electron
microscopy (cryo-EM), due to dramatic advances in
the resolution and ability to study the structures from
various organisms under conditions maximally close
to the cellular environment [9-11]. More recently,
cryo-electron tomography has made it possible to vi-
sualize the structure of functional ribosomes in their
native state, in the cytoplasm or organelles. These
developments supplemented by novel physical and
computational approaches, have allowed to integrate
structural ribosomal data with the results of decades
of biochemical and genetic studies (see Flis et al. [12]
and Nishima et al. [13]).
In this review, we discuss the problem of the
ribosomal E-site based on the conclusion of recent
studies and analysis of structural data deposited in
the RCSB Protein Data Bank (PDB).
HOW DOES tRNA MOVE INTO THE E-SITE?
Even when studying the mechanism of protein
synthesis by classical biochemical, biophysical, and ge-
netic methods, researchers have established the view
that ribosome, as a molecular machine, undergoes
a series of diverse dynamic transformations at each
step of polypeptide synthesis [14, 15]. These trans-
formations are reversible structural rearrangements,
such as partial rotation of the ribosomal SSU relative
to the LSU, displacement of the SSU “head” relative
to its “body,” reversible large-scale movements of the
LSU L1 and L7 protuberances, changes in the relative
positions of the translation factor domains, and, final-
ly, translocation of mRNA and tRNA from the A-site to
the P-site and from the P-site to the E-site (see reviews
by Noller etal. [16], Korostelev [17], and Lindahl [18]).
Recently developed methods have allowed not
only to visualize these large-scale conformational
changes, but also to reveal their previously unknown
details [19].
In the classical ribosome configuration, when its
subunits are not rotated relative to each other, the
anticodon and acceptor segments of tRNA molecules
interact with the corresponding A-, P-, and E-sites of
the SSU and LSU. These arrangements are referred to
as classical and designated as A/A, P/P, and E/E, where
the first letter refers to the SSU and the second – to
the LSU [20]. It is important to keep in mind that at
any given time, only two tRNAs are present in the
functional ribosome: either A- and P-tRNAs, or P- and
E-tRNAs. (However, it should be noted, that in many
structural studies, ribosome–tRNA complexes for sub-
sequent analysis were obtained in vitro using a 3 to
4-fold excess of deacylated tRNA relative to the pepti-
dyl- or aminoacyl-tRNA. In such “artificial” complexes,
tRNAs may occupy all three sites; see Seely etal. [21]).
During the PTR, the growing polypeptide is trans-
ferred from the P-site tRNA to the amino acid residue
of the A-site tRNA. Moreover, the acceptor end of the
A-tRNA molecule, which is located on the LSU and
now carries the growing polypeptide chain, moves
toward the P-site of this subunit and adopts the so-
called hybrid, or intermediate, A/P state (since the
anticodon portion of this tRNA remains bound to the
A-site of the SSU). At the same time, the 3′ acceptor
end of the P-site tRNA moves into a specific functional
site on the LSU – the E-site (its structure and charac-
teristics will be discussed below), while the anticodon
part remains associated with the P-site of the SSU.
Therefore, the tRNA also adopts an intermediate state,
in this case referred to as the P/E state. The formation
of the intermediate states of the two tRNAs is accom-
panied by a limited rotation of the SSU relative to
the LSU. The ribosome acquires a state poised for the
translocation, i.e., becomes ready to move both tRNAs
together with the bound mRNA by exactly one codon
in a strictly defined direction. The elementary act of
translocation ultimately ends with the transition of
the peptidyl-tRNA and deacylated tRNA from the in-
termediate states into the classical P/P and E/E states,
respectively (see review by Korostelev [17]).
CONTACTS OF E-tRNA WITH THE RIBOSOME
In the classical state, the E-site tRNA forms min-
imal contacts with the mRNA anticodon on the SSU
and two specific segments of the rRNA on the LSU. Let
us consider these contacts in detail. Figure 1 shows
the structure of Escherichia coli tRNA and its prin-
cipal contacts with mRNA and 23S rRNA in the E/E
state. This structure was obtained by high-resolution
cryo-EM [22] and selected from a series of functional
ribosome complexes representing the early steps of
the polypeptide chain elongation.
As can be seen in Fig. 1, the trinucleotide anti-
codon segment of the tRNA forms a full codon–an-
ticodon complex with the complementary codon in
the mRNA. This fully supports the main conclusion of
Wilson and Nierhaus [4], who stated that the princi-
pal function of the deacylated tRNA–E-site complex
is to maintain correct reading frame.
At the same time, our analysis of numerous struc-
tures of E-tRNAs in the E/E state in prokaryotic, eu-
karyotic, and mitochondrial ribosomes obtained by
both X-ray crystallography and cryo-EM, has shown
that a complete codon–anticodon complex is observed
only in rare cases [22]. More often, there is only a sin-
gle hydrogen bond between the tRNA anticodon and
mRNA codon, or the contact between the E-tRNA and
mRNA is absent. This can be explained by the fact
that, unlike the codon–anticodon complexes formed
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Fig. 1. Three main contacts of E-tRNA with mRNA and rRNA in the classical E/E state (E. coli; PDB ID: 7N31). In addition
to the codon–anticodon complex (enlarged view, lower left inset), the figure shows the Watson–Crick GC base pair formed
through the tertiary interactions in the tRNA “elbow,” its stacking with G2112 and G2168 of the L1 protuberance of the
23S rRNA (enlarged view, right inset), and contacts of the 3′-CpA terminal group of E-tRNA with nucleotide residues of the
3′A pocket and A2432 of the 23S rRNA (enlarged view, upper left inset). In this and all subsequent figures, hydrogen bonds
and intermolecular aromatic contacts are shown as green and red dashed lines, respectively. Construction, analysis, and
visualization of RNA spatial structures were carried out with Discovery Studio Visualizer v.21.1.0.20298.
by the A- and P-site tRNAs, the transient complex be-
tween the E-tRNA and mRNA is not stabilized by direct
interactions with 16S rRNA or proteins of the SSU.
As a result, the anticodon loop of the E-tRNA is
the first to lose the contact with the ribosome, which
precedes its exit (Fig. 2) [23].
The second contact of the E-tRNA with the ribo-
some involves the so-called tRNA “elbow,” formed by
its T- and D-loops (Fig. 1). The tRNA elbow interacts
with the tip of the L1 protuberance of the LSU, which
is composed of protein L1, and with nucleotide resi-
dues of the 23S rRNA that are not immediate neigh-
bors in the polynucleotide chain. These nucleotides
belong to the loops flanking helix H77 in the second-
ary structure. In the 3D ribosome structure, these res-
idues are brought into a close proximity and, accord-
ing to several published ribosomal structures, form
both Watson–Crick and non-canonical base pairs [24]
(see Lehmann et al. [25]). The intermolecular tRNA–
rRNA contacts that form in this structure are stacking
interactions between heterocyclic bases of nucleotides
that are not directly adjacent in the primary RNA
structure. This motif is common among RNAs of var-
ious classes and plays an important role in shaping
the 3D structure of tRNAs and rRNAs, as well as in
their functioning [26-28].
As mentioned earlier, translation is accompanied
by reversible large-scale movements of the L1 protu-
berance relative to the “body” of the LSU. The state
in which the protuberance is maximally displaced
from the LSU is referred to as the “out” state, while
the maximally closed conformation is termed the “in”
state. The elbow of the E-tRNA interacts with the L1
protuberance only in its “in” state. Structural analy-
sis of ribosomes at various functional stages reveals
either complete (double) or partial (single) contacts
between the E-tRNA and the L1 protuberance. Single
contacts most likely correspond to the early stages
of deacylated tRNA entry into the E-site (i.e., the
P/E state) and, definitively, to the initial steps of its
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Fig. 2. The entry (a) of E-tRNA into the ribosomal E-site (PDB ID: 5QU7) and the beginning of its exit (b) (PDB ID: 5UQ8).
(These events were captured because mRNA had a well-developed secondary structure near the 3′-end that slowed its entry
into and movement through the ribosome [25]).
Fig. 3. Contacts between the E-tRNA elbow and nucleotide residues of the L1 protuberance. Full contact: a)PDB ID: 7SSN;
partial contacts: b) PDB ID: 7ST6, c) PDB ID: 7ST2. d) Secondary structure of the 23S rRNA segment containing G2112 and
G2168 [29].
departure from this site. Figure 3 shows examples of
such states in E. coli ribosomes observed by cryo-EM
[29]. Similar states have been previously detected by
X-ray crystallography in archaeal ribosomes [30].
The third contact of deacylated tRNA with the
E-site shown in Fig. 1 deserves special attention.
It occurs within the functional center of the ribosome
(hereafter referred to as the 3′A pocket) formed by
a specific segment of the LSU rRNA that possesses
a unique spatial configuration and serves to firmly
anchor the 3′-terminal adenosine residue of the tRNA.
This pocket is composed of two adjacent rRNA nucle-
otides (G2421 and C2422) and is stabilized by the hy-
drogen bonding with the trinucleotide CCA segment
of the same rRNA, as well as by stacking interactions
with neighboring rRNA bases [26, 28]. Remarkably,
the structure of this pocket remains unchanged and
can be observed even in ribosomes lacking tRNA.
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The requirement for the 3′-terminal adenosine
of the E-tRNA for its binding to the E-site was first
demonstrated using tRNA molecule lacking this nu-
cleotide [31] and later confirmed directly by chemical
probing and mutational analysis [32-34]. However, the
detailed structure of the 3′A pocket became known
only after X-ray crystallography studies of ribosomes
and their complexes with model poly- and oligonu-
cleotides mimicking the 3′-terminus of tRNA [35].
These structural studies also showed that irreversible
binding of synthetic tRNA mimetics to the 3′A pocket
completely blocked translocation [35]. In other words,
the CCA-end of the E-site tRNA must be completely
released from the ribosome for a single translocation
event to proceed without hindrance.
Conversely, any interference with the tRNA bind-
ing to the vacant 3′A pocket caused by disruption of
its native structure (the effect of antibiotics and oth-
er E-site inhibitors on this pocket will be discussed
below) also markedly suppresses or even completely
halts translocation. This occurs, for example, when
the structure of the 3′A pocket is altered by the de-
letion of a nitrogenous base from one of its forming
nucleotides [36] or through mutagenesis of the 3′A
pocket nucleotide residues critical for the interaction
with the 3′-terminal adenosine of tRNA [37].
As already noted, the E-tRNA–3′A pocket complex
is formed during the movement of deacylated tRNA
from the P- to the E-site, i.e., it stabilizes tRNA in
the P/E state. When the E-tRNA dissociates from the
ribosome, its 3′-end is the last to be released from
the 3′A pocket. This curious fact has been established
when the resolution of cryo-EM ribosome structures
reached 2 Å [38].
In the 3D structures of ribosomes from E. coli
and several other bacteria, partial dissociation of the
E-tRNA sometimes leaves only its 3′-terminal CA seg-
ment bound to the 3′A pocket in the same conforma-
tion as in the full E/E state (see Watson etal. [38]; PDB
ID: 7K00). Such retention of the 3′-terminal dinucleo-
tide of the E-tRNA is extremely rare in archaeal and
eukaryotic ribosomes.
It should be noted that in archaeal and eukary-
otic ribosomes (both cytoplasmic and mitochondri-
al), one of the LSU proteins is positioned in a close
proximity to the 3′A pocket. In contrast, in eubacterial
ribosomes, proteins are located at a considerable dis-
tance from this site. As a result, the conformation of
the 3′-CA-end of the E-tRNA in eubacterial ribosomes
differs markedly from that in archaeal, eukaryotic,
and mitochondrial ribosomes (Fig. 4).
Indeed, comparison of structures shown in Fig. 4
reveals that in eubacterial ribosomes, the heterocyclic
bases of the 3′-terminal CA segment of tRNA lie ap-
proximately in the same plane, with the nitrogenous
base of C75 stacked against A2432 (E. coli numbering).
In turn, A2432 stacks with A2433, thus forming (to-
gether with C75) a five-nucleotide stack. In ribosomes
from non-bacterial sources, C75 is positioned roughly
as in the 3′-terminus of free tRNA – its base plane is
approximately parallel to that of C74. In all known
cases, A76 occupies a similar position relative to the
3′A pocket bases with which it stacks. The identity of
these rRNA bases may vary (and some can be modi-
fied), but the cytidine residue C2394 of the 23S rRNA,
which forms a network of specific hydrogen bonds
with A76 in the 3′A pocket, is strictly conserved.
Therefore, after dissociating from its codon–anti-
codon complex with mRNA, the E-tRNA is not immedi-
ately released from the ribosome but retains specific
contacts with the LSU and maintains a defined spa-
tial position for some time. The possible functional
significance of this phenomenon is discussed in the
concluding section of this article.
E-SITE INHIBITORS
Ribosomes are targeted by a large number of
natural and synthetic bioactive compounds, including
numerous antibiotics. Most inhibitors of protein bio-
synthesis bind to the A- and P-sites of the ribosome
within its decoding center, as well as in the peptidyl
transferase center and the tunnel through which na-
scent polypeptide chains exit from the ribosome [39].
Antibiotics that specifically target the E-site are
much less common [40]. However, some well-known
antibiotics (e.g., aminoglycoside kasugamycin, penta-
peptide edeine, and tetrapeptide GE81112) which had
been originally assumed to act as translation initia-
tion inhibitors [39], in fact overlap with a significant
portion of the mRNA-binding channel on the SSU in
the P-site and E-site regions [41].
The antibiotic amicoumacin A (AMI) exhibits a
higher selectivity toward the E-site region of the mR-
NA-binding channel [42, 43]. AMI does not interact di-
rectly with E-tRNA. The mechanism of its inhibitory
activity lies in the ability to form multiple contacts
with rRNA residues constituting the E-site region of
the SSU and simultaneously bind to mRNA within
the decoding center of this region, thereby effectively
“gluing” the mRNA to the rRNA and halting translo-
cation [42, 43]. AMI inhibits translation not only in
eubacteria and archaea but also in eukaryotes, and
is therefore considered to be a potential anticancer
agent [44].
In this regard, the well-known antibiotic cyclohex-
imide (CHX) demonstrates a much greater selectivity
toward ribosomes from the three major evolutionary
domains of life: it suppresses protein synthesis in ar-
chaea and eukaryotes, but has little or no inhibitory
effect on bacterial ribosomes [45-47].
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Fig. 4. The 3′A pocket and its environment in ribosomes from different sources. a)E. coli without E-tRNA (PDB ID: 9NL5);
b) E. coli with E-tRNA (PDB ID: 7K00); c) Thermus thermophilus (PDB ID: 5UQ7); d) Saccharomyces cerevisiae (PDB ID:
8T3A); e) Nicotiana tabacum (PDB ID: 8B2L); f) human mitochondrial ribosome (PDB ID: 7QI5). Green, CpA; light brown,
proteins; blue, rRNA of LSU.
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Fig. 5. Antibiotics interacting with the mRNA region of the ribosomal E-site: a)kasugamycin (KSG), PDBID: 9FCO; b)amicou-
macin A (AMI), PDB ID: 4W2F; c) cycloheximide (CHX), PDB ID: 7R81. Amino acid residues in protein L44 whose mutations
result in the resistance to CHX are highlighted in red.
According to the data from PubMed Central
(PMC), the number of publications mentioning CHX
has exceeded 3000 annually over the past decade.
Therefore, here we briefly summarize only the main
details of its interaction with the ribosomes sensitive
to this antibiotic.
The binding site of CHX within the ribosomal
E-site is located in the 3′A pocket and its environment.
As noted above, the architecture of the 3′A pocket is
highly conserved. However, unlike in bacteria, the 3′A
pocket in archaeal and eukaryotic ribosomes (includ-
ing mitochondrial ones) is surrounded by proteins,
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Fig. 6. Interaction of the antibiotic manikomycin A (MCM) with E. coli ribosome: a) MCM overlapping with the 3′CA-end of
E-tRNA; b)shielding of A2432, which otherwise forms a stacking interaction with C75 of E-tRNA; c)chemical structure of MCM.
and at least one of these proteins is directly involved
in specific CHX recognition. This is evidenced by the
fact that mutations in several amino acid residues of
protein L44, situated near the 3′A pocket, result in the
resistance to CHX (Fig. 5c).
Until very recently, no protein biosynthesis in-
hibitors acting selectively on the E-site of the LSU of
bacterial ribosome have been known (although theo-
retical analysis suggested that such selective inhibi-
tors could be designed [47, 48]). Only recently, Wright
etal. [49] identified an inhibitor produced by Strepto-
myces rimosus. This compound, a depsipeptide named
manikomycin A (MCM), binds selectively to the 3′A
pocket, thereby preventing interaction of the CCA-end
of E-tRNA with its primary binding site within the
E-site of bacterial ribosome (Fig. 6).
At the same time, proteins surrounding this pock-
et in archaeal and eukaryotic ribosomes either hinder
MCM binding or make it entirely impossible. Analy-
sis of regions of ribosome stalling induced by MCM
revealed the enrichment of Pro codons in the P- and
A-sites of ribosomes blocked by this compound. [49].
So far, there is no explanation for this phenomenon.
The authors suggest that since translation of mRNA
regions containing Pro codons proceeds more slow-
ly, the period during which the ribosomal E-site re-
mains unoccupied by E-tRNA (and, therefore, remains
accessible to the antibiotic) is prolonged. It is also
possible that the observed effects are related to the
function of bacterial translation factor EF-P, which is
activated when the PTR rate markedly decreases due
to the presence of Pro or other amino acids form-
ing the so-called “problematic” amino acid sequenc-
es. EF-P restores the PTR rate within a time period
that is shorter than a single translocation step and
is released from the ribosome [50]. The binding of
EF-P to the ribosome leaves the 3′A pocket accessible
for the MCM binding [51].
Finally, we would like to draw attention to the
observation which, at the first glance, may seem
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Fig. 7. ATP molecule in the 3′A pocket of the human ribo-
some (PDB ID: 8QYX). Note the interaction between the ami-
no group of ATP and one of the G-pocket residues, as well
as the π–anion interaction between the same adenine base
and the phosphate group.
unrelated to the inhibitors of ribosomal E-site. While
analyzing the 3D structure of the isolated human 60S
ribosomal subunit (PDB ID: 8QYX), we unexpectedly
found an ATP molecule within its 3′A pocket (Fig. 7)
[52]. The ribosomal preparation used for the struc-
tural analysis was obtained in the studies of subunit
biogenesis, and the authors of the original paper did
not comment on this finding.
Interestingly, although the complexes formed by
the 3′A pocket with the 3′-terminal adenosine of the
E-site tRNA and with adenosine moiety of ATP share
certain structural similarities, their conformations
differ markedly. Although adenine bases of both nu-
cleosides exist in a weakly pronounced anti-confor-
mation, they are oriented in the opposite directions
relative to the bases of the 23S rRNA that form the
pocket. Consequently, the nature of hydrogen bonds
formed by these heterocyclic bases with the cytosine
residue of the pocket (C4341) also differs.
Cellular extracts used for the isolation of 60S
subunits undoubtedly contained free ATP [52]. Never-
theless, even if the observed ATP–3′A pocket complex
in the 60S subunit represented a crystallography arti-
fact, the obtained structural information may prove to
be valuable for the rational design of new synthetic
antibiotics targeting protein biosynthesis.
INSTEAD OF A CONCLUSION
In this review, we would like to emphasize once
again that the translocation of tRNA from the P-site
to the E-site represents one of the key stages of pro-
tein biosynthesis. This step is accomplished through
the large-scale movements of ribosomal subunits
anddomains relative to each other, as well as through
the formation of numerous strong and specific con-
tacts between the E-tRNA and specialized functional
centers of the ribosome. First, E-tRNA participates in
the movement of the codon–anticodon complex along
the ribosome while maintaining the correct reading
frame [4]. Second, we assume that the precisely de-
fined topology and dynamics of tRNA within the E-site
contribute to the ribosomal functioning after tRNA
dissociation from the E-site. It should be noted that
tRNA occupies this position even after the transla-
tion termination, when its participation in the mRNA
translocation is no longer required [53].
It is also important to mention numerous trans-
lation initiation, elongation, and termination fac-
tors, various quality control factors that ensure
proper ribosome function [54], and a group of pro-
tein factors finalizing maturation of newly synthe-
sized polypeptides directly on the ribosomal surface.
Together, these components constitute the so-called
ribosome interactome, which, in the case of eukary-
otic ribosomes, includes over a hundred proteins
and RNAs [55].
The attempts to establish a direct functional link
between the ribosome and ARSs have been made
already in the early studies into the mechanism of
protein synthesis [56]. With accumulation of data on
the ribosomal interactomes, it has become clear that
ARSs are not only components of these complexes
(as was expected) but can also associate with vari-
ous ribosomal components [57-60]. It was proposed
that, as soon as free deacylated tRNA is released from
the ribosome, it is immediately captured by the cog-
nate ARS [58].
Analysis of tRNA positioned in the E-site in the
classic E/E state shows that it lies within a shallow
depression and remains accessible from the ribosomal
surface. Its anticodon loop is also accessible. As noted
above, it loses contact with mRNA shortly after transi-
tion from the P/E to the E/E state. It is well established
that the anticodon within this loop is the first and
most important structural element recognized by an
ARS [61]. Therefore, it is reasonable to suggest that
ARSs can interact with their cognate tRNAs while the
latter are still located in the E-site. Furthermore, ARS
might dissociate together with tRNA into the periribo-
somal space, where it can complete the aminoacyla-
tion reaction and, at an appropriate moment, deliver
tRNA to the elongation factorI (EF-Tu in prokaryotes).
Such process will undoubtedly be advantageous both
kinetically and thermodynamically.
If our hypothesis is experimentally confirmed,
this would imply that an important, perhaps, even
the primary function of the ribosomal E-site is di-
rect preparation of tRNA for participation in the
new rounds of translation.
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Abbreviations
ARS aminoacyl-tRNA synthetases
CHX cycloheximide
E-tRNA deacylated tRNA
LSU large ribosomal subunit
MCM manikomycin
PTR peptidyl transferase reaction
SSU small ribosomal subunit
Acknowledgments
The authors thank A. S. Mankin and reviewer for care-
ful reading of the manuscript and constructive sugges-
tions.
Contributions
V.M. analyzed the data and prepared all figures; A.B.
designed the project. Both authors contributed sub-
stantially to the analysis of literature and writing
ofthe manuscript.
Funding
The study was conducted under the state assignment
of Lomonosov Moscow State University, project no.
121031300037-7.
Ethics approval and consent to participate
This work does not contain any studies involving hu-
man and animal subjects.
Conflict of interest
The authors of this work declare that they have
noconflicts of interest.
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