X-Ray Analysis of Prokaryotic and Eukaryotic Ribosomes - Biophysical Approaches to Translational Control of Gene Expression - page 13

(Schurr et al. 1993 ; Ma et al. 2002 ). The E-site codons in those complexes and in the
present initiation complex were found in a conformation not favorable for codon-
anticodon interaction. These results agree fully with the accepted concept of transla-
tion initiation where deacylated tRNA should not appear in the E site until after the
first translocation event. In the initiation complex, we observed that the SD duplex
anchors the 5¢ end of the mRNA onto the platform of the 30S subunit, where the SD
is positioned close to proteins S11 and S18 on the platform (Fig. 1.6d ).
Contrary to the initiation state, the SD duplex assumes a different position on the
platform in the elongation state, where it contacts ribosomal protein S2 (Fig. 1.6c ).
The mRNA is in a “relaxed” conformation where the distance between the SD core
adenosine (−11) and the P-site codon (+1) is increased from seven to ten nucle-
otides, resulting in an enlargement of the SD duplex to 12 nucleotides, although
classical Watson-Crick base-paring in the double helix occurs in only nine pairs
(Fig. 1.6a , d). Thus, almost all nucleotides (from 1,531 to 1,542) of the single-
stranded 3¢ end of 16S rRNA are involved in the formation of the SD duplex. As a
consequence of the mRNA relaxation, the E-site codon adopts a conformation that
is closer to the classic A-helical conformation (Fig. 1.6a ), which leads to formation
of a base pair between the first position of the E-site codon and position 36 of the
cognate E-site tRNA Phe (Fig. 1.5d ). This base pair is stabilized by G693 of 16S
rRNA and the 2-methylthio group of the ms 2 i 6 A37 tRNA modi fi cation. Whether the
observed codon-anticodon interaction in the E site would exist without stabilization
by the modification remains uncertain. No base pairs are observed for the second
and third positions of the E-site codon which are too distant from the E-site tRNA
to form standard Watson-Crick pairs. Additionally, the base of mRNA nucleotide −4
interacts with A1507 of 16S rRNA in the elongation state immediately upstream of
the E-site codon.
The “tense” and “relaxed” mRNA conformations may delimit the extent of the
movement that the SD duplexes can undergo on the platform of the ribosome, so
that the SD helix can take intermediate positions between these two extremes. In
support of this notion, crystal structures of the 30S subunit (Kaminishi et al. 2007 )
and the 70S ribosome (Korostelev et al. 2006 ) report positions of the SD duplex that
are between or near the ones observed here for the initiation and elongation states.

1.2.7 mRNA Movement on the Ribosome

During the past years we have employed structural methods to study how the mRNA
interacts with the ribosome at different translational states. These various structures
represent snapshots of the working ribosome and as such can be used to propose a
trajectory for the process. We suggest the following simplified scheme for how
the mRNA moves on the ribosome at the different states of translation (Fig. 1.7 )
(Jenner et al. 2010b, 2007 ; Yusupova et al. 2006 ) .
In the first step of initiation complex formation, the mRNA binds to the ribo-
some and establishes the SD duplex between the 5¢-untranslated region and the