Biomedical Engineering Reference
In-Depth Information
The 3 ¢ end of the mRNA enters the ribosome through a tunnel formed by
ribosomal proteins S3, S4, and S5 (mRNA nucleotides +10 to +12) after which the
mRNA passes a layer formed by 16S rRNA elements that are capable of contracting
around the mRNA (mRNA nucleotides +7 to +9). The A- (+4 to +6), P- (+1 to +3),
and E-site (−3 to −1) codons interact with the respective tRNAs on the interface
between the ribosomal subunits. Finally the mRNA emerges on the platform of the
16S subunit where the 5¢ end of the mRNA upstream of the E-site codon along with
3¢-terminal tail of 16S rRNA forms the SD duplex (Shine and Dalgarno
1974
) .
1.2.4
Domain Closure
Comparison of two crystal structures of the ribosome modeling the initiation and
elongation states reveals that, upon transition from initiation to elongation, the 30S
subunit undergoes a conformational change whereupon helices 15-18 from the body
of the 30S subunit contract towards the 30S neck (Fig.
1.3b
, c) (Jenner et al.
2010b
) .
The remaining part of the body and most of the head of the 30S subunit remain
immobile. This domain closure results in a contraction by 1-2 Å of the mRNA tun-
nel immediately downstream of the A-site codon causing it to grip the template
more tightly in the elongation state than in the initiation state (Fig.
1.3d
). A similar
conformational change was seen in studies of the isolated 30S subunit with an anti-
codon stem-loop bound in the A site (Ogle et al.
2002
). From those studies it was
hypothesized that domain closure occurs only when a cognate tRNA is bound in
order to signal correct decoding. Unexpectedly, our results with the full functional
Fig. 1.3
(continued) nucleotide 37 of the P-site tRNA through Mg(H
2
O)
6
2+
and stabilization of the
mRNA kink between the P- and A-site codons via interactions with nucleotides from h44 (16S
rRNA); (6) stacking of the base of mRNA position −1 with G926 from h28 (16S rRNA); (7) the
mRNA A codon interactions with nucleotides G530, A1492, and A1493 (16S rRNA); (8) C1397
from 16S RNA; (9) aromatic stacking network between mRNA and U1196 and C1054 (16S
rRNA); (10) ribosomal proteins S3, S4, and S5. (
b
,
c
) Conformational changes of the 70S ribo-
some. The 30S structure is colored according to the difference between phosphate and C
a
positions
in the initiation and elongation complexes, ranging from
blue
(0 Å difference) to
red
(8 Å differ-
ence).
Arrows
indicate the direction of movement of the domain closure during transition from the
initiation to elongation state. The downstream mRNA tunnel has been marked with a white outline.
From the superposition it is clear that only the shoulder of the 30S subunit moves, whereas the
other parts of the 30S subunit remain immobile, and that the resulting movement leads to a contrac-
tion of the mRNA tunnel downstream of the A-site codon. (
d
) Detailed view of the RNA-layer part
of the downstream mRNA tunnel seen from the solvent side of the 30S subunit. The RNA chains
with the largest movements are shown in
white
(initiation) and color (elongation) with difference
vectors marking the changes in position. The contraction of the downstream mRNA tunnel leads
to a narrowing of the tunnel diameter by 1-3 Å, tightening the ribosome grip on the mRNA.
(
e
) Superpostion of cognate A-tRNA (
green
) and vacant A-site (
blue
) states. The
black arrows
indicate the general movement of the 30S subunit domain towards the neck region of the subunit.
(
f
) Superposition of cognate A-tRNA (
green
) and near-cognate A-tRNA (
red
) states
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