An
Introduction to Ribosome Structure
David Marcey
© 2006
I.
Introduction
II. Subunit Structure
III. tRNA Binding and Codon Recognition
IV. References
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I.
Introduction
Ribosomes are
the large, ribonucleoprotein factories in which proteins are synthesized.
In this process, messenger RNA (mRNA) codons are read by the anticodons
of adaptor, transfer RNAs (tRNAs) that carry codon-specific amino
acids. These amino acids are added to a growing protein chain by peptide
bond formation in the heart of the ribosome.
The massive, macromolecular
assemblage at left is the crystal structure of the 70S ribosome from
Thermus thermophilus, an archaebacterium. The structure contains
42 proteins
and 3 ribosomal RNAs (rRNA).
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II. Subunit Structure
The 70S
ribosome comprises two subunits: a large 50S
subunit, and a small 30S subunit. The 50S
subunit contains a 23S and a 5S
rRNA plus over 30
proteins, 22 of which are resolved
in the crystal structure. The 30S subunit contains
a 16S rRNA plus 20
proteins. The RNAs of each subunit serve as the core
structural and functional components of the ribosome. The ribosomal
proteins are involved in subunit bridges and tRNA contact, and support
the key roles of the RNAs in each subunit. The
positions and conformations of the rRNA components of each subunit
can be visualized as follows:
-
The 16S
rRNA of the small, 30S subunit
folds into four domains: 5', central,
3' major, and 3'
minor. The structural autonomy of these domains implies that
they move relative to one another during protein synthesis. Viewed
from the subunit interface, the 16S
rRNA forms most of the interface
surface, with proteins located mainly
at the periphery.
-
The 23S
rRNA of the large, 50S subunit folds
into six secondary structural domains containing over 130 RNA helices:
I, II,
III, IV,
V, VI.
These six domains, unlike those of the 16S
rRNA of the small subunit, are thoroughly
intertwined. The 5S rRNA
forms a seventh domain of rRNA tertiary structure in the large subunit.
Like the RNA of the small subunit, the rRNAs
of the large subunit form most of the subunit interface surface,
with proteins located mainly at the
periphery.
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III. tRNA Binding
and Codon Recognition
3
tRNAs associate with the ribosome in the cavity between the
50S and
30S subunits.
Each tRNA is bound in a
distinctive site made from structural elements contributed by both
ribosomal subunits.
The A-site
tRNA, P-site tRNA, and E-site
tRNA exhibit slight conformational differences. However, all
adopt the classical "L shape" tertiary structure. Their
3' ends are bound by the 50S
subunit and attach to amino acids and
peptides through an acyl bond. Their anticodon
stem-loops point into binding pockets of the 30S
subunit . These
features can be seen by briefly focusing on the P-site
tRNA.
Note the
tight juxtaposition of the 3' ends of
the A-site and
P-site
tRNAs in the peptidyl transferase
site of the 50S subunit (not shown). The A-site
tRNA bears an incoming amino acid (not
shown), and the P-site tRNA
carries the growing peptide chain (not shown). Peptide bond formation
attaches the peptide to the A-site tRNA's
amino acid. The P-site
tRNA then moves to the E-site
(E stands for "exit"), replacing the former, uncharged E-site
tRNA. The A-site tRNA,
now bearing the growing peptide, is shifted into the P
position. A new tRNA bearing the next amino acid is then brought
into the A-site.
Turning
now to codon recognition, it can be seen that the 30S
subunit binds the anticodon stem loops
of the tRNAs as well as the mRNA being translated
(two, triplet codons are shown).
The A-site
and P-site
tRNAs (phe-tRNAs in the
structure shown at left) bear the anticodon residues (AAG)
that hydrogen bond with the two UUU codons of the mRNA:
The
G-U bonding in third position of each codon is an example of "wobble"
base pairing. Wobble pairing allows some codons that differ in the
third, 3' base to be recognized by the same tRNA anticodon. This,
together with examples of isoaccepting tRNAs that carry the same amino
acid but whose anticodons differ in the wobble base, allows for the
high degree of degeneracy found in the genetic code.
The conformation
of the mRNA and the A-
and P-site
tRNA anticodons helps to ensure that there is no confusion as to which
codon should be bound to which tRNA. The conformation is partially
achieved by a significant kinking of
the mRNA backbone. This
results in a significant distancing of the A- and P-site anticodons.
The distance between the 5'G of the P-site
anticodon and the 3'A of the A-site
anticodon is ~14 Angstroms (1.4 nm), much larger than the separation
needed if the mRNA were not kinked.
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IV. References
Yusupov, M. M.,
Yusupova, G. Z., Baucom, A., Lieberman, K., Earnest, T. N., Cate,
J. H. D., Noller, H. F.: Crystal Structure of the Ribosome at 5.5
A Resolution. Science 292:883-896 (2001).
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