The improved structure resolution allows construction of the first
all-atom model of a ribosome functional complex containing its
mRNA and tRNA substrates. This provided two kinds of information
crucial to the understanding of the protein synthesis mechanism:
(1) details of molecular interactions between the ribosome and
its substrate RNAs, and (2) ways in which the structures of both
the ribosome and the tRNAs are altered by their functional interactions.
During protein synthesis, the genetic code is used to translate
the sequence of nucleotides in a mRNA into the sequence of amino
acids in the protein. Groups of three nucleotides (codons) in the
mRNA are read by base pairing with a complementary three-nucleotide
sequence of nucleotides (anticodon) in the tRNAs, which carry the
growing protein chain during synthesis. There are three binding
sites for tRNA in the ribosome, called the A (aminoacyl), P (peptidyl)
and E (exit) sites. In the crystals that were used for the structure
determination, tRNAPhe was bound to the P site and noncognate endogenous
tRNA to the E site of the ribosome, in addition to a 10-nucleotide
mRNA fragment. The tRNA is bound most tightly to the ribosomal
P site, which is responsible for maintaining the translational
reading frame of the mRNA and for holding the growing protein chain
in the ribosome via the peptidyl-tRNA. The structure reveals a
high density of contacts between the tRNA and ribosomal RNA bases
and backbone, as well as ribosomal proteins, explaining the high
affinity of the P site for tRNA. Catalysis of peptide bond formation
takes place on the 50S subunit by a ribosomal activity called peptidyl
transferase. In the new structure, an intriguing structural rearrangement
is observed in the peptidyl transferase center.
Interactions of the anticodon stem-loop (ASL) of elongator tRNAPhe
(orange) and mRNA (green) with 16S rRNA (cyan) and small-subunit
proteins (blue) in the 30S subunit P site.
In the course of protein synthesis, tRNAs move through the
ribosome, coupled to movement of mRNA like an assembly line, in
a process called translocation. Translocation of tRNA from the
P to the E site is crucial for the energetics of this process,
and requires that the terminal nucleotide A76 of tRNA is deacylated—i.e., no
longer contains a bound protein chain, which is its chemical state
following peptide bond formation. The new structure explains this
requirement, showing that binding of tRNA to the E site requires
hydrogen bonding between the ribose moiety of A76 and C2394 of
23S rRNA; the presence of a peptidyl, aminoacyl, or even a methyl
group bound to the terminal ribose would thus prevent these interactions.
Structural changes in the peptidyl transferase center.
View of the T. thermophilus 70S ribosomal complex
containing deacylated tRNA bound to the P site (blue)
compared with the H. marismortui 50S subunit
model complex (magenta).
Future ribosome structure studies that include functional states
may eventually lead to an atomic-resolution 3D "movie"—the
ultimate description of the molecular mechanism of protein synthesis.
E-site tRNA interactions. (a) Interaction of
the elbow of E-site tRNA (red) with 23S rRNA (blue) in the L1
stalk region, showing the large-scale displacement of the stalk
relative to its position in the vacant ribosome, induced by tRNA
binding. The blue arrow indicates the extreme compression of
the major groove of helix 76 of 23S rRNA that accompanies this
movement. (b) Interactions of the CCA tail of E-site tRNA
with the large subunit.
Research conducted by A. Korostelev, S. Trakhanov, M. Laurberg,
and H.F. Noller (University of California, Santa Cruz).
Research funding: National Institutes of Health and the Agouron
Institute. Operation of the ALS is supported by the U.S. Department
of Energy, Office of Basic Energy Sciences (BES).
Publication about this research: A. Korostelev, S. Trakhanov,
M. Laurberg and H. Noller, "Crystal structure of a 70S ribosome-tRNA
complex reveals functional interactions and rearrangements," Cell 126,
1065–1077 (2006).
ALSNews Vol. 277, June 27, 2007 |