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A structural understanding of the dynamic ribosome machine

Key Points

  • The ribosome consists of two ribonucleoprotein subunits. The small subunit mediates the interactions between the anticodons of the tRNAs and the codons in the mRNA that they are translating to determine the order of amino acids in the protein being synthesized. The large subunit contains the peptidyl-transferase centre (PTC), which catalyses the formation of peptide bonds in the growing polypeptide.

  • An incoming tRNA is delivered to the A site in complex with elongation factor (EF)-Tu–GTP. Correct codon–anticodon pairing activates the GTPase centre of the ribosome that causes hydrolysis of GTP and EF-Tu to release the aminoacyl end of the tRNA.

  • Watson–Crick base pairs are formed between the mRNA and the P-site tRNA, which positions the peptidyl-tRNA, but unlike the A site, the rRNA does not make interactions with the codon–anticodon base-paired triplets that 'check' the accuracy of this interaction.

  • Binding of tRNA induces conformational changes in ribosomal (r)RNA that optimally orientates the peptidyl-tRNA and aminoacyl-tRNA for the peptidyl-transferase reaction to occur, which involves the transfer of the peptide chain onto the A-site tRNA. The ribosome must then shift in the 3′ mRNA direction so that it can decode the next mRNA codon.

  • Translocation of the tRNAs and mRNA is facilitated by binding of the GTPase EF-G, which causes the P-site deacylated tRNA to move to the E site and the A-site peptidyl-tRNA to move to the P site on GTP hydrolysis. The ribosome is then ready for the next round of elongation.

  • When a stop codon in the mRNA reaches the A site of the ribosome at the end of the elongation phase of protein synthesis, translocational release factors catalyse the hydrolysis and release of the ester-linked polypeptide on the P-site tRNA.

Abstract

Ribosomes, which are central to protein synthesis and convert transcribed mRNAs into polypeptide chains, have been the focus of structural and biochemical studies for more than 50 years. The structure of its larger subunit revealed that the ribosome is a ribozyme with RNA at the heart of its enzymatic activity that catalyses peptide bond formation. Numerous initiation, elongation and release factors ensure that protein synthesis occurs progressively and with high specificity. In the past few years, high-resolution structures have provided molecular snapshots of different intermediates in ribosome-mediated translation in atomic detail. Together, these studies have revolutionized our understanding of the mechanism of protein synthesis.

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Figure 1: An overview of ribosomal structure and mRNA translation.
Figure 2: Recognition of codon–anticodon interactions by the ribosome.
Figure 3: P-site–tRNA interactions in the ribosome.
Figure 4: Substrate-induced rearrangements in the peptidyl-transferase centre promote peptide chain formation and suppress hydrolysis.
Figure 5: Different interactions of the tRNA with the E site across kingdoms.
Figure 6: Space-filling models of the polypeptide exit tunnel.
Figure 7: An overview of termination of translation.

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DATABASES

Entrez Taxonomy

Deinococcus radiodurans

Haloarcula marismortui

Thermus thermophilus

FURTHER INFORMATION

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Glossary

Anticodon

A unit that is composed of three nucleotides in the tRNA that are complementary to and recognize the three bases of the codon on the mRNA.

A site

The site on the ribosome that binds aminoacyl-tRNA.

Aminoacyl-tRNA

A tRNA attached to an amino acid, which is ester linked to the sugar of the 3′ nucleotide.

P site

The site on the ribosome that binds peptidyl-tRNA.

Peptidyl-tRNA

A tRNA with the peptide being synthesized linked to the 3′ nucleotide.

70S ribosome

The complete prokaryotic ribosome particle, which is composed of the small (30S) subunit and large (50S) subunit.

Ribosomal RNA

(rRNA). A type of RNA that is synthesized in the nucleolus by RNA polymerase I. Approximately 65% of a ribosome is composed of rRNA.

Peptidyl-transferase centre

(PTC). The active site of the ribosome where peptide bond formation occurs.

E site

The site on the ribosome that binds the deacylated tRNA before it leaves the ribosome.

EF-Tu

Elongation factor Tu (temperature unstable), known as EF-1 in other kingdoms, delivers the aminoacyl tRNA to the ribosome in a codon-specific manner.

EF-G

Elongation factor G (GTPase), known as EF-2 in other kingdoms, binds to the ribosome and promotes tRNA and mRNA translocation powered by GTP hydrolysis.

Stop codon

A codon that codes for the end of the message that is recognized by the release factor.

Release factor

(RF). A protein factor that recognizes a stop codon in mRNA and catalyses the deacylation of the peptidyl-tRNA.

GTPase centre

The region of the ribosome 50S subunit that includes the sarcin–ricin RNA and stimulates the GTPase activity of elongation factors.

Stem-loop

The structure that is formed when a self-complementary nucleic acid sequence forms a duplex joined by a loop.

Type I A–minor interaction

A specific hydrogen-bonding interaction between an A base and a G–C base pair through the minor groove of duplex RNA.

Watson–Crick base pairs

The complementary hydrogen bond between bases A and T (or U) and G and C that form duplex nucleic acids.

Type II A–minor interaction

A second type of specific hydrogen bonding between an A base and a G–C base pair through the minor groove of duplex RNA.

Wobble base pair

A non-Watson–Crick base pair such as G–U.

D stem

One of the three stem-loops of the tRNA cloverleaf that stacks on the anticodon stem, forming one arm of the tRNA molecule.

Ribozyme

A ribosome is classified as a ribozyme (ribonucleic acid enzyme) because its active site is composed of RNA.

Nucleophilic attack

A reaction whereby an electron-rich atom (such as nitrogen) attacks an electropositive group.

Trigger factor

A prokaryotic protein that binds to the ribosome tunnel exit and assists in nascent polypeptide folding.

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Steitz, T. A structural understanding of the dynamic ribosome machine. Nat Rev Mol Cell Biol 9, 242–253 (2008). https://doi.org/10.1038/nrm2352

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