InterPro domain: IPR000231

Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [ 1 , 2 ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.

Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [ 3 , 3 ].

A number of eukaryotic, bacterial and archaebacterial ribosomal proteins can be grouped on the basis of sequence similarities. One of these families consists of:

• Mammalian L30 [ 4 ].
• Leishmania major L30.
• Yeast YL32 [ 5 ].
• Bacillus subtilis proteins YbxF and YlxQ [ 6 ].
• Thermococcus celer L30 [ 7 ].
• A probable ribosomal protein (ORF 1) from Methanococcus vannielii [ 8 ].
• A probable ribosomal protein (ORF 104) from Sulfolobus acidocaldarius [ 9 ].

These proteins, of the L30e family, have 82 to 114 amino-acid residues.

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2. The ribosome in focus. Cell 104, 813-6
3. The end of the beginning: structural studies of ribosomal proteins. Curr. Opin. Struct. Biol. 10, 633-6
4. Molecular cloning and nucleotide sequences of cDNAs specific for rat liver ribosomal proteins S17 and L30. Gene 35, 289-96
5. The yeast ribosomal protein L32 and its gene. J. Biol. Chem. 262, 16055-9
6. YbxF and YlxQ are bacterial homologs of L7Ae and bind K-turns but not K-loops. RNA 18, 759-70
7. Nucleotide sequence of the genes encoding the L30, S12 and S7 equivalent ribosomal proteins from the archaeum Thermococcus celer. Nucleic Acids Res. 19, 6047
8. Organization and nucleotide sequence of a transcriptional unit of Methanococcus vannielii comprising genes for protein synthesis elongation factors and ribosomal proteins. J. Mol. Evol. 29, 20-7
9. Organization and nucleotide sequence of the genes encoding the large subunits A, B and C of the DNA-dependent RNA polymerase of the archaebacterium Sulfolobus acidocaldarius. Nucleic Acids Res. 17, 4517-34