S
IPR020929

Large ribosomal subunit protein uL5, conserved site

InterPro entry
Short nameRibosomal_uL5_CS

Description

This entry represents a short conserved sequence found in the N-terminal region of the members of the large ribosomal subunit protein uL5 family.

Large ribosomal subunit protein uL5, previously known as Ribosomal protein L5, is ~180 amino acids in length. In Escherichia coli, uL5 is known to be involved in binding 5S RNA to the large ribosomal subunit
[4]
.

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
[2, 3]
.

References

1.Atomic structures at last: the ribosome in 2000. Ramakrishnan V, Moore PB. Curr. Opin. Struct. Biol. 11, 144-54, (2001). View articlePMID: 11297922

2.The ribosome in focus. Maguire BA, Zimmermann RA. Cell 104, 813-6, (2001). View articlePMID: 11290319

3.The end of the beginning: structural studies of ribosomal proteins. Chandra Sanyal S, Liljas A. Curr. Opin. Struct. Biol. 10, 633-6, (2000). View articlePMID: 11114498

4.On the interaction of ribosomal protein L5 with 5S rRNA. Iwasaki K, Kikukawa S, Kawamura S, Kouzuma Y, Tanaka I, Kimura M. Biosci Biotechnol Biochem 66, 103-9, (2002). PMID: 11866091

Further reading

5. Structure and evolution of the Tetrahymena thermophila gene encoding ribosomal protein L21. Rosendahl G, Andreasen PH, Kristiansen K. Gene 98, 161-7, (1991). View articlePMID: 2016059

6. The structure of the gene for ribosomal protein L5 in the archaebacterium Sulfolobus acidocaldarius. Yang D, Gunther I, Matheson AT, Auer J, Spicker G, Bock A. Biochimie 73, 679-82, (1991). View articlePMID: 1840500

7. Amino acid sequences of the ribosomal proteins HL30 and HmaL5 from the archaebacterium Halobacterium marismortui. Hatakeyama T, Hatakeyama T. Biochim. Biophys. Acta 1039, 343-7, (1990). View articlePMID: 2198942

GO terms

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