Summary: Ribosomal protein S5, N-terminal domain
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Ribosomal protein S5, N-terminal domain Provide feedback
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This tab holds annotation information from the InterPro database.
InterPro entry IPR013810
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 [PUBMED:11297922, PUBMED:11290319]. 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 [PUBMED:11290319, PUBMED:11114498].
Ribosomal protein S5 is one of the proteins from the small ribosomal subunit, and is a protein of 166 to 254 amino-acid residues. In Escherichia coli, S5 is known to be important in the assembly and function of the 30S ribosomal subunit. Mutations in S5 have been shown to increase translational error frequencies. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [PUBMED:, PUBMED:2247072], groups bacterial, cyanelle, red algal chloroplast, archaeal and fungal mitochondrial S5; mammalian, Caenorhabditis elegans, Drosophila and plant S2; and yeast S4 (SUP44).
This entry represents the N-terminal domain of ribosomal protein S5, which has an alpha-beta(3)-alpha structure that folds into two layers, alpha/beta.
|Cellular component||ribosome (GO:0005840)|
|Molecular function||RNA binding (GO:0003723)|
|structural constituent of ribosome (GO:0003735)|
|Biological process||translation (GO:0006412)|
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|Author:||Finn RD, Griffiths-Jones SR|
|Number in seed:||13|
|Number in full:||5805|
|Average length of the domain:||66.50 aa|
|Average identity of full alignment:||52 %|
|Average coverage of the sequence by the domain:||34.20 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||15|
|Download:||download the raw HMM for this family|
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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Ribosomal_S5 domain has been found. There are 202 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
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