Ribosomal_S4 Ribosomal protein S4/S9 N-terminal domain
SMART ACC:	SM001390
Description:	This family includes small ribosomal subunit S9 from prokaryotes and S16 from metazoans. This domain is predicted to bind to ribosomal RNA (PMID:9707415). This domain is composed of four helices in the known structure. However the domain is discontinuous in sequence and the alignment for this family contains only the first three helices.
InterPro ACC:	IPR001912
InterPro abstract:	This entry represents the domain found at the N terminus of the small ribosomal subunit uS4. Small ribosomal subunit protein uS4 was previously known as Ribosomal protein S4 in bacteria and plants and S9 in fungi and animals. S4 is known to bind directly to 16S ribosomal RNA. The crystal structure of a bacterial S4 protein revealed a two domain molecule. The first domain is composed of … expand This entry represents the domain found at the N terminus of the small ribosomal subunit uS4. Small ribosomal subunit protein uS4 was previously known as Ribosomal protein S4 in bacteria and plants and S9 in fungi and animals. S4 is known to bind directly to 16S ribosomal RNA. The crystal structure of a bacterial S4 protein revealed a two domain molecule. The first domain is composed of four helices in the known structure. The second domain is an insertion within domain 1 and displays some structural homology with the ETS DNA binding domain [ PUBMED:9707415 ]. 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 ]. collapse
GO function:	rRNA binding (GO:0019843)
Family alignment:	View the Family alignment or the Alignment consensus sequence
There are 26 315 Ribosomal_S4 domains in 26 312 proteins in SMART's NRDB database.

Taxonomic distribution of proteins containing Ribosomal_S4 domains

The tree below includes only several representative species and genera. The complete taxonomic breakdown of all proteins containing Ribosomal_S4 domains can be accessed here. Click the counts or percentage values to display the corresponding proteins.

Predicted cellular role

Cellular role:	Translation
Binding / catalysis:	Ribosomal RNA

Relevant references for this domain

Primary literature for the Ribosomal_S4 domain is listed below. Automatically-derived, secondary literature is also available.

KEGG pathways involving proteins which contain this domain

This information is based on the mapping of SMART genomic protein database to KEGG orthologous groups. Percentages are related to the number of proteins containing a Ribosomal_S4 domain which could be assigned to a KEGG orthologous group, and not all proteins containing Ribosomal_S4 domains. Please note that proteins can be included in multiple pathways, ie. the numbers below will not add to 100%.

KEGG pathways

Some of these pathways are included in the interactive Pathways Explorer overview maps. Select an overview map and click the button below to highlight them in iPath.

KEGG orthologous groups

Some of these KOs are included in the interactive Pathways Explorer overview maps. Select an overview map and click the button below to highlight them in iPath.

3D structures in PDB containing this domain

Links to other resources describing this domain

Pfam	Ribosomal_S4
InterPro	IPR001912