Summary: S4 domain
This is the Wikipedia entry entitled "S4 protein domain". More...
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S4 protein domain Edit Wikipedia article
In molecular biology, S4 domain refers to a small protein domain found in a large ribosomal protein named S4. The S4 domain is a small domain, approximately 60-65 amino acid residues long, occurs in a single copy at various positions in different proteins and was originally found in pseudouridine synthases, a bacterial ribosomal protein.  The function of the ribosome is to read RNA and synthesise the correct protein. The S4 domain functions in RNA binding. By improving RNA binding it aids the process of protein synthesis and leads to fewer errors. Since the S4 domain is a ribosomal protein, this function is fundamental to protein synthesis.
Proteins S4 helps initiate assembly of the 16S rRNA, are located at junctions of five RNA helices. 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.
The function of the S4 domain is to be an RNA-binding protein. S4 is a multifunctional protein, and it must bind to the which binds to 16S ribosomal RNA. In addition, the S4 domain binds a complex pseudoknot and represses translation. More specifically, this protein domain delivers nucleotide-modifying enzymes to RNA and to regulates translation through structure specific RNA binding. 
- Aravind L, Koonin EV (March 1999). "Novel predicted RNA-binding domains associated with the translation machinery". J. Mol. Evol. 48 (3): 291–302. doi:10.1007/pl00006472. PMID 10093218.
- Maguire BA, Zimmermann RA (March 2001). "The ribosome in focus". Cell 104 (6): 813–6. doi:10.1016/s0092-8674(01)00278-1. PMID 11290319.
- Chandra Sanyal S, Liljas A (December 2000). "The end of the beginning: structural studies of ribosomal proteins". Curr. Opin. Struct. Biol. 10 (6): 633–6. doi:10.1016/S0959-440X(00)00143-3. PMID 11114498.
- Davies C, Gerstner RB, Draper DE, Ramakrishnan V, White SW (1998). "The crystal structure of ribosomal protein S4 reveals a two-domain molecule with an extensive RNA-binding surface: one domain shows structural homology to the ETS DNA-binding motif.". EMBO J 17 (16): 4545–58. doi:10.1093/emboj/17.16.4545. PMC 1170785. PMID 9707415.
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S4 domain Provide feedback
The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterized, small proteins that may be involved in translation regulation . The S4 domain probably mediates binding to RNA.
Davies C, Gerstner RB, Draper DE, Ramakrishnan V, White SW; , EMBO J 1998;17:4545-4558.: The crystal structure of ribosomal protein S4 reveals a two-domain molecule with an extensive RNA-binding surface: one domain shows structural homology to the ETS DNA-binding motif. PUBMED:9707415 EPMC:9707415
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR002942
The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterised, small proteins that may be involved in translation regulation [PUBMED:10093218]. The S4 domain probably mediates binding to RNA [PUBMED:9707415].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||RNA binding (GO:0003723)|
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
- the number of residues in the sequence
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We make a range of alignments for each Pfam-A family:
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Curation and family details
|Number in seed:||155|
|Number in full:||36010|
|Average length of the domain:||47.10 aa|
|Average identity of full alignment:||28 %|
|Average coverage of the sequence by the domain:||18.58 %|
|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:||20|
|Download:||download the raw HMM for this family|
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There are 2 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 S4 domain has been found. There are 225 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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