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225  structures 10093  species 2  interactions 36010  sequences 39  architectures

Family: S4 (PF01479)

Summary: S4 domain

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This is the Wikipedia entry entitled "S4 protein domain". More...

S4 protein domain Edit Wikipedia article

S4
PDB 2qoy EBI.png
Identifiers
Symbol S4
Pfam PF01479
Pfam clan CL0492
InterPro IPR002942
PROSITE PDOC00549
MEROPS S41
SCOP 1c06
SUPERFAMILY 1c06

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. [1] 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.[1]

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.[2][3]

Function[edit]

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. [1]

Structure[edit]

The S4 protein domain is composed of three alpha helices and five beta strands. It is organized as an antiparallel sheet in a Greek key motif. [4]

References[edit]

  1. ^ a b c Aravind L, Koonin EV (March 1999). "Novel predicted RNA-binding domains associated with the translation machinery". J. Mol. Evol. 48 (3): 291–302. PMID 10093218. 
  2. ^ Maguire BA, Zimmermann RA (March 2001). "The ribosome in focus". Cell 104 (6): 813–6. PMID 11290319. 
  3. ^ 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. 
  4. ^ 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. 

This article incorporates text from the public domain Pfam and InterPro IPR002942

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

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 [1]. The S4 domain probably mediates binding to RNA.

Literature references

  1. Aravind L, Koonin EV; , J Mol Evol 1999;48:291-302.: Novel predicted RNA-binding domains associated with the translation machinery. PUBMED:10093218 EPMC:10093218

  2. 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].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan S4 (CL0492), which has the following description:

This superfamily includes diverse proteins related to the ribosomal S4 protein.

The clan contains the following 2 members:

S4 S4_2

Alignments

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(155)
Full
(36010)
Representative proteomes NCBI
(24712)
Meta
(7637)
RP15
(2224)
RP35
(4271)
RP55
(5635)
RP75
(6709)
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Format an alignment

  Seed
(155)
Full
(36010)
Representative proteomes NCBI
(24712)
Meta
(7637)
RP15
(2224)
RP35
(4271)
RP55
(5635)
RP75
(6709)
Alignment:
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Order:
Sequence:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(155)
Full
(36010)
Representative proteomes NCBI
(24712)
Meta
(7637)
RP15
(2224)
RP35
(4271)
RP55
(5635)
RP75
(6709)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

HMM logo

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Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Medline:99193178
Previous IDs: none
Type: Domain
Author: Bateman A
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 information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.0 22.0
Trusted cut-off 22.0 22.0
Noise cut-off 21.9 21.9
Model length: 48
Family (HMM) version: 20
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 2 interactions for this family. More...

S4 tRNA-synt_1b

Structures

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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