Summary: S4 domain
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This is the Wikipedia entry entitled "S4 protein domain". More...
S4 protein domain Edit Wikipedia article
![]() | It has been suggested that this article be merged into 40S ribosomal protein S4, Y isoform 1. (Discuss) Proposed since October 2019. |
S4 | |||||||||
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Identifiers | |||||||||
Symbol | S4 | ||||||||
Pfam | PF01479 | ||||||||
Pfam clan | CL0492 | ||||||||
InterPro | IPR002942 | ||||||||
PROSITE | PDOC00549 | ||||||||
MEROPS | S41 | ||||||||
SCOPe | 1c06 / SUPFAM | ||||||||
CDD | cd00165 | ||||||||
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In molecular biology, S4 domain refers to a small RNA-binding protein domain found in a ribosomal protein named S4. The S4 domain is 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 ribosome-associated protein.[1]
The S4 protein helps to initiate assembly of the 16S rRNA. In this way proteins serve to organise and stabilise the rRNA tertiary structure.[2][3]
Function
The function of the S4 domain is to be an RNA-binding protein. S4 is a multifunctional protein, and it must bind to the 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
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
- ^ a b Aravind L, Koonin EV (March 1999). "Novel predicted RNA-binding domains associated with the translation machinery" (PDF). 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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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
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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
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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
Internal database links
SCOOP: | Ribosomal_S4 S4_2 TyrRSs_C |
Similarity to PfamA using HHSearch: | S4_2 TyrRSs_C |
External database links
HOMSTRAD: | S4 |
SCOP: | 1c06 |
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.
Molecular function | RNA binding (GO:0003723) |
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 4 members:
Ribosomal_S4 S4 S4_2 TyrRSs_CAlignments
We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
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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 (116) |
Full (43618) |
Representative proteomes | UniProt (210163) |
NCBI (242029) |
Meta (7290) |
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RP15 (5643) |
RP35 (20325) |
RP55 (40867) |
RP75 (70664) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
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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 (116) |
Full (43618) |
Representative proteomes | UniProt (210163) |
NCBI (242029) |
Meta (7290) |
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---|---|---|---|---|---|---|---|---|---|
RP15 (5643) |
RP35 (20325) |
RP55 (40867) |
RP75 (70664) |
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Raw Stockholm | |||||||||
Gzipped |
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logo
HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...
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.
Note: You can also download the data file for the tree.
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
Seed source: | Medline:99193178 |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Bateman A |
Number in seed: | 116 |
Number in full: | 43618 |
Average length of the domain: | 46.90 aa |
Average identity of full alignment: | 26 % |
Average coverage of the sequence by the domain: | 17.51 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 48 | ||||||||||||
Family (HMM) version: | 26 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Interactions
There are 18 interactions for this family. More...
Ribosomal_S30 PseudoU_synth_2 EFG_IV Ribosomal_S24e RS4NT Ribosomal_S4e Ribosomal_L5 KOW Ribosomal_S30 S4 Ribosomal_S4 RS4NT Ribosomal_S7e Ribosomal_S24e Ribosomal_L5_C FtsJ Ribosom_S12_S23 PseudoU_synth_2Structures
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 1201 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 sequence.
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