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970  structures 9273  species 15  interactions 13173  sequences 82  architectures

Family: Ribosomal_S2 (PF00318)

Summary: Ribosomal protein S2

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Ribosomal protein S2 Provide feedback

No Pfam abstract.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001865

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 S2 proteins have been shown to belong to a family that includes 40S ribosomal subunit 40kDa proteins, putative laminin-binding proteins, NAB-1 protein and 29.3kDa protein from Haloarcula marismortui [PUBMED:1531984, PUBMED:8119397]. The laminin-receptor proteins are thus predicted to be the eukaryotic homologue of the eubacterial S2 risosomal proteins [PUBMED:7899076].

Ribosomal protein S2 (RPS2) are involved in formation of the translation initiation complex, where it might contact the messenger RNA and several components of the ribosome. It has been shown that in Escherichia coli RPS2 is essential for the binding of ribosomal protein S1 to the 30s ribosomal subunit. In humans, most likely in all vertebrates, and perhaps in all metazoans, the protein also functions as the 67 kDa laminin receptor (LAMR1 or 67LR), which is formed from a 37 kDa precursor, and is overexpressed in many tumors. 67LR is a cell surface receptor which interacts with a variety of ligands, laminin-1 and others. It is assumed that the ligand interactions are mediated via the conserved C terminus, which becomes extracellular as the protein undergoes conformational changes which are not well understood. Specifically, a conserved palindromic motif, LMWWML, may participate in the interactions. 67LR plays essential roles in the adhesion of cells to the basement membrane and subsequent signalling events, and has been linked to several diseases. Some evidence also suggests that the precursor of 67LR, 37LRP is also present in the nucleus in animals, where it appears associated with histones [PUBMED:18464793, PUBMED:18269348, PUBMED:18063583, PUBMED:9718729, PUBMED:10188208, PUBMED:18573314, PUBMED:15473865, PUBMED:3905390, PUBMED:6272196, PUBMED:1586449, PUBMED:10566557, PUBMED:12068815, PUBMED:12422231, PUBMED:17051149].

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 SIS (CL0067), which has the following description:

This catalytic domain catalyses isomerisation reactions of a variety of sugars [1].

The clan contains the following 8 members:

bact-PGI_C DUF2529 HobA PGI Phosphatase Ribosomal_S2 SIS SIS_2

Alignments

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
(469)
Full
(13173)
Representative proteomes UniProt
(36842)
NCBI
(33186)
Meta
(2987)
RP15
(3777)
RP35
(8632)
RP55
(12562)
RP75
(16842)
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PP/heatmap 1                

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(469)
Full
(13173)
Representative proteomes UniProt
(36842)
NCBI
(33186)
Meta
(2987)
RP15
(3777)
RP35
(8632)
RP55
(12562)
RP75
(16842)
Alignment:
Format:
Order:
Sequence:
Gaps:
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Download options

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
(469)
Full
(13173)
Representative proteomes UniProt
(36842)
NCBI
(33186)
Meta
(2987)
RP15
(3777)
RP35
(8632)
RP55
(12562)
RP75
(16842)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

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 View help on the curation process

Seed source: Prosite
Previous IDs: S2;
Type: Family
Sequence Ontology: SO:0100021
Author: Finn RD
Number in seed: 469
Number in full: 13173
Average length of the domain: 168.00 aa
Average identity of full alignment: 35 %
Average coverage of the sequence by the domain: 73.05 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 26.1 26.1
Trusted cut-off 26.1 26.1
Noise cut-off 25.8 26.0
Model length: 215
Family (HMM) version: 20
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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Interactions

There are 15 interactions for this family. More...

Ribosomal_S3_C Ribosomal_S9 Ribosomal_S21e Ribosomal_S17e Ribosomal_S8 WD40 Ribosomal_L3 WD40 Ribosomal_S2 Ribosomal_S5 Ribosomal_S5 Ribosomal_S21 Ribosomal_S17e Ribosomal_S26e Ribosomal_S28e

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 Ribosomal_S2 domain has been found. There are 970 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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