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0  structures 122  species 0  interactions 125  sequences 3  architectures

Family: L31 (PF09784)

Summary: Mitochondrial ribosomal protein L31

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This is the Wikipedia entry entitled "Ribosomal protein". More...

Ribosomal protein Edit Wikipedia article

Mitochondrial ribosomal protein L31
Identifiers
Symbol L31
Pfam PF09784
InterPro IPR016340
PROSITE PDOC00880
SCOP 1m90
SUPERFAMILY 1m90

A ribosomal protein is any of the proteins that, in conjunction with rRNA, make up the ribosomal subunits involved in the cellular process of translation. A large part of the knowledge about these organic molecules has come from the study of E. coli ribosomes. Most ribosomal proteins have been isolated and specific antibodies have been produced. These, together with electronic microscopy and the use of certain reactives, have allowed for the determination of the topography of the proteins in the ribosome.

Proteins in E. coli ribosomes

The ribosome of E. coli has about 22 proteins in the small subunit (labelled S1 to S22) and 34 proteins in the large subunit (L1 to L36). All of them are different with three exceptions: one protein is found in both subunits (S20 and L26), L7 and L12 are acetylated and methylated forms of the same protein, and L8 is a complex of L7/L12 and L10. In addition, L31 is known to exist in two forms, the full length at 7.9 kilodaltons (kDa) and fragmented at 7.0 kDa. This is why the number of proteins in a ribosome is of 56. Except for S1 (with a molecular weight of 61.2 kDa), the other proteins range in weight between 4.4 and 29.7 kDa.[1]

Disposition in the small ribosomal subunit

In the small (30S) subunit of E. coli ribosomes, the proteins denoted S4, S7, S8, S15, S17, S20 bind independently to 16S rRNA. After assembly of these primary binding proteins, S5, S6, S9, S12, S13, S16, S18, and S19 bind to the growing ribosome. These proteins also potentiate the addition of S2, S3, S10, S11, S14, and S21. Protein binding to helical junctions is important for initiating the correct tertiary fold of RNA and to organize the overall structure. Nearly all the proteins contain one or more globular domains. Moreover, nearly all contain long extensions that can contact the RNA in far-reaching regions. Additional stabilization results from the proteins' basic residues, as these neutralize the charge repulsion of the RNA backbone. Protein-protein interactions also exist to hold structure together by electrostatic and hydrogen bonding interactions. Theoretical investigations pointed to correlated effects of protein-binding onto binding affinities during the assembly process [2]

See also

References

  1. ^ Arnold RJ, Reilly JP. (1999) "Observation of Escherichia coli ribosomal proteins and their posttranslational modifications by mass spectrometry." Anal Biochem. v269(1): pp 105-12. PMID 10094780
  2. ^ Hamacher K, Trylska J, McCammon JA. (2006) "Dependency Map of Proteins in the Small Ribosomal Subunit." PLoS Comput. Biol. v2(2): e10. PMID 16485038
  • De Robertis and De Robertis, Biología Celular y Molecular 10th ed., El Ateneo, Buenos Aires, 1982, ISBN 950-02-0027-9 (in Spanish)
  • Monika Martick, Lucas H. Horan, Harry F. Noller and William G. Scott. A discontinuous hammerhead ribozyme embedded in a mammalian messenger RNA. doi:10.1038/nature07117

External links

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.

Mitochondrial ribosomal protein L31 Provide feedback

This is a family of mitochondrial ribosomal proteins. L31 is essential for mitochondrial function in yeast [2].

Literature references

  1. Grohmann L, Graack HR, Kitakawa M; , Eur J Biochem. 1989;183:155-160.: Molecular cloning of the nuclear gene for mitochondrial ribosomal protein YmL31 from Saccharomyces cerevisiae. PUBMED:2666132 EPMC:2666132

  2. Graack HR, Grohmann L, Kitakawa M; , Biochimie. 1991;73:837-844.: The nuclear coded mitoribosomal proteins YmL27 and YmL31 are both essential for mitochondrial function in yeast. PUBMED:1764528 EPMC:1764528


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR016340

This group represents a predicted mitochondrial ribosomal protein L31, fungal type [PUBMED:2666132, PUBMED:1764528].

Domain organisation

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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.

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Full
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Representative proteomes NCBI
(120)
Meta
(0)
RP15
(26)
RP35
(57)
RP55
(86)
RP75
(100)
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  Seed
(10)
Full
(125)
Representative proteomes NCBI
(120)
Meta
(0)
RP15
(26)
RP35
(57)
RP55
(86)
RP75
(100)
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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.

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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

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Curation View help on the curation process

Seed source: Pfam-B_24102 (release 21.0)
Previous IDs: none
Type: Family
Author: Mistry J, Wood V
Number in seed: 10
Number in full: 125
Average length of the domain: 106.30 aa
Average identity of full alignment: 53 %
Average coverage of the sequence by the domain: 91.26 %

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 20.5 20.5
Trusted cut-off 20.5 31.5
Noise cut-off 19.3 20.4
Model length: 103
Family (HMM) version: 4
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Species distribution

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