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1  structure 307  species 0  interactions 788  sequences 4  architectures

Family: L51_S25_CI-B8 (PF05047)

Summary: Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Thioredoxin fold". More...

Thioredoxin fold Edit Wikipedia article

Thioredoxin
Thioredoxin-fold-1ert.png
One molecule of human thioredoxin (PDB ID 1ERT), a canonical example of the thioredoxin fold class.
Identifiers
Symbol Thioredoxin
Pfam PF00085
Pfam clan CL0172
InterPro IPR013766
PROSITE PDOC00172
SCOP 3trx
SUPERFAMILY 3trx
CDD cd01659

The thioredoxin fold is a protein fold common to enzymes that catalyze disulfide bond formation and isomerization. The fold is named for the canonical example thioredoxin and is found in both prokaryotic and eukaryotic proteins. It is an example of an alpha/beta protein fold that has oxidoreductase activity. The fold's spatial topology consists of a four-stranded antiparallel beta sheet sandwiched between three alpha helices. The strand topology is 2134 with 3 antiparallel to the rest.

Contents

[edit] Sequence conservation

Despite sequence variability in many regions of the fold, thioredoxin proteins share a common active site sequence with two reactive cysteine residues: Cys-X-Y-Cys, where X and Y are often but not necessarily hydrophobic amino acids. The reduced form of the protein contains two free thiol groups at the cysteine residues, whereas the oxidized form contains a disulfide bond between them.

[edit] Disulfide bond formation

Different thioredoxin fold-containing proteins vary greatly in their reactivity and in the pKa of their free thiols, which derives from the ability of the overall protein structure to stabilize the activated thiolate. Although the structure is fairly consistent among proteins containing the thioredoxin fold, the pKa is extremely sensitive to small variations in structure, especially in the placement of protein backbone atoms near the first cysteine.

[edit] Examples

Human proteins containing this domain include:

[edit] References

  • Creighton TE. (2000). Protein folding coupled to disulphide-bond formation. In Mechanisms of Protein Folding 2nd ed. Editor RH Pain. Oxford University Press.

[edit] 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 L51 / S25 / CI-B8 domain Provide feedback

The proteins in this family are located in the mitochondrion. The family includes ribosomal protein L51, and S25. This family also includes mitochondrial NADH-ubiquinone oxidoreductase B8 subunit (CI-B8) EC:1.6.5.3. It is not known whether all members of this family form part of the NADH-ubiquinone oxidoreductase and whether they are also all ribosomal proteins.

Literature references

  1. Gan X, Kitakawa M, Yoshino KI, Oshiro N, Yonezawa K, Isono K; , Eur J Biochem 2002;269:5203-5214.: Tag-mediated isolation of yeast mitochondrial ribosome and mass spectrometric identification of its new components. PUBMED:12392552 EPMC:12392552

  2. Koc EC, Burkhart W, Blackburn K, Moseley A, Koc H, Spremulli LL; , J Biol Chem 2000;275:32585-32591.: A proteomics approach to the identification of mammalian mitochondrial small subunit ribosomal proteins. PUBMED:10938081 EPMC:10938081

  3. Ton C, Hwang DM, Dempsey AA, Liew CC; , Biochem Biophys Res Commun 1997;241:589-594.: Identification and primary structure of five human NADH-ubiquinone oxidoreductase subunits. PUBMED:9425316 EPMC:9425316


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007741

Proteins containing this domain are located in the mitochondrion and include ribosomal protein L51, and S25. This domain is also found in mitochondrial NADH-ubiquinone oxidoreductase B8 subunit (CI-B8) EC. It is not known whether all members of this family form part of the NADH-ubiquinone oxidoreductase and whether they are also all ribosomal proteins.

Domain organisation

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

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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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

View options

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
(67)
Full
(788)
Representative proteomes NCBI
(748)
Meta
(8)
RP15
(164)
RP35
(279)
RP55
(432)
RP75
(534)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(67)
Full
(788)
Representative proteomes NCBI
(748)
Meta
(8)
RP15
(164)
RP35
(279)
RP55
(432)
RP75
(534)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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
(67)
Full
(788)
Representative proteomes NCBI
(748)
Meta
(8)
RP15
(164)
RP35
(279)
RP55
(432)
RP75
(534)
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

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: Pfam-B_9461 (release 7.6)
Previous IDs: none
Type: Domain
Author: Wood V, Bateman A, Finn RD
Number in seed: 67
Number in full: 788
Average length of the domain: 54.90 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 38.29 %

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 21.0 21.0
Trusted cut-off 21.2 21.2
Noise cut-off 20.9 20.6
Model length: 52
Family (HMM) version: 11
Download: download the raw HMM for this family

Species distribution

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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 L51_S25_CI-B8 domain has been found. There are 1 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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