Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
178  structures 1453  species 0  interactions 4072  sequences 41  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 "NADH dehydrogenase (ubiquinone)". More...

NADH dehydrogenase (ubiquinone) Edit Wikipedia article

  • From a page move: This is a redirect from a page that has been moved (renamed). This page was kept as a redirect to avoid breaking links, both internal and external, that may have been made to the old page name.

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

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
SymbolThioredoxin, Trx
PfamPF00085
Pfam clanCL0172
InterProIPR013766
PROSITEPDOC00172
SCOPe3trx / SUPFAM
CDDcd01659
Membranome337
Thioredoxin
Identifiers
SymbolTrx
Membranome260

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.

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.

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.

Examples

Human proteins containing this domain include:

References

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

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. Structurally related to thioredoxin-fold.

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


Internal 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...

Loading domain graphics...

Pfam Clan

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 and the UniProtKB 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
(61)
Full
(4072)
Representative proteomes UniProt
(6623)
RP15
(775)
RP35
(1800)
RP55
(3020)
RP75
(4153)
Jalview View  View  View  View  View  View  View 
HTML View  View           
PP/heatmap 1 View           

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

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

Format an alignment

  Seed
(61)
Full
(4072)
Representative proteomes UniProt
(6623)
RP15
(775)
RP35
(1800)
RP55
(3020)
RP75
(4153)
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
(61)
Full
(4072)
Representative proteomes UniProt
(6623)
RP15
(775)
RP35
(1800)
RP55
(3020)
RP75
(4153)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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: Pfam-B_9461 (release 7.6)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Wood V , Bateman A , Finn RD
Number in seed: 61
Number in full: 4072
Average length of the domain: 55.30 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 37.49 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 24.0 24.0
Trusted cut-off 24.2 24.1
Noise cut-off 23.9 23.9
Model length: 52
Family (HMM) version: 19
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

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

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

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...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

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 178 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.

Loading structure mapping...

AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A096PS68 View 3D Structure Click here
A0A0P0W8G3 View 3D Structure Click here
A0A0R0J5B1 View 3D Structure Click here
A0A1D6J4I7 View 3D Structure Click here
A0A1D6NEY6 View 3D Structure Click here
A0A1D8PQU3 View 3D Structure Click here
A4I6T3 View 3D Structure Click here
B4FA94 View 3D Structure Click here
B6TDN0 View 3D Structure Click here
B6TLX0 View 3D Structure Click here
C6SYI2 View 3D Structure Click here
C6SZP7 View 3D Structure Click here
C6Y4D2 View 3D Structure Click here
D3ZI75 View 3D Structure Click here
D3ZS58 View 3D Structure Click here
D3ZXF8 View 3D Structure Click here
F4J9E4 View 3D Structure Click here
I1K2A2 View 3D Structure Click here
I1MVQ6 View 3D Structure Click here
K7K9M8 View 3D Structure Click here
K7KXR0 View 3D Structure Click here
O02220 View 3D Structure Click here
O43678 View 3D Structure Click here
P0CB79 View 3D Structure Click here
P32388 View 3D Structure Click here
P82663 View 3D Structure Click here
P82669 View 3D Structure Click here
Q02370 View 3D Structure Click here
Q06090 View 3D Structure Click here
Q07842 View 3D Structure Click here
Q0MQ92 View 3D Structure Click here
Q1ZXN5 View 3D Structure Click here
Q4QR80 View 3D Structure Click here
Q4R5E2 View 3D Structure Click here
Q4VBI5 View 3D Structure Click here
Q54D02 View 3D Structure Click here
Q54RB6 View 3D Structure Click here
Q567W4 View 3D Structure Click here
Q5AH35 View 3D Structure Click here
Q6DH43 View 3D Structure Click here