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32  structures 2058  species 1  interaction 2635  sequences 24  architectures

Family: Rdx (PF10262)

Summary: Rdx family

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Rdx family Provide feedback

This entry is an approximately 100 residue region of selenoprotein-T, conserved from plants to humans. The protein binds to UDP-glucose:glycoprotein glucosyltransferase (UGTR), the endoplasmic reticulum (ER)-resident protein, which is known to be involved in the quality control of protein folding [1]. Selenium (Se) plays an essential role in cell survival and most of the effects of Se are probably mediated by selenoproteins, including selenoprotein T. However, despite its binding to UGTR and that its mRNA is up-regulated in extended asphyxia, the function of the protein and hence of this region of it is unknown [2]. Selenoprotein W contains selenium as selenocysteine in the primary protein structure and levels of this selenoprotein are affected by selenium [3].

Literature references

  1. Korotkov KV, Kumaraswamy E, Zhou Y, Hatfield DL, Gladyshev VN; , J Biol Chem. 2001;276:15330-15336.: Association between the 15-kDa selenoprotein and UDP-glucose:glycoprotein glucosyltransferase in the endoplasmic reticulum of mammalian cells. PUBMED:11278576 EPMC:11278576

  2. Ikematsu K, Tsuda R, Tsuruya S, Nakasono I; , Forensic Sci Int. 2007;169:168-172.: Identification of novel genes expressed in hypoxic brain condition by fluorescence differential display. PUBMED:17034973 EPMC:17034973

  3. Gu QP, Ream W, Whanger PD; , Biometals 2002;15:411-420.: Selenoprotein W gene regulation by selenium in L8 cells. PUBMED:12405536 EPMC:12405536

  4. Dikiy A, Novoselov SV, Fomenko DE, Sengupta A, Carlson BA, Cerny RL, Ginalski K, Grishin NV, Hatfield DL, Gladyshev VN; , Biochemistry. 2007;46:6871-6882.: SelT, SelW, SelH, and Rdx12: genomics and molecular insights into the functions of selenoproteins of a novel thioredoxin-like family. PUBMED:17503775 EPMC:17503775


This tab holds annotation information from the InterPro database.

InterPro entry IPR011893

This entry represents the Rdx family of selenoproteins, which includes mammalian selenoproteins SelW, SelV, SelT and SelH, bacterial SelW-like proteins and cysteine-containing proteins of unknown function in all three domains of life. Mammalian Rdx12 and its fish selenoprotein orthologues are also members of this family [PUBMED:17503775]. These proteins possess a thioredoxin-like fold and a conserved CXXC or CxxU (U is selenocysteine) motif near the N terminus, suggesting a redox function. Rdx proteins can use catalytic cysteine (or selenocysteine) to form transient mixed disulphides with substrate proteins. Selenium (Se) plays an essential role in cell survival and most of the effects of Se are probably mediated by selenoproteins.

Selenoprotein W (SelW) plays an important role in protection of neurons from oxidative stress during neuronal development [PUBMED:19466610], [PUBMED:12405536].

Selenoprotein T (SelT) is conserved from plants to humans. SelT is localized to the endoplasmic reticulum through a hydrophobic domain. The protein binds to UDP-glucose:glycoprotein glucosyltransferase (UGTR), the endoplasmic reticulum (ER)-resident protein, which is known to be involved in the quality control of protein folding [PUBMED:11278576, PUBMED:19747065]. The function of SelT is unknown, although it may have a role in PACAP signaling during PC12 cell differentiation [PUBMED:17034973, PUBMED:18198219].

Selenoprotein H (SelH) protects neurons against UVB-induced damage by inhibiting apoptotic cell death pathways, by preventing mitochondrial depolarization, and by promoting cell survival pathways [PUBMED:19766117].

Domain organisation

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Pfam Clan

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.

  Seed
(263)
Full
(2635)
Representative proteomes UniProt
(5924)
NCBI
(7114)
Meta
(67)
RP15
(622)
RP35
(1475)
RP55
(2347)
RP75
(3285)
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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
(263)
Full
(2635)
Representative proteomes UniProt
(5924)
NCBI
(7114)
Meta
(67)
RP15
(622)
RP35
(1475)
RP55
(2347)
RP75
(3285)
Alignment:
Format:
Order:
Sequence:
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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
(263)
Full
(2635)
Representative proteomes UniProt
(5924)
NCBI
(7114)
Meta
(67)
RP15
(622)
RP35
(1475)
RP55
(2347)
RP75
(3285)
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.

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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: KOGs (KOG3286) & COG3526
Previous IDs: SelT;
Type: Family
Sequence Ontology: SO:0100021
Author: KOGs, Finn RD , Coggill P
Number in seed: 263
Number in full: 2635
Average length of the domain: 87.90 aa
Average identity of full alignment: 32 %
Average coverage of the sequence by the domain: 59.62 %

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 22.1 22.1
Trusted cut-off 22.1 22.1
Noise cut-off 21.9 22.0
Model length: 74
Family (HMM) version: 9
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

Rdx

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 Rdx domain has been found. There are 32 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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