Summary: Thioredoxin-like domain
This is the Wikipedia entry entitled "Thioredoxin fold". More...
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Thioredoxin fold Edit Wikipedia article
One molecule of human thioredoxin (PDB ID 1ERT), a canonical example of the thioredoxin fold class.
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.
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.
Human proteins containing this domain include:
- P4HB; P5; PDIA2; PDIA3; PDIA4; PDIA5; PDIA6; PDILT
- QSOX1; QSOX2
- TXN; TXN2; TXNDC1; TXNDC10; TXNDC11; TXNDC13; TXNDC14; TXNDC15; TXNDC16; TXNDC2; TXNDC3; TXNDC4; TXNDC5; TXNDC6; TXNDC8; TXNL1; TXNL3
- Creighton TE. (2000). Protein folding coupled to disulphide-bond formation. In Mechanisms of Protein Folding 2nd ed. Editor RH Pain. Oxford University Press.
Thioredoxin-like domain Provide feedback
No Pfam abstract.
Internal database links
|SCOOP:||Thioredoxin_7 Thioredoxin_8 Thioredoxin_9|
|Similarity to PfamA using HHSearch:||Thioredoxin Thioredoxin Calsequestrin|
External database links
This tab holds annotation information from the InterPro database.
No InterPro data for this Pfam family.
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
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This clan contains families related to the thioredoxin family. Thioredoxins are small enzymes that are involved in redox reactions via the reversible oxidation of an active centre disulfide bond. The thioredoxin fold consists of a 3 layer alpha/beta/alpha sandwich and a central beta sheet.
The clan contains the following 52 members:2Fe-2S_thioredx AhpC-TSA AhpC-TSA_2 Aminopep ArsC ArsD Calsequestrin DIM1 DSBA DUF1223 DUF1525 DUF1687 DUF2703 DUF2847 DUF4174 DUF836 DUF899 DUF953 ERp29_N Glutaredoxin GSHPx GST_N GST_N_2 GST_N_3 HyaE KaiB L51_S25_CI-B8 Metallopep MRP-S23 MRP-S25 Peptidase_M76 Phosducin Redoxin SCO1-SenC SelP_N Sep15_SelM SH3BGR T4_deiodinase Thioredox_DsbH Thioredoxin Thioredoxin_2 Thioredoxin_3 Thioredoxin_4 Thioredoxin_5 Thioredoxin_6 Thioredoxin_7 Thioredoxin_8 Thioredoxin_9 Tom37 TraF YtfJ_HI0045 Zincin_1
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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Curation and family details
|Number in seed:||47|
|Number in full:||2777|
|Average length of the domain:||177.00 aa|
|Average identity of full alignment:||17 %|
|Average coverage of the sequence by the domain:||36.98 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||2|
|Download:||download the raw HMM for this family|
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There are 3 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 Thioredoxin_6 domain has been found. There are 39 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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