Summary: Thioredoxin 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 domain Provide feedback
No Pfam abstract.
Internal database links
|SCOOP:||Thioredoxin_4 TraF Thioredoxin_5 Thioredoxin_6 Thioredoxin_7 Thioredoxin_8 Thioredoxin_9|
|Similarity to PfamA using HHSearch:||Thioredoxin Glutaredoxin DUF836 ArsD Thioredoxin_2 Thioredoxin_4 TraF|
This tab holds annotation information from the InterPro database.
InterPro entry IPR012336
Several biological processes regulate the activity of target proteins through changes in the redox state of thiol groups (S2 to SH2), where a hydrogen donor is linked to an intermediary disulphide protein. Such processes include the ferredoxin/thioredoxin system, the NADP/thioredoxin system, and the glutathione/glutaredoxin system [PUBMED:15862094]. Several of these disulphide proteins share a common structure, consisting of a three-layer alpha/beta/alpha core. Proteins that contain domains with a thioredoxin-like fold include:
- Arsenate reductase (ArsC) [PUBMED:11709171]
- Calsequestrin (contains three tandem repeats of this fold) [PUBMED:9628486]
- Circadian oscillation regulator KaiB [PUBMED:15071498]
- Disulphide bond isomerase DsbC and DsbG (C-terminal domain) [PUBMED:10700276, PUBMED:15184683]
- Disulphide bond facilitator DsbA (contains an alpha-helical insertion) [PUBMED:9300489]
- Endoplasmic reticulum protein ERP29 (N-terminal domain) [PUBMED:11435111]
- Glutathione S-transferase (GST) (N-terminal domain) [PUBMED:16597834]
- Mitochondrial ribosomal protein L51/S25/CI-B8 domain (variable positions for Cys residues in active site) [PUBMED:15341729]
- Phosducin [PUBMED:8898209]
- Protein disulphide isomerase (PDI) (contains two tandem repeats of this fold) [PUBMED:10383197]
- Glutathione peroxidase-like enzymes [PUBMED:6852035]
- Selenoprotein W-related [PUBMED:16319061]
- SH3-binding glutamic acid-rich protein like (SH3BGR) (lacks both conserved Cys residues) [PUBMED:15120624]
- Spliceosomal protein U5-15Kd [PUBMED:10610776]
- Thioltransferases, including thioredoxin [PUBMED:2181145], glutaredoxon [PUBMED:1304339], hybrid peroxiredoxin hyPrx5 [PUBMED:12529327]
- Thioredoxin-like 2Fe-2S ferredoxin [PUBMED:12089152]
- 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
- the number of residues in the 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 57 members:2Fe-2S_thioredx AhpC-TSA AhpC-TSA_2 Aminopep ArsC ArsD Calsequestrin DIM1 DSBA DUF1223 DUF1462 DUF1525 DUF1687 DUF2703 DUF2847 DUF4174 DUF836 DUF899 DUF953 ERp29_N GILT Glutaredoxin GSHPx GST_N GST_N_2 GST_N_3 GST_N_4 HyaE KaiB L51_S25_CI-B8 Metallopep MRP-S23 MRP-S25 OST3_OST6 Peptidase_M76 Phosducin Rdx 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 UniProtKB sequence database using the family HMM
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
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Curation and family details
|Number in seed:||78|
|Number in full:||1513|
|Average length of the domain:||77.10 aa|
|Average identity of full alignment:||25 %|
|Average coverage of the sequence by the domain:||27.87 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||4|
|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_3 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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