This is the Wikipedia entry entitled "Transaldolase". More...
The Wikipedia text that you see displayed here is a download from Wikipedia. This means that the information we display is a copy of the information from the Wikipedia database. The button next to the article title ("Edit Wikipedia article") takes you to the edit page for the article directly within Wikipedia. You should be aware you are not editing our local copy of this information. Any changes that you make to the Wikipedia article will not be displayed here until we next download the article from Wikipedia. We currently download new content on a nightly basis.
Does Pfam agree with the content of the Wikipedia entry ?
Pfam has chosen to link families to Wikipedia articles. In some case we have created or edited these articles but in many other cases we have not made any direct contribution to the content of the article. The Wikipedia community does monitor edits to try to ensure that (a) the quality of article annotation increases, and (b) vandalism is very quickly dealt with. However, we would like to emphasise that Pfam does not curate the Wikipedia entries and we cannot guarantee the accuracy of the information on the Wikipedia page.
Editing Wikipedia articles
Before you edit for the first time
Wikipedia is a free, online encyclopedia. Although anyone can edit or contribute to an article, Wikipedia has some strong editing guidelines and policies, which promote the Wikipedia standard of style and etiquette. Your edits and contributions are more likely to be accepted (and remain) if they are in accordance with this policy.
You should take a few minutes to view the following pages:
How your contribution will be recorded
Anyone can edit a Wikipedia entry. You can do this either as a new user or you can register with Wikipedia and log on. When you click on the "Edit Wikipedia article" button, your browser will direct you to the edit page for this entry in Wikipedia. If you are a registered user and currently logged in, your changes will be recorded under your Wikipedia user name. However, if you are not a registered user or are not logged on, your changes will be logged under your computer's IP address. This has two main implications. Firstly, as a registered Wikipedia user your edits are more likely seen as valuable contribution (although all edits are open to community scrutiny regardless). Secondly, if you edit under an IP address you may be sharing this IP address with other users. If your IP address has previously been blocked (due to being flagged as a source of 'vandalism') your edits will also be blocked. You can find more information on this and creating a user account at Wikipedia.
If you have problems editing a particular page, contact us at email@example.com and we will try to help.
The community annotation is a new facility of the Pfam web site. If you have problems editing or experience problems with these pages please contact us.
Transaldolase Edit Wikipedia article
The following chemical reaction is catalyzed by transaldolase:
The pentose phosphate pathway has two metabolic functions: (1) generation of nicotinamide adenine dinucleotide phosphate (reduced NADPH), for reductive biosynthesis, and (2) formation of ribose, which is an essential component of ATP, DNA, and RNA. Transaldolase links the pentose phosphate pathway to glycolysis. In patients with deficiency of transaldolase, there's an accumulation of erythritol (from erythrose 4-phosphate), D-arabitol, and ribitol.
The deletion in 3 base pairs in the TALDO1 gene results in the absence of serine at position 171 of the transaldolase protein, which is part of a highly conserved region, suggesting that the mutation causes the transaldolase deficiency that is found in erythrocytes and lymphoblasts. The deletion of this amino acid can lead to liver cirrhosis and hepatosplenomegaly (enlarged spleen and liver) during early infancy. Transaldolase is also a target of autoimmunity in patients with multiple sclerosis.
Transaldolase is a single domain composed of 337 amino acids. The core structure is an α/β barrel, similar to other class I aldolases, made up of eight parallel β-sheets and seven α-helices. There are also seven additional α-helices that are not part of the barrel. Hydrophobic amino acids are located between the β-sheets in the barrel and the surrounding α-helices to contribute to packing, such as the area containing Leu-168, Phe-170, Phe-189, Gly-311, and Phe-315. In the crystal, human transaldolase forms a dimer, with the two subunits connected by 18 residues in each subunit. See mechanism to the left for details.
The active site, located in the center of the barrel, contains three key residues: lysine-142, glutamate-106, and aspartate-27. The lysine holds the sugar in place while the glutamate and aspartate act as proton donors and acceptors.
Mechanism of catalysis
The residue of lysine-142 in the active site of transaldolase forms a Schiff base with the keto group in sedoheptulose-7-phosphate after deprotonation by another active site residue, glutamate-106. The reaction mechanism is similar to the reverse reaction catalyzed by aldolase: The bond joining carbons 3 and 4 is broken, leaving dihydroxyacetone joined to the enzyme via a Schiff base. This cleavage reaction generates the unusual aldose sugar erythrose-4-phosphate. Then transaldolase catalyzes the condensation of glyceraldehyde-3-phosphate with the Schiff base of dihydroxyacetone, yielding enzyme-bound fructose 6-phosphate. Hydrolysis of the Schiff base liberates free fructose 6-phosphate, one of the products of the pentose phosphate pathway.
- PDB 1F05; Thorell S, Gergely P, Banki K, Perl A, Schneider G (June 2000). "The three-dimensional structure of human transaldolase". FEBS Lett. 475 (3): 205–8. doi:10.1016/S0014-5793(00)01658-6. PMID 10869557.
- Molecular graphics images were produced using the UCSF Chimera package from the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (October 2004). "UCSF Chimera–a visualization system for exploratory research and analysis". J Comput Chem 25 (13): 1605–12. doi:10.1002/jcc.20084. PMID 15264254.
- "Entrez Gene: transaldolase 1".
- Banki K, Eddy RL, Shows TB, Halladay DL, Bullrich F, Croce CM, Jurecic V, Baldini A, Perl A (October 1997). "The human transaldolase gene (TALDO1) is located on chromosome 11 at p15.4-p15.5". Genomics 45 (1): 233–8. doi:10.1006/geno.1997.4932. PMID 9339383.
- Verhoeven NM, Huck JH, Roos B, Struys EA, Salomons GS, Douwes AC, van der Knaap MS, Jakobs C (May 2001). "Transaldolase deficiency: liver cirrhosis associated with a new inborn error in the pentose phosphate pathway". Am. J. Hum. Genet. 68 (5): 1086–92. doi:10.1086/320108. PMC 1226089. PMID 11283793.
- Perl A (June 2007). "The pathogenesis of transaldolase deficiency". IUBMB Life 59 (6): 365–73. doi:10.1080/15216540701387188. PMID 17613166.
- Niland B, Perl A (2004). "Evaluation of autoimmunity to transaldolase in multiple sclerosis". Methods Mol. Med. 102: 155–71. doi:10.1385/1-59259-805-6:155. PMID 15286385.
- Jia J, Schörken U, Lindqvist Y, Sprenger GA, Schneider G (January 1997). "Crystal structure of the reduced Schiff-base intermediate complex of transaldolase B from Escherichia coli: mechanistic implications for class I aldolases". Protein Sci. 6 (1): 119–24. doi:10.1002/pro.5560060113. PMC 2143518. PMID 9007983.
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.
Transaldolase Provide feedback
No Pfam abstract.
Choi KH, Shi J, Hopkins CE, Tolan DR, Allen KN; , Biochemistry 2001;40:13868-13875.: Snapshots of catalysis: the structure of fructose-1,6-(bis)phosphate aldolase covalently bound to the substrate dihydroxyacetone phosphate. PUBMED:11705376 EPMC:11705376
Schorken U, Thorell S, Schurmann M, Jia J, Sprenger GA, Schneider G; , Eur J Biochem 2001;268:2408-2415.: Identification of catalytically important residues in the active site of Escherichia coli transaldolase. PUBMED:11298760 EPMC:11298760
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR001585
Transaldolase (EC) catalyses the reversible transfer of a three-carbon ketol unit from sedoheptulose 7-phosphate to glyceraldehyde 3-phosphate to form erythrose 4-phosphate and fructose 6-phosphate. This enzyme, together with transketolase, provides a link between the glycolytic and pentose-phosphate pathways. Transaldolase is an enzyme of about 34 kDa whose sequence has been well conserved throughout evolution. A lysine has been implicated [PUBMED:8109173] in the catalytic mechanism of the enzyme; it acts as a nucleophilic group that attacks the carbonyl group of fructose-6-phosphate.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Biological process||carbohydrate metabolic process (GO:0005975)|
- 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
- the Pfam graphic itself.
Loading domain graphics...
This large superfamily of TIM barrel enzymes all contain a common phosphate binding site. The phosphate is found in a variety of cofactors and ligands such as FMN [1,2].
The clan contains the following 57 members:Ala_racemase_N ALAD Aldolase AP_endonuc_2 BtpA CdhD CutC DAHP_synth_1 DAHP_synth_2 DeoC DHDPS DHO_dh DHquinase_I DUF1341 DUF2090 DUF556 DUF561 DUF692 DUF993 Dus F_bP_aldolase FMN_dh G3P_antiterm Glu_syn_central Glu_synthase His_biosynth HMGL-like IGPS IMPDH iPGM_N MtrH NanE NAPRTase NeuB NMO OMPdecase Orn_Arg_deC_N Oxidored_FMN PcrB PdxJ PhosphMutase PRAI Pterin_bind QRPTase_C Racemase_4 RhaA Ribul_P_3_epim SOR_SNZ Tagatose_6_P_K ThiG TIM TIM-br_sig_trns TMP-TENI Transaldolase Trp_syntA UvdE UxuA
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:
- Pfam viewer
- an HTML-based viewer that uses DAS to retrieve alignment fragments on request
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
If you find these logos useful in your own work, please consider citing the following article:
Note: You can also download the data file for the tree.
Curation and family details
|Seed source:||Pfam-B_787 (release 3.0)|
|Author:||Bateman A, Griffiths-Jones SR|
|Number in seed:||131|
|Number in full:||6718|
|Average length of the domain:||256.10 aa|
|Average identity of full alignment:||30 %|
|Average coverage of the sequence by the domain:||91.25 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||14|
|Download:||download the raw HMM for this family|
Weight segments by...
Change the size of the sunburst
selected sequences to HMM
a FASTA-format file
- 0 sequences
- 0 species
How the sunburst is generated
Colouring and labels
Anomalies in the taxonomy tree
Missing taxonomic levels
Unmapped species names
Too many species/sequences
The tree shows the occurrence of this domain across different species. More...
You can use the tree controls to manipulate how the interactive tree is displayed:
- show/hide the summary boxes
- highlight species that are represented in the seed alignment
- expand/collapse the tree or expand it to a given depth
- select a sub-tree or a set of species within the tree and view them graphically or as an alignment
- save a plain text representation of the tree
There is 1 interaction 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 Transaldolase domain has been found. There are 128 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.
Loading structure mapping...