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301  structures 8641  species 0  interactions 49496  sequences 274  architectures

Family: Transket_pyr (PF02779)

Summary: Transketolase, pyrimidine binding domain

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Transketolase, pyrimidine binding domain Provide feedback

This family includes transketolase enzymes, pyruvate dehydrogenases, and branched chain alpha-keto acid decarboxylases.

Literature references

  1. Nikkola M, Lindqvist Y, Schneider G; , J Mol Biol 1994;238:387-404.: Refined structure of transketolase from Saccharomyces cerevisiae at 2.0 A resolution. PUBMED:8176731 EPMC:8176731

  2. Lindqvist Y, Schneider G, Ermler U, Sundstrom M; , EMBO J 1992;11:2373-2379.: Three-dimensional structure of transketolase, a thiamine diphosphate dependent enzyme, at 2.5 A resolution. PUBMED:1628611 EPMC:1628611


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR005475

Transketolase EC (TK) catalyzes the reversible transfer of a two-carbon ketol unit from xylulose 5-phosphate to an aldose receptor, such as ribose 5-phosphate, to form sedoheptulose 7-phosphate and glyceraldehyde 3- phosphate. This enzyme, together with transaldolase, provides a link between the glycolytic and pentose-phosphate pathways. TK requires thiamine pyrophosphate as a cofactor. In most sources where TK has been purified, it is a homodimer of approximately 70 Kd subunits. TK sequences from a variety of eukaryotic and prokaryotic sources [ PUBMED:1567394 , PUBMED:1737042 ] show that the enzyme has been evolutionarily conserved. In the peroxisomes of methylotrophic yeast Pichia angusta (Yeast) (Hansenula polymorpha), there is a highly related enzyme, dihydroxy-acetone synthase (DHAS) EC (also known as formaldehyde transketolase), which exhibits a very unusual specificity by including formaldehyde amongst its substrates.

1-deoxyxylulose-5-phosphate synthase (DXP synthase) [ PUBMED:9371765 ] is an enzyme so far found in bacteria (gene dxs) and plants (gene CLA1) which catalyzes the thiamine pyrophosphoate-dependent acyloin condensation reaction between carbon atoms 2 and 3 of pyruvate and glyceraldehyde 3-phosphate to yield 1-deoxy-D- xylulose-5-phosphate (dxp), a precursor in the biosynthetic pathway to isoprenoids, thiamine (vitamin B1), and pyridoxol (vitamin B6). DXP synthase is evolutionary related to TK. The N-terminal section, contains a histidine residue which appears to function in proton transfer during catalysis [ PUBMED:1628611 ]. In the central section there are conserved acidic residues that are part of the active cleft and may participate in substrate-binding [ PUBMED:1628611 ]. This family includes transketolase enzymes EC and also partially matches to 2-oxoisovalerate dehydrogenase beta subunit SWISSPROT EC . Both these enzymes utilise thiamine pyrophosphate as a cofactor, suggesting there may be common aspects in their mechanism of catalysis.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan THDP-binding (CL0254), which has the following description:

This clan includes pyruvate dehydrogenases, branched chain alpha-keto acid decarboxylases, phosphoketolases and the pyrimidine binding region of transketolases.

The clan contains the following 10 members:

DXP_synthase_N E1_dh PDH_E1_M POR_N TPP_enzyme_C TPP_enzyme_N Transket_pyr Transketolase_N XFP XFP_N

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...

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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
(80)
Full
(49496)
Representative proteomes UniProt
(200696)
RP15
(6580)
RP35
(22809)
RP55
(47997)
RP75
(79322)
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PP/heatmap 1            

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

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

Format an alignment

  Seed
(80)
Full
(49496)
Representative proteomes UniProt
(200696)
RP15
(6580)
RP35
(22809)
RP55
(47997)
RP75
(79322)
Alignment:
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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
(80)
Full
(49496)
Representative proteomes UniProt
(200696)
RP15
(6580)
RP35
(22809)
RP55
(47997)
RP75
(79322)
Raw Stockholm Download   Download   Download   Download   Download   Download    
Gzipped 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: Prosite
Previous IDs: transketolaseD2; transket_pyr;
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A , Finn RD , Griffiths-Jones SR
Number in seed: 80
Number in full: 49496
Average length of the domain: 176.50 aa
Average identity of full alignment: 24 %
Average coverage of the sequence by the domain: 29.15 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.4 20.4
Trusted cut-off 20.4 20.4
Noise cut-off 20.3 20.3
Model length: 178
Family (HMM) version: 26
Download: download the raw HMM for this family

Species distribution

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Selections

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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 Transket_pyr domain has been found. There are 301 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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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
A0A0P0W9W2 View 3D Structure Click here
A0A0R0FHC7 View 3D Structure Click here
A0A0R0G7H4 View 3D Structure Click here
A0A0R0GCP9 View 3D Structure Click here
A0A0R0GVA0 View 3D Structure Click here
A0A0R0GVA0 View 3D Structure Click here
A0A0R0IAU8 View 3D Structure Click here
A0A0R4IP01 View 3D Structure Click here
A0A0R4J2U8 View 3D Structure Click here
A0A0R4J653 View 3D Structure Click here
A0A1D6ECJ6 View 3D Structure Click here
A0A1D6EEB5 View 3D Structure Click here
A0A1D6HUR1 View 3D Structure Click here
A0A1D6I872 View 3D Structure Click here
A0A1D6IA31 View 3D Structure Click here
A0A1D6KKD1 View 3D Structure Click here
A0A1D6LLS4 View 3D Structure Click here
A0A1D6M458 View 3D Structure Click here
A0A1D6NVN3 View 3D Structure Click here
A0A1D6NVZ7 View 3D Structure Click here
A0A1D6PBQ8 View 3D Structure Click here
A0A1D8PJ26 View 3D Structure Click here
A0A1I9LTC7 View 3D Structure Click here
A0A2R8QUY1 View 3D Structure Click here
A2ATU0 View 3D Structure Click here
A4I115 View 3D Structure Click here
A4I1L9 View 3D Structure Click here
A4I2P6 View 3D Structure Click here
A4IAQ6 View 3D Structure Click here
A4ID50 View 3D Structure Click here
A8JNU6 View 3D Structure Click here
B4FUC1 View 3D Structure Click here
B6T565 View 3D Structure Click here
B7ZWU6 View 3D Structure Click here
C6KSV3 View 3D Structure Click here
C6T827 View 3D Structure Click here
C6TGA9 View 3D Structure Click here
D3ZHE7 View 3D Structure Click here
D3ZPV2 View 3D Structure Click here
D3ZQD3 View 3D Structure Click here
E5RPJ6 View 3D Structure Click here
E7EZ05 View 3D Structure Click here
E7F8S4 View 3D Structure Click here
E7FGK9 View 3D Structure Click here
E9Q7L0 View 3D Structure Click here
F4IW47 View 3D Structure Click here
F4IWV2 View 3D Structure Click here
I1JDR2 View 3D Structure Click here
I1JJD2 View 3D Structure Click here
I1JM18 View 3D Structure Click here
I1KN45 View 3D Structure Click here
I1KRU1 View 3D Structure Click here
I1KX60 View 3D Structure Click here
I1LFG4 View 3D Structure Click here
I1M1A4 View 3D Structure Click here
I1M6N5 View 3D Structure Click here
I1M8Z1 View 3D Structure Click here
I1MRC8 View 3D Structure Click here
I1MSU3 View 3D Structure Click here
I1N1T9 View 3D Structure Click here
I1NF12 View 3D Structure Click here
K7KIL5 View 3D Structure Click here
K7KTK7 View 3D Structure Click here
K7L9B1 View 3D Structure Click here
K7LPA3 View 3D Structure Click here
K7MVB9 View 3D Structure Click here
K7TJV6 View 3D Structure Click here
O17759 View 3D Structure Click here
O22567 View 3D Structure Click here
O44451 View 3D Structure Click here
O50408 View 3D Structure Click here
O61199 View 3D Structure Click here
O64688 View 3D Structure Click here
O74378 View 3D Structure Click here
P0AFG3 View 3D Structure Click here
P11177 View 3D Structure Click here
P20967 View 3D Structure Click here
P21953 View 3D Structure Click here
P23254 View 3D Structure Click here
P27302 View 3D Structure Click here
P29401 View 3D Structure Click here
P32473 View 3D Structure Click here
P33315 View 3D Structure Click here
P33570 View 3D Structure Click here
P35738 View 3D Structure Click here
P40142 View 3D Structure Click here
P49432 View 3D Structure Click here
P50137 View 3D Structure Click here
P51854 View 3D Structure Click here
P77488 View 3D Structure Click here
P9WG25 View 3D Structure Click here
P9WIS1 View 3D Structure Click here
P9WIS5 View 3D Structure Click here
P9WNS3 View 3D Structure Click here
Q02218 View 3D Structure Click here
Q09171 View 3D Structure Click here
Q0DEU8 View 3D Structure Click here
Q0J0H4 View 3D Structure Click here
Q10G39 View 3D Structure Click here
Q23629 View 3D Structure Click here
Q2FY53 View 3D Structure Click here
Q2FYM1 View 3D Structure Click here
Q2FYT8 View 3D Structure Click here
Q2G2A5 View 3D Structure Click here
Q2QM55 View 3D Structure Click here
Q38799 View 3D Structure Click here
Q38854 View 3D Structure Click here
Q4CMR4 View 3D Structure Click here
Q4CTE8 View 3D Structure Click here
Q4CW17 View 3D Structure Click here
Q4CYI3 View 3D Structure Click here
Q4DB91 View 3D Structure Click here
Q4DCI2 View 3D Structure Click here
Q4DEQ0 View 3D Structure Click here
Q4DKY2 View 3D Structure Click here
Q4DU82 View 3D Structure Click here
Q4DXQ0 View 3D Structure Click here
Q4KLP0 View 3D Structure Click here
Q54JE4 View 3D Structure Click here
Q54VG0 View 3D Structure Click here
Q556J0 View 3D Structure Click here
Q55FN7 View 3D Structure Click here
Q58092 View 3D Structure Click here
Q5A5V6 View 3D Structure Click here
Q5A750 View 3D Structure Click here
Q5PRA2 View 3D Structure Click here
Q5XI78 View 3D Structure Click here
Q60597 View 3D Structure Click here
Q69LD2 View 3D Structure Click here
Q6P3A8 View 3D Structure Click here
Q6PHI8 View 3D Structure Click here
Q6YU51 View 3D Structure Click here
Q6Z1G7 View 3D Structure Click here
Q6Z3X5 View 3D Structure Click here
Q7K5K3 View 3D Structure Click here
Q7PLE6 View 3D Structure Click here
Q7SIC9 View 3D Structure Click here
Q7T368 View 3D Structure Click here
Q7XWP9 View 3D Structure Click here
Q86HX0 View 3D Structure Click here
Q8I0X1 View 3D Structure Click here
Q8I6S5 View 3D Structure Click here
Q8IDW0 View 3D Structure Click here
Q8IL09 View 3D Structure Click here
Q8RWV0 View 3D Structure Click here
Q93619 View 3D Structure Click here
Q95T35 View 3D Structure Click here
Q96HY7 View 3D Structure Click here
Q99MX0 View 3D Structure Click here
Q9C6Z3 View 3D Structure Click here
Q9D051 View 3D Structure Click here
Q9D4D4 View 3D Structure Click here
Q9FLH2 View 3D Structure Click here
Q9H0I9 View 3D Structure Click here
Q9LDY2 View 3D Structure Click here
Q9LFL9 View 3D Structure Click here
Q9SAV3 View 3D Structure Click here
Q9ULD0 View 3D Structure Click here
Q9URM2 View 3D Structure Click here
Q9VA02 View 3D Structure Click here
Q9VHN7 View 3D Structure Click here
Q9VVP4 View 3D Structure Click here
Q9ZQY2 View 3D Structure Click here