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173  structures 5038  species 4  interactions 20295  sequences 58  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


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 9 members:

DXP_synthase_N E1_dh 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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

View options

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
(93)
Full
(20295)
Representative proteomes NCBI
(15647)
Meta
(10577)
RP15
(1847)
RP35
(3551)
RP55
(4709)
RP75
(5571)
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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
(93)
Full
(20295)
Representative proteomes NCBI
(15647)
Meta
(10577)
RP15
(1847)
RP35
(3551)
RP55
(4709)
RP75
(5571)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

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
(93)
Full
(20295)
Representative proteomes NCBI
(15647)
Meta
(10577)
RP15
(1847)
RP35
(3551)
RP55
(4709)
RP75
(5571)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

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
Author: Bateman A, Finn RD, Griffiths-Jones SR
Number in seed: 93
Number in full: 20295
Average length of the domain: 175.70 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 29.45 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -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 20.2
Model length: 178
Family (HMM) version: 19
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 4 interactions for this family. More...

Transket_pyr Transketolase_N E1_dh Transketolase_C

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 173 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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