Transket_pyrTransketolase, pyrimidine binding domain |
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| SMART accession number: | SM00861 |
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| Description: | Transketolase (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 show that the enzyme has been evolutionarily conserved. In the peroxisomes of methylotrophic yeast Hansenula polymorpha, there is a highly related enzyme, dihydroxy-acetone synthase (DHAS) (also known as formaldehyde transketolase), which exhibits a very unusual specificity by including formaldehyde amongst its substrates. |
| Family alignment: |
There are 3670 Transket_pyr domains in 3670 proteins in SMART's nrdb database.
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- Evolution (species in which this domain is found)
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Go to specific node: Anopheles gambiae, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, Mus musculus, Rattus norvegicus, Saccharomyces cerevisiae, Takifugu rubripes - Cellular role (predicted cellular role)
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Cellular role: metabolism
- Literature (relevant references for this domain)
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Primary literature is listed below; Automatically-derived, secondary literature is also avaliable.
- Nikkola M, Lindqvist Y, Schneider G
- Refined structure of transketolase from Saccharomyces cerevisiae at 2.0 Aresolution.
- J Mol Biol. 1994; 238: 387-404
- Display abstract
The crystal structure of transketolase from Saccharomyces cerevisiae hasbeen refined to a crystallographic residual of 15.7% at 2.0 A resolutionusing the program package X-PLOR. The refined model of the transketolasehomodimer, corresponding to 1356 amino acid residues in the asymmetricunit, consists of 10,396 protein atoms, 1040 solvent molecules, 52thiamine diphosphate atoms and two calcium ions. All amino acid residuesexcept for the two N-terminal residues of the two subunits are defined inthe electron density maps and refined. The estimated root-mean-square(r.m.s.) error of the model is less than 0.2 A as deduced from Luzzatiplots. The r.m.s. deviation from ideality is 0.017 A for bond distancesand 3.1 degrees for bond angles. The main-chain torsion angles ofnon-glycine residues lie within the allowed regions of the Ramachandranplots. The model shows a very good fit to the electron density maps. Theaverage B-factor for all protein atoms in the first subunit is 19 A2, and15A2 in the second. The average B-factor for solvent atoms is 32A2. Thetwo subunits of transketolase were refined independently and have nearlyidentical structures with an r.m.s. deviation of 0.24 A for C alpha atoms3 to 680, and slightly less when aligning the individual domains. A fewexceptions from the 2-fold symmetry are found, mostly in the surfaceresidues. The thiamine diphosphate cofactors have identical conformations.The cofactor is shielded from solvent except for the C-2 atom of thethiazolium ring. A calcium ion is bound to the diphosphate group ofthiamine and protein ligands. The metal binding site and the interactionsof thiamine diphosphate with protein residues are described. A network ofhydrogen bonds consisting of glutamic acid residues and internal watermolecules connects the two thiamine diphosphate molecules. Its structureand possible functional implications are discussed.
- Lindqvist Y, Schneider G, Ermler U, Sundstrom M
- Three-dimensional structure of transketolase, a thiamine diphosphatedependent enzyme, at 2.5 A resolution.
- EMBO J. 1992; 11: 2373-9
- Display abstract
The crystal structure of Saccharomyces cerevisiae transketolase, athiamine diphosphate dependent enzyme, has been determined to 2.5 Aresolution. The enzyme is a dimer with the active sites located at theinterface between the two identical subunits. The cofactor, vitamin B1derived thiamine diphosphate, is bound at the interface between the twosubunits. The enzyme subunit is built up of three domains of thealpha/beta type. The diphosphate moiety of thiamine diphosphate is boundto the enzyme at the carboxyl end of the parallel beta-sheet of theN-terminal domain and interacts with the protein through a Ca2+ ion. Thethiazolium ring interacts with residues from both subunits, whereas thepyrimidine ring is buried in a hydrophobic pocket of the enzyme, formed bythe loops at the carboxyl end of the beta-sheet in the middle domain inthe second subunit. The structure analysis identifies amino acids criticalfor cofactor binding and provides mechanistic insights into thiaminecatalysis.
- Structure (3D structures containing this domain)
3D Structures of Transket_pyr domains in PDB
PDB code Main view Title 1ay0 
Identification of catalytically important residues in yeast transketolase 1dtw 
Human branched-chain alpha-keto acid dehydrogenase 1gpu 
Transketolase complex with reaction intermediate 1ik6 
3d structure of the e1beta subunit of pyruvate dehydrogenase from the archeon pyrobaculum aerophilum 1itz 
Maize transketolase in complex with tpp 1ngs 
Complex of transketolase with thiamin diphosphate, ca2+ and acceptor substrate erythrose-4-phosphate 1ni4 
Human pyruvate dehydrogenase 1ols 
Roles of his291-alpha and his146-beta' in the reductive acylation reaction catalyzed by human branched-chain alpha- ketoacid dehydrogenase 1olu 
Roles of his291-alpha and his146-beta' in the reductive acylation reaction catalyzed by human branched-chain alpha- ketoacid dehydrogenase 1olx 
Roles of his291-alpha and his146-beta' in the reductive acylation reaction catalyzed by human branched-chain alpha- ketoacid dehydrogenase 1qgd 
Transketolase from escherichia coli 1qs0 
Crystal structure of pseudomonas putida 2-oxoisovalerate dehydrogenase (branched-chain alpha-keto acid dehydrogenase, e1b) 1r9j 
Transketolase from leishmania mexicana 1tka 
Specificity of coenzyme binding in thiamin diphosphate dependent enzymes: crystal structures of yeast transketolase in complex with analogs of thiamin diphosphate 1tkb 
Specificity of coenzyme binding in thiamin diphosphate dependent enzymes: crystal structures of yeast transketolase in complex with analogs of thiamin diphosphate 1tkc 
Specificity of coenzyme binding in thiamin diphosphate dependent enzymes: crystal structures of yeast transketolase in complex with analogs of thiamin diphosphate 1trk 
Refined structure of transketolase from saccharomyces cerevisiae at 2.0 angstroms resolution 1u5b 
Crystal structure of the human mitochondrial branched-chain alpha-ketoacid dehydrogenase 1um9 
Branched-chain 2-oxo acid dehydrogenase (e1) from thermus thermophilus hb8 in apo-form 1umb 
Branched-chain 2-oxo acid dehydrogenase (e1) from thermus thermophilus hb8 in holo-form 1umc 
Branched-chain 2-oxo acid dehydrogenase (e1) from thermus thermophilus hb8 with 4-methylpentanoate 1umd 
Branched-chain 2-oxo acid dehydrogenase (e1) from thermus thermophilus hb8 with 4-methyl-2-oxopentanoate as an intermediate 1v11 
Crosstalk between cofactor binding and the phosphorylation loop conformation in the bckd machine 1v16 
Crosstalk between cofactor binding and the phosphorylation loop conformation in the bckd machine 1v1m 
Crosstalk between cofactor binding and the phosphorylation loop conformation in the bckd machine 1v1r 
Crosstalk between cofactor binding and the phosphorylation loop conformation in the bckd machine 1w85 
The crystal structure of pyruvate dehydrogenase e1 bound to the peripheral subunit binding domain of e2 1w88 
The crystal structure of pyruvate dehydrogenase e1(d180n, e183q) bound to the peripheral subunit binding domain of e2 1wci 
Reactivity modulation of human branched-chain alpha- ketoacid dehydrogenase by an internal molecular switch 1x7w 
Crystal structure of the human mitochondrial branched-chain alpha-ketoacid dehydrogenase 1x7x 
Crystal structure of the human mitochondrial branched-chain alpha-ketoacid dehydrogenase 1x7y 
Crystal structure of the human mitochondrial branched-chain alpha-ketoacid dehydrogenase 1x7z 
Crystal structure of the human mitochondrial branched-chain alpha-ketoacid dehydrogenase 1x80 
Crystal structure of the human mitochondrial branched-chain alpha-ketoacid dehydrogenase 2beu 
Reactivity modulation of human branched-chain alpha- ketoacid dehydrogenase by an internal molecular switch 2bev 
Reactivity modulation of human branched-chain alpha- ketoacid dehydrogenase by an internal molecular switch 2bew 
Reactivity modulation of human branched-chain alpha- ketoacid dehydrogenase by an internal molecular switch 2bfb 
Reactivity modulation of human branched-chain alpha- ketoacid dehydrogenase by an internal molecular switch 2bfc 
Reactivity modulation of human branched-chain alpha- ketoacid dehydrogenase by an internal molecular switch 2bfd 
Reactivity modulation of human branched-chain alpha- ketoacid dehydrogenase by an internal molecular switch 2bfe 
Reactivity modulation of human branched-chain alpha- ketoacid dehydrogenase by an internal molecular switch 2bff 
Reactivity modulation of human branched-chain alpha- ketoacid dehydrogenase by an internal molecular switch 2bp7 
New crystal form of the pseudomonas putida branched-chain dehydrogenase (e1) 2e6k 
X-ray structure of thermus thermopilus hb8 tt0505 2j9f 
Human branched-chain alpha-ketoacid dehydrogenase- decarboxylase e1b 2jgd 
E. coli 2-oxoglutarate dehydrogenase (e1o) 2o1s 
1-deoxy-d-xylulose 5-phosphate synthase (dxs) from escherichia coli 2o1x 
1-deoxy-d-xylulose 5-phosphate synthase (dxs) from deinococcus radiodurans 2ozl 
Human pyruvate dehydrogenase s264e variant 2r5n 
Crystal structure of transketolase from escherichia coli in noncovalent complex with acceptor aldose ribose 5-phosphate 2r8o 
Transketolase from e. coli in complex with substrate d- xylulose-5-phosphate 2r8p 
Transketolase from e. coli in complex with substrate d- fructose-6-phosphate 3duf 
3dv0 
3dva 
3exe 
3exf 
3exg 
3exh 
3exi 
3hyl 
3k95 
- Links (links to other resources describing this domain)
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PFAM Transket_pyr
