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1.2.4.1: pyruvate dehydrogenase (acetyl-transferring)

This is an abbreviated version!
For detailed information about pyruvate dehydrogenase (acetyl-transferring), go to the full flat file.

Word Map on EC 1.2.4.1

Reaction

pyruvate
+
[dihydrolipoyllysine-residue acetyltransferase] lipoyllysine
=
[dihydrolipoyllysine-residue acetyltransferase] S-acetyldihydrolipoyllysine
 +
CO2

Synonyms

aceE, AcoA, CTHT_0006350, CTHT_0069820, dehydrogenase, pyruvate, E1 component of pyruvate dehydrogenase, E1 component of pyruvate dehydrogenase multienzyme complex, E1 component of the pyruvate dehydrogenase multienzyme complex, E1 component subunit alpha, E1 component subunit beta, E1alpha, E1ec, E1p, IAR4, MAB1, MdeB, mitochondrial pyruvate dehydrogenase, More, MtPDC, OsI_14647, OsI_31986, Pda1, PDC, PDH, PDH E1alpha, PDH subunit E1-beta, PDH-A1, PDHa, PdhA1, PDHA1a, PdhB, PDHC, PDHc E1, PDHc-E1, PdhE, PDHE1alpha, PdhH, PH2, pyruvate decarboxylase, pyruvate dehydrogenase, pyruvate dehydrogenase complex, pyruvate dehydrogenase complex E1 component, pyruvate dehydrogenase complex,, pyruvate dehydrogenase E1, pyruvate dehydrogenase E1 alpha subunit, pyruvate dehydrogenase E1 component, pyruvate dehydrogenase E1 component subunit beta, pyruvate dehydrogenase multienzyme complex, pyruvate dehydrogenase multienzyme complex E1, pyruvate dehydrogenase, E1, pyruvate:NAD oxidoreductase, pyruvate:[dihydrolipoyllysine-residue acetyltransferase]-lipoyllysine 2-oxidoreductase (decarboxylating, acceptor-acetylating), pyruvic acid dehydrogenase, pyruvic dehydrogenase, thiamin diphosphate-dependent pyruvate dehydrogenase, thiamin-dependent pyruvate dehydrogenase, thiamine diphosphate-dependent 2-oxo acid decarboxylase, VEG220, Vegetative protein 220

ECTree

     1 Oxidoreductases
         1.2 Acting on the aldehyde or oxo group of donors
             1.2.4 With a disulfide as acceptor
                1.2.4.1 pyruvate dehydrogenase (acetyl-transferring)

Crystallization

Crystallization on EC 1.2.4.1 - pyruvate dehydrogenase (acetyl-transferring)

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
in complex with phosphonolactylthiamine diphosphate as structural and electrostatic analogue of alpha-lactylthiamin diphosphate. Presence of phosphonolactylthiamin diphosphate causes large conformational changes
preparation of catalytic subunit E1 of pyruvate dehydrogenase complex, without cofactors thiamine diphosphate and Mg2+, no evidence of disorder/order loop transformations. Comparison with holo-E1 enzyme and in an inhibitor complex with thiamine 2-thiazolone diphosphate
purified enzyme E1 in complex with inhibitor thiamine thiazolone diphosphate and Mg2+, sitting drop vapour diffusion method, reservoir solution: 15-20% PEG 2000 monomethyl ether, 5-10% 2-propanol, 0.2% NaN3, 100 mM HEPES, pH 7.00, 22°C, 4 weeks, X-ray diffraction structure determination and analysis at 2.09 A resolution, comparison with structure determined with bound cofactor thiamine diphosphate
purified recombinant pyruvate dehydrogenase multienzyme complex component E1, sitting drop vapor diffusion method, mixing of equal amounts of protein and precipitant solution of 0.006-0.01 ml, the latter containing 15-20% PEG2000 monomethyl ether, 10% propanol, 0.2% NaN3, and 60 mM HEPES, pH 7.1, 22°C, 2-5 weeks, native and selenomethionine crystals, X-ray diffraction structure determination and analysis at 1.85 A resolution
sitting drop vapour diffusion method with 15-20% PEG2000 monomethyl ether, 10% propanol, 0.2% NaN3 in 60 mM HEPES buffer (pH 7.05)
modeling of the beta-subunit of the pyruvate decarboxylase component of the pyruvate dehydrogenase complex based on the crystal structures of the homologous 2-oxoisovalerate decarboxylase of Pseudomonas putida and Homo sapiens. The negatively charged side chain of Glu285 and the hydrophobic side chain of Phe324 are of particular importance in the interaction with the peripheral subunit-binding domain of the dihydrolipoyl acetyltransferase component of the complex
full and dynamic structural model of full human pyruvate dehydrogenase complex, including binding of the linking arms to the surrounding E1 (pyruvate decarboxylase) and E3 (dihydrolipoamide dehydrogenase) enzymes via their binding domains with variable stoichiometries. An optimalsetting of approximately 30 copies of E1 ensures stability of the surrounding E1 and E3 clouds. Decreasing the number of E1s increases the flexibility of the now nonoccupied arms. Their flexibility depends on the presence of other E1s and E3s in the vicinity, even if they are associated with other arms. As one consequence, the radius of gyration decreases with decreasing number of E1s
-
recombinant enzyme, orthorhombic crystals in polyethylene glycol 3350 by vapor-diffusion method, space group P222
-
vapour diffusion method with 14-18% PEG 3350, 0.1 mM sodium azide, and 200 mM NaSCN in 50 mM potassium phosphate (pH 8.0)
homology modeling and docking of inhibitor N-((1-((4-amino-2-methylpyrimidin-5-yl)methyl)-5-iodo-1H-1,2,3-triazol-4-yl)methyl)-4-nitrobenzenesulfonamide. The compound can inhibit PDH subunit E1 by occupying the thiamin diphosphate-binding pocket and then blocking PDH E1 bound to thiamin diphosphate as competitive inhibitor
asymmetric reconstruction of the active, native pyruvate dehydrogenase complex by cryo-EM as a dynamic assembly. Enzyme clusters form a transient catalytic nanocompartment. The flexible parts of the dehydrogenase factory are notably restricted by a density cloud surrounding single E1p and E3 subunits. This density cloud presumably is composed of E1p and E3. The E1p and E3 proteins are not observed to interact directly with the E2p core but are spatially confined in relative proximity
Thermochaetoides thermophila